Home

User`s Manual

1. Ene fi L visual templates in MapMaker see section 2 14 or as predefined selections in MRFinder see section 4 5 You can now for example import administrative boundaries for a country adding them under the node of this country following more or less the same steps of this example There are more useful features when importing predefined selections For example you can make that when a tree node is selected it automatically selects all the subnodes it contains This can be useful for example if you add a node Provinces for a country and then you add subnodes with all the provinces If you want that when selecting the node Provinces ModestR add to the map all the provinces edit the Provinces node and check the option Select childs of this node when selecting it 128 ModestR Software Quick start tutorial It can be also pointed out that you can delete nodes using the Delete selection button but be careful because all subnodes of a node will be also deleted F Select chiiis ofthis node when seleciing i To reorganize nodes such as moving a node to another parent you can edit the node and select its new parent You will see that the No data in this selection Category field of the node changes to the new t parent Then save it You can also just drag and drop nodes to move them from one parent to Adding new selection another 4 12 Other tools 4 12 1 Simplifying selections MRFinder searc
2. Options x To make easier browsing predefined selections an active map is shown by default on the right side of the dialog This active map shows a preview when available of the element selected in the left tree Moreover this preview can be interactive in some case For example if you select Word countries in the left tree a world map will be shown on the right panel You can double click on a continent to see details of this continent As you can see this active preview panel is synchronized with the left tree the way that when you select an element on one of them this element will also be selected on the other one To add a selection to the map you just have to check it on the tree You can also right click on the left active preview an select the element in the context menu Add a stored selection VQ Algeria 4 H E Angola E Benin jn E Burkina Faso Zoom into sublements N Burundi Go upper level Cameroon E Cape Verde Central African Republic VI Chad Comoros Congo Congo The Democratic Republic of the J E C te d Ivoire Djibouti T Egypt F Equatorial Guinea Eritrea Ethiopia E Gabon Gambia F Ghana 4 Options Some nodes of the tree can be not checkable as they are just here to group selections And other ones can automatically include other nodes when checked For example a node Europe can automatically add all the Europ
3. Once found the ranks you are interested in you can select them on the left side tree Clicking on the Export button located on the bottom right corner all selected branches will be exported to a CSV file If you enabled the option for the exported data to be imported to currently opened ModestR database DataManager will directly start the importation of this same file to the current ModestR database 108 ModestR Software Quick start tutorial 3 18 Taxonomy searching and checking utility One quite frequent problem when using taxonomy data from A different sources is the discrepancy between those sources Other OriginalName P Anguilla anguilla times the problem is that we have for example a list of species ania Entomacrodus solus but not the rest of the taxonomic levels that ModestR requires to add them to a database class order etc To try to help solving Anisotremus moricandi those kind of issues a simple tool has been added to eae eae Epinephelus marginatus 0 Mycteroperca fusca of species in GBIF online database 11 Hippoglossus hippoglossus 12 Sebastes fasciatus 13 Alytes muletensis 14 Rana pyrenaica 1 4 5 Limbochromis robertsi 6 7 9 DataManager that allows searching for taxonomic data for a list The first step is preparing a file in CSV format containing the list of species to be checked This can be done with any text editor or gt C lotriton arnoldi 16 Aquila adalberti a worksheet l
4. v 3 2 4 ay 1 2 Mode ModestR Software and documentation University of Vigo C Guisande et al WebSite http www ipez es ModestR If you use ModestR software and you publish any results or images obtained by means of ModestR software you can cite it in your work as E Garcia Rosello et al 2013 ModestR a software tool for managing and analyzing species distribution map databases Ecography 36 11 1202 1207 online in http onlinelibrary wiley com doi 10 1111 j 1600 0587 2013 00374 x abstract D O I 10 1111 j 1600 0587 2013 00374 x ModestR Software Quick start tutorial Contents Me WARY OC Naas seen cet ace cere E ew oe eeneneaectenneneeiaeeeseecace 8 1 1 POG SER SS UNV CONN S ete secnete senna ccresteecanatecsatensectesseaeaeeseieeasentavect sn tcenannsasarduiescsseanees 8 2 First steps With MapMaker scsccscecsccscscsccccccsceccccccscsceccecscscescececsceseccecces 11 2 1 Opening MapMaker and moving across the world Ma ccccccsssececeesecceeeeseeeeeeeeees 11 2 2 Making a range distribution Map IN MapMaker cccccccesseccecesseceeeesececeeseceeeeeceeseees 12 2 3 Making an occurrence based distribution map in MapMakeP ccc csseceeeeseeeeeeees 14 2 4 Modifying Samples in a map 0 c ccc01es T NRIs svc neuvsrencassrenvensrsenensurencaverensans 18 2 5 Importing data to a MapMaker Map u ccccccssscccsscscesecseeneseceeecseesceseueceeeeceeeeseneneeees 20 2 6 Data
5. 3 17 Extracting taxonomy data from ITIS database DataManager integrates an easy to use tool to browse the ITIS taxonomy database and export data from this database to a CSV file Those exported data can be used to subsequently import them to a ModestR database but also for any other purpose The ITIS taxonomy database can be found on the ITIS website http www itis gov DataManager supports browsing ITIS database in sqlite format You can find instructions to download this database in the DataManager main menu option mport Taxonomy From ITIS database How to use ITIS database Once downloaded you can browse its contents going to the menu option mport Taxonomy From ITIS database ITIS database browser tool You ll have to select the ITIS database file in Sqlite format A browser will be displayed ITIS Taxonomy database export tool Select ranks to be exported Purses Export options Search tool a y Plantae Select levels to be included H Animalia cel ee Fungi Taxonomy Level H E Protozoa E Kingdom e Chromista T Subkingdom H A Archaea L Infrakingdom Superdivision E Division Subdivision E Parvdivision T Infradivision Superphylum L Phylum Z Subphylum C Infraphylum Parvphylum F Superclass 7 Class F Subclass E Infraclass Qi imarardar W Exportation options Field separator V Require TWG standards Import options Import to current database 107
6. Import fle C Usererselobesurasishapefiles courties shp fieldlist s compined in te te l land os a b utto n Ayanda g e e 17 mien a in ea 220 3 Akala Ps meian Samos AND COUNTRY andor OR Optonal teing crferna jsf Hsn to inees all ENGLISH Ania KIT LOCAL Angus IH k UWF RAFH Aas S CONTINENT Snes Rovhe wt c LIWAELS7 4 ni j E Caii E wri q 4 qj You can also directly write a condition in the textbox The syntax of the conditions is similar to the syntax of a WHERE clause in SQL If you want to import all data just Accept this dialog box e f the shapefile contains data fields which is the most usual ModestR will show you the list of fields to allow you selecting the field that will be used to assign names to the imported selections Otherwise you can select Default In this dialog box you can explore fields values clicking on the field on the left list to see its values on the right one this makes easier to find the correct field to be used to assign names to the imported selections Select field to use as name The file you are importing contains data fields for each selection You can select the field to be used to name the selections or select Default to use default names Fields contained in the file Values OBJECTID ISO3 ISO FIPS COUNTRY ENGLISH LOCAL SOVEREIGN ancti CONTINENT Antigua and Barbuda UNREG1 Argentina Armenia Aruba Ashmore and Cartier Islands a FRENCH i S
7. placing the mouse on an element opi e sm mple a nd pres s Delete key WV Valid V Invalid gt Detail Lever U Viewing 7 180 100 0346 to 180 100 0346 Ready 2 1 OpeningMapMakerandmoving across the world map When you open MapMaker it will automatically show the world map in a full view with a lower detail level You can zoom in any part of the map selecting the Zoom Select tool in the left tool panel and then selecting the zone in the world map When the wanted zone is selected press the Zoom button or select the Zoom option on the contextual menu You can also use the mouse wheel to zoom in and out click first on the map to set the focus on it but this option can perform very slowly depending on your computer capabilities Finally you can use the lateral Zoom trackbar to modify the zoom level MapMaker have several detail levels from O lower to 4 highest It will automatically changes to a higher or a lower detail level regarding the deep of the zoom Anyway you can force a detail level using the Detail Level trackbar at the top of the left tools panel Take into account that the higher the level the slower will be displaying the map and moving across it MapMaker will display the current level of detail in the bottom status bar You can select the elements that will be shown on the map in the Show groupbox left tool panel such as borders or freshwater habitats Freshwater habitats are only vi
8. AND Sample 4 IOR Sample 5 NOT Sample 6 IN Sample 7 Sample 8 Sample 9 Sample 10 3 If you are familiar with shapefile format you can also add importation criteria to filter which data will be imported To do that use the See hide fieldlist button to see the list of fields contained in the shapefile Then you can select a field to see the values it takes and add criteria that will be used as filter when importing You can also directly write a condition in the textbox The syntax of the conditions is similar to the syntax of a WHERE clause in SQL If the imported shapefile contains several shapes which is quite usual once imported a dialog box will ask you if you want to add a single selection that include all shapes contained in the shapefile or to split them in several selections As explained in 4 6 as MRFinder can search for species discriminating several selections the difference is that if you add a single selection even if it contains several shapes you can only obtain the species in the selection as a whole If you add several selections you can obtain search results grouped by selection 184 ModestR Software Quick start tutorial Warning Imported selection data contains several selections Do you want to split A and import each selection as a distinct selection Press Mo to store imported selection as a whole a If you select to split the shapes in several selections a dialog box will show the fi
9. In the case you click on the Calculate VIF button the VIF of each variable will be shown in the list VIF can be useful to detect high correlated variables and then decide to remove some variables To remove a variable just select in on the list and use the Delete selected button Environmental layer generation Select Variables Analysis Order Processing Scale Options Correlation and variable redundancy analysis Selected Variables Bathymetry Calcite CDOM Chla Cloud cover Colineanty analysis Delete Full extent 0 Extent of occurence J ren one D Similarly to the Layer extent option described in the previous step VIF can be calculated for the full extent for a visual template or for the EOO given that a visual template or occurrence data are present on the map as explained before Take into account that extent used to calculate VIF can be different from the extent selected for the environmental layer ModestR doesn t establish any limitation in this sense so the convenience of using one or another option is left to the user Click on Continue button to go to next step If occurrence data are present on the map when you started to create the environmental layer the next step will allow you to perform a contribution analysis In other case this step will be automatically skipped If occurrence data are present on the map you can opt
10. Variable Analysis Hull Processing Inflation Factor VIF A VIF value higher than 30 is Select the variables to be used to calculate contribution commonly considered an indicator of collinearity Envi tal Variabl A nd u marine among the variables Thus you have the change choice V Bathymetry f ee Tle Cate of removing those variables significantly related and Wi CDOM ase W Chia therefore that are redundant But this is an optional Cloud cover i i T DA i step If you just want to include all variables you can Depth W D0 simply continue Take into account that if two variables i Nitrate 7 Wi PAR are very highly correlated the way that one of them if Ee pH FJ Phosphate a linear function of the other one VIF cannot be Fle Poc i FO Sainty calculated Involved variables will be marked to allow F Silicate EJO Temperature you to remove one of them if you want W 5 Prueba Fle batycsv AFU Terrestrial Click on Continue button to go to next step x Cancel Contribution of variables to species distribution Select Variables Vanable Analysis Hull Processing Correlation and variable redundancy analysis Selected Variables Finally you have to select the maps to be processed Depth only sample maps only areas range maps or all of oo DA them Pan DO Nitrate Cloud cover You have to select the EOO mode for sam
11. wew gbif org dataset 83a8cOda f762 11e1 2439 00145eb45e9a http www gbif org dataset 830b4af8 f762 11e1 a439 00145eb45e9a Mm 27 This requires installing the last software updates If you want to distinguish freshwaters you also have to install freshwater data in ModestR available in ModestR website Anyway as freshwater habitats are still being reviewed and updated in some areas checking feature may only distinguishes between land and sea habitats 145 ModestR Software Quick start tutorial 6 8 Importing samples from CSV files You can import samples and create maps importing data from CSV files containing samples occurrences for one or more species This can be done using the mport Import presence data From CSV sample files A similar option but limiting the species to be imported to a specific branch of the taxonomic tree can be found in the contextual menu clicking with left mouse button on the desired element of the tree selecting the option mport presence data for this branch From CSV sample files This option will import sample data from a CSV file Expected format is a list of samples in the form Species Longitude Latitude or Species Latitude Longitude This way you can import a single file containing occurrences for several species but only species already existing in the database will be imported that is species in the database with exactly the same name than the specified in the i
12. x1 cells which results in a very long and rarely useful report 2 7 Data cleaning using custom validation rules Besides automatic cleaning MapMaker incorporates the possibility of using custom validation rules to determine the validity of samples as well as areas of presence according to environmental variables As mentioned before in section 2 6 environmental data needed to use this features are not included in ModestR so they have to be provided by the user as data files in ESRI ASCII or CSV format and integrated in ModestR as explained in section 6 26 Once environmental data available to ModestR validation rules can be added using the menu Mapping Data Cleaning Custom environmental based cleaning of MapMaker A dialog box like the shown below will appear 26 ModestR Software Quick start tutorial E Set validation rules with environmental variables Rule assistant Environmental Variables 5g Marine Bathymetry Calcite Chlorophyll a Sea surface temperature W Silicate Salinity Phosphate pH Missing value action PAR Clean data Dont clean data Nitrate Cloud cover Samples Validation E er Vali da airy to Pr Pmi ox To all samples Only to invalid samples Dont validate samples Diffuse attenuation Add Placemarks orm To validated samples ea v To invalidated samples ma cDOM Bathymetry 6x6 J Delete previously existing placemarks Placemark size
13. ModestR Software Quick start tutorial don t check this option all samples will be imported and added to the map even if they are duplicated e Make the sample habitat auto checked using this option a sample will be automatically checked by DataManager to determine if it is situated in a valid or invalid habitat and therefore it will be considered valid or invalid with a precision of aprox 1 seconds You can set different colors for valid an invalid samples to easily distinguish them in the Options Preferences option on the main menu of DataManager Moreover only valid samples will be used when processing and extracting data from a map like presence or richness data If on the contrary you don t set a sample as dynamic it will be considered as manually validated invalidated By default it will be valid and you have to manually set it as invalid if needed Therefore we recommend you to try the dynamic validation e Select valid habitats for the samples you have to select which habitats are valid for the Samples you are importing this option appears on the left tool panel when manually adding Samples You can select one or more samples but it is mandatory to select at least one habitat If you selected to make the samples as habitat auto checked those habitats will be used to validate invalidate a sample If you don t selected to make the samples as dynamic this information will NOT be used as samples have to be manually valida
14. Pleuronectif Pleuronectic Hippoglossu Hippoglossu Actinoptery ScorpaeniforSebastidae Sebastes ata a mic A B C D 701 Reptilia Testudines Cheloniidae Chelonia 702 Reptilia 703 Streptophyt Apiales 704 Magnoliopsi Asterales 705 Magnoliopsi Asterales 706 Magnoliopsi Lamiales 707 Magnoliopsi Lamiales Callitrichace Callitriche 708 Magnoliopsi Lamiales Plantaginace Cymbalaria 709 Streptophyt Lamiales Plantaginace Linaria 710 Filicopsida IDicksoniales Culcitaceae Culcita Apiaceae Eryngium Asteraceae Inula Asteraceae Sonchus Callitrichace Callitriche a adm E Chelonia my Testudines Cheloniidae Eretmochely Eretmochely Eryngium grc Inula bifrons Sonchus pus Callitriche lu Callitriche re Cymbalaria Linaria benit Culcita macr Sebastes fas 1 Chelonia my 1 Eretmochely 0 Eryngium grc 1 Inula bifrons 1 Sonchus pus 0 Callitriche lu 0 Callitriche re 1 Cymbalaria 0 Linaria benit 0 Culcita macri oicoioioioisoisoisois iso 1 Entomacrodt 1 Limbochrom 1 Anisotremus 1 Thunnus thy 1 Epinephelus 1 Epinephelus 1 Mycteroperc 1 Hippoglossu 1 Sebastes fas 100 100 100 100 100 100 100 100 Poo c eo oc oO Oo 8 8 8 pPioioioioioioioico o o o 0 BACKBONE_MATCH_FUZZY Class not found using phylum 0 0 0 BACKBONE_MATCH_NONE 0 BACKBONE_MATCH_NONE 0 0 BACKBONE_MATCH_NONE Class not found using phylum 0 BACKBONE _MATCH_NONE Not found Not found Not found Not found Not found Not found Not fou
15. Then you will have a copy of the map now associated to a different species B You can finally use DataManager to delete the first map which was linked to species A 3 5 Opening a map from DataManager Once a map is stored in a ModestR database you can open it and modify it in MapMaker To do that you can just select the species in the taxonomic tree and use Edit Open selected map in MapMaker menu option or Open map in MapMaker option in the context menu 78 ModestR Software Quick start tutorial Of course you can also independently open MapMaker and load the map from the database as explained in 2 19 ModestR DataManager C ModestRProject BD Elasmobranchii DB File Edit Import Export Process Options Tools Help Database Taxonomy Classification S i Elasmobranchi S i Batoids Pristiformes B Pristidae E Anoxypristis EEE Anoxypristis cuspidata l Pristis Rajiformes Process this map waa e Open the map of this species in MapMaker Change node name Cut node Delete this node Export map Show map data Export taxonomy of this branch Import presence data for this branch Set samples from maps of this branch Apply convex hull to this branch Process maps for this branch 3 6 Processing maps ModestR maps are basically stored in an XML based format either in a database or in a standalone file This XML file contains a declarative description of the taxonomy presence are
16. Wetlands Small rivers E Large Channels Large Ditches E Large Drains Reservoirs E Large rivers The accepted format is a list of samples in the form Species Longitude Latitude Species field is optional or Species Latitude Longitude Species field is optional In the dialog box you can select the correct options for the format of the CSV file to import e The order of the coordinates in the CSV file Longitude Latitude or vice versa e f the first columns contains the species name e lf the first row contains headers in that case first row will be skipped e Decimal separator and field separator More details about CSV samples importation are explained in section 2 3 7 2 Importing samples from GBIF online database You can import samples from the GBIF online database to a MapMaker map On the main menu select File Import Samples from online GBIF database or the equivalent button of the toolbar You will have to write the desired species name alternatively you can select it from a ModestR database Then you can choose if you want MapMaker to look for synonyms in GBIF database More details about GBIF samples importation are explained in section 2 3 175 ModestR Software Quick start tutorial 7 3 Importing areas from ESRI ASCII probability distribution models You can import distribution data from distribution models with a ESRI ASC raster probability format like the obtained usi
17. When using this feature you have to set the criterion to decide when a species is considered as rare To do that use the button at left of this checkbox that will show a dialog box where you can set the criteria applied to determine if a species is rare Select the filters to apply to the species found Taxonomy filter Rare species filter Categories filter Filtered results Export data be Beryciformes 10000 he Cetomimiformes UUUU 0 Lophiiformes CE NE En SE __ V Filter only rare species Taxonomy level to calculate or rare species i i Elasmobranchii GBIF E ia Actinopterygii Maximum Area of occupancy AOO Ateleopodiformes Percentage of species with the lowest AOO Scientific name 2R 25 E 3 Level O Maximum Extent of occurrence E00 10000 Percentage of species with the lowest EQO a of species 25 Y This tree allows to select which Results taxonomic group of species will be used to determine the EOO AOO in percent based criterias relative x Si Total species in region 222 Species matching criteria 15 Region Bounds Long 86 19 to 77 48 Lat 0 31 to 73 43 The available options are e Maximum Area of Occupancy AOO a species will be considered rare if its total presence area all over the world AOO is less than the value you can enter in Km e Perce
18. World Basins Basins of Africa 8 World Basins Basins of Africa 9 4 WW Options The button Show on the bottom right side allows showing in the world map the graph corresponding to the one that is currently shown in the right panel The button Export exports to a folder image files for the data and density graphs corresponding to each one of the visual templates of the left list 2 16 Other useful features 2 16 1 Other map elements Besides samples and presence areas other elements can be added to the map mainly for informative purposes On the left tool panel you ll find options to add arrows placemarks and text to a map The operation with those tools is very straightforward you essentially have to select a tool and then click on the map to add the corresponding element For arrows you have to click on the starting point and drag until the end point for example Any of those elements can be selectively deleted from a map either by selecting any area using the Freehand or the Rectangle tools and clicking the Delete objects button located on the left tool panel Alternatively going to the Edit menu where options exist to delete in a single step all the elements of any type arrows placemarks 66 ModestR Software Quick start tutorial 2 16 2 Querying distance between two points You can query for the approximate distance between two points in the map using the Show distance tool located in the Ma
19. are preserved e Edit Set samples of the selected branch To manually validated samples set all samples occurrences of the maps of the selected branch as manually validated samples That implies that all samples contained in a map will be considered as valid even if they are located in habitats not valid for the species See section 2 4 for more details about Sample management in ModestR e Edit Set samples of the selected branch To manually unvalidated samples set all samples occurrences of the maps of the selected branch as manually unvalidated samples That implies that all samples contained in a map will be considered as invalid regardless of the habitat they are located in See section 2 4 for more details about sample management in ModestR e Edit Set samples of the selected branch To habitat auto checked samples set all samples occurrences of the maps of the selected branch as auto validated samples That implies that ModestR will check if samples are located in habitats valid for the species to consider them valid or invalid See section 2 4 for more details about sample management in ModestR e Edit Set samples of the selected branch Modify samples valid habitats allow modifying the habitats that will be considered as valid for the occurrences of the selected species presence areas of range maps will not be affected See section 2 4 for more details about sample management in ModestR e Edit Set samples of the selected branch
20. details about how to integrate environmental data in ModestR are explained in section 6 26 Environmental layer generation Select Variables Analysis Environmental Variables E Marine ied Bathymetry Calcite F CDOM Cha F gt Cloud cover DA F Depth i do Nitrate PAR E pH Phosphate Poc gt Salinity Silicate Temperature MGi Prueba ApparentOxygenUtilization_at_depth 5500 batyCSV Nitrate_at_depth_ 5500 PercentOxygenSaturation_at_depth_ 5500 Phosphate_at_depth_ 5500 Salinity_at_depth_ 5500 j JAA 1 P j Full extent Visual template Extent of occurence Occupied river basins In this dialog box you can also select the Layer extent which can be e Full extent the layer will be calculated for the area for which selected environmental data is available For example if you selected environmental variables that cover the entire world the environmental layer to be created will also cover the entire world e Visual template selecting this option a right panel will appear where you ll have to select a visual template The layer will be calculated only within the bounds of this visual template 101 ModestR Software Quick start tutorial e Extent of Occurrence selecting this option a right panel will appear where you ll have to select the EOO calculation method The l
21. dp G Bathymetry _ P Calcite Chlorophyl a G Sea surface temperature Fla Silicate L Poc 2 CDM 1 BathymetryBis Variable que falla E Baty0 50 2 al Terrestrial Althymetry i d In this dialog box you can select on the tree the variables you want to use in the data cleaning Besides the environmental variables you have integrated in ModestR you could see three specifically calculated variables related to dispersal capacity which are also available mean distance latitudinal dispersion and longitudinal dispersion Mean distance for each occurrence record is calculated as the mean distance from this record to all the other records Latitudinal dispersion and longitudinal dispersion merely are the latitude or longitude value of each occurrence record These variables allow validating records basing on their relative geographical dispersion so records excessively distant from the others will be cleaned It must be pointed out that those variables can only be used on maps that contain samples but not on range maps Once all whished variables selected click on the Continue button to go to the next step ModestR will then determine the range of values took by the selected variables on the current presence 6 Take into account that using longitudinal dispersion which is merely the longitude value of each occurrence to perform da
22. higher percentage contribution to the instability index can be considered as those more affecting the most the distribution of the species This analysis is used as part of calculations such as environmental occurrence see 2 9 and 3 11 and Niche of Occurrence using a per species layer see 3 13 to select the variables that affect the most the distribution of the species But you can also perform this analysis independently from Environmental Occurrence or Niche of Occurrence features a report about variable contribution for any rank species can also be exported from DataManager using the menu Export Export maps of the selected branch To variables contribution report In the first step you have to select the variables for which you want to calculate their contribution index You have to select at least 2 variables 23 Dubois D M 1973 An index of fluctuations Do connected with diversity and stability of ecosystems applications in the Lotka Volterra model and in an experimental distribution of species Rapport de syth se III Programme National sur l environment Physique et Biologique Project Mer Commision Interminist rielle de la Politique Scientifique Li ge Guisande C Barreiro A Maneiro I Riveiro I Vergara A R Vaamonde A 2006 Tratamiento de datos Ediciones Diaz de Santos 367 pp 161 ModestR Software Quick start tutorial guuna Next step allows you to optionally calculate Variance Select Variables
23. ooo W Leptocharias smithii H El Proscylidae H Pseudotriakidae H O Scyliorhinidae a e Sphyrnidae ao Triakidae E TEF Heterodontiformes HC Hexanchiformes a l Lamniformes amp Orectolobiformes HO Pristiophoriformes HO Squaliformes Hf 1 Squatiniformes The counter shows how many Add mode Add as individual maps Add as single map Group by Gate lt f Order Selected species 68 ie Genus To illustrate those different options of adding data to the map next an example is described The following maps contain the same data corresponding to the distribution maps of seven species of the Pristiformes order In the first one the data where added using the option Add as individual maps So each species distribution is added as a separated dataset with its own name and settings 26 You can find the Elasmobranchii database for ModestR from which those data came from in the ModestR website It is available as a sample database that contains expert range maps for all the species of Elasmobranchii class 133 ModestR Software Quick start tutorial File Edit Samples View Layers ModestR tools Options Help ADMIN Y PRUEBAS REEE F acma BPI a St tx A 2 mt Map M RMamping Options Encircle checked items in map Detail Level 0 Viewing from 180 100 0346 to 180 100 0346 Ready In the second one the same data where added using the option Add as single ma
24. with the value if it exists of this variable at the coordinates of the pseudosample The exported format will be the same than for the previously described option of valid samples exportation excepted for the CoordLastModified column that obviously will not appear e Presence areas coordinates this option will generate a CSV with the description of each polygonal area selected in the map as occupied by the species Warning This polygon will not be clipped to the selected habitat it will contain all the coordinates selected by the user regardless of the habitat A Outer Hole column indicates it the coordinates correspond to the outer limits of the polygon or to an inner hole The type indicates the habitat selected for this zone A blank line separates each polygon Valid samples contained in the map will also be exported each one in a line with the FillSample type Environmental data cannot be added when using this exportation option 154 ModestR Software Quick start tutorial Outer 1 pr PT ES ES Class Order Family Genus Species 56 13 54 79 1 o sea _ ActinopterygiiAcipenseriformes Acipenseridae cipenserAcipenser brevirostrum 56 13 55 13 EEEE er e emery ee a ere reer sa aa a o sea fetmoptervgihacioenserormeshcinenseridaefictpensepAcipenser brevrossrun 59 83 47 73 1 o sea _ ActinopterygitAcipenseriformes Acipenseridae Acipenser Acipenser brevirostrum 60 17 47 rf 0 se heimonaan penarine hepnar ir
25. 0 30031 Overlapping 0 64946 Spatial overlapping report between Anoxypristis cuspidata and Pristis microdon Total spatia 2295411 29 Overlapping 2293411 29 Total spatia 0 45494 Total spatia 0 49778 9 2 191 Quick start tutorial Percent Overlap Percent Overlap Distribution1 0 Importing file of visual template names 0 30031 0 43494 0 43842 0 0 04915 0 586 0 58388 0 33421 0 0 21877 0 Distribution2 0 0 64946 0 49778 0 17305 0 0 03712 0 5864 0 30899 0 061 0 0 0764 Large rivers Smallrivers Lentic water Small chanr Large chann Small ditche Large ditche Small drain 0 ModestR Software Quick start tutorial 10 Checking for updates ModestR is regularly updated to add new features Therefore regular updates are released You can check for updates directly from any ModestR application using Help Check for updates menu option This makes that the application connects online to ModestR website to download data and check for available updates for your installation no data are sent from your computer to the Web If there are new updates a dialog box with a list of updates will be displayed You can also make that ModestR applications check automatically for updates setting this options in the Options Preferences menu item of any of those applications Updates have to be downloaded from ModestR website and installed on your computer taking into account the path where you have instal
26. 0 coordinates E Consider and remove duplicated samples if they are equal until 4 th decimal Data cleaning options Mean distance E Latitudinal dispersion E Longitudinal dispersion Select valid habitats for the species Sea FP Land All freshwaters C Lentic habitats Small Channels O Small Ditches C Small Drains Wetlands O Small rivers E Large Channels Large Ditches E Large Drains Reservoirs E Large rivers Use first and foremost data from existing maps when available to determine valid habitats for a species 143 ModestR Software Quick start tutorial This option will download sample data from GBIF for each species of the selected branch and process them regarding the options you set in the dialog box that will be shown previously According to the settings you select new maps can be created existing maps can be overwritten or new data can be added to existing maps for example A brief explanation of each option of this dialog box will be shown in an emerging tooltip if you place the mouse on it Several options are already described in section 2 3 and in section 6 8 below Here we summarize the most relevant ones e Download data only for species without map in the selected branch Download only data for species that still not have maps in the selected branch This option avoids overwriting already existing maps e Download data only for species with map in the selected branch Download data only
27. 100 atelopues maxent gj Terrestrial Althymetry 6101 BI02 Population 6x6 x Cancel G Apply In this dialog box you can select any environmental variable and add it to the expression that will be used as validation rule You can either use the Rule assistant that helps you to construct the rule or just write it into the validation rule box To use the Rule assistant follow those steps e Select the environmental variable in the tree e Click on the Add button aside the Rule assistant e Select the adequate relation operation gt lt and enter a value to compare to e Select it the rule will be added to the validation rule as an AND or an OR rule only relevant when there are more than one rule e Click on the button to Add this rule to Validation The rule part will be added to the validation rule textbox Alternatively you can directly write or modify a validation rule in the Validation rule textbox using the lower Add button to add variables from the tree to the expression Validation expression have to be logical or Boolean that is evaluated as true or false Variables used in the expression have to be written inside brackets this will be automatically done if you use the Add buttons to add them AND and OR operators are allowed Using the right mouse button on the validation rule box a contextual menu will appear showing more options and Operators Once a valid rule introduced you have
28. 19 to 77 48 Lat 0 31 to 73 43 The available exportation options are e Export Metrics generates and exports metrics about species such as richness rarity patch index etc e Export gradients generates and exports latitudinal gradients for several metrics e Export Stats generates and exports statistical data about species like occupied area maximum and minimum latitude and longitude real area reference area ratio etc e Export Maps exports selected species maps in several formats e Export taxonomy exports taxonomy of the selected species in several formats e Export region cords exports the coordinates of the region selected in the map In most of the cases the exported data will be by default clipped to the selected regions either to the exact regions such as for richness metric or to the rectangle that circumscribes the selected areas such as for environmental variables or areas by habitat You can optionally disable this clipping to export data about the species found but for the entire world for example If you need to clip any raster data e g environmental data in raster format to selected areas you can use the clipping feature described below in 4 12 3 More details about those options and the exported formats can be found in section 8 Besides exporting search results data you can also export the current map view to an image file using the main menu option File Export Current map view as image 4 10 S
29. 2 6 MapMaker is able to perform automatic data cleaning of the presence data in a species distribution map But if you want to apply this transformation to numerous maps ina batch mode it may be easierto _ do it in a single operation from Data Cleaning calculation DataManager in turn of doing it for each iene map in MapMaker If you are not familiar Select the varisbles te be used to cakulaie the Data Cleaning with ModestR data cleaning features E l a Environmental Variables please read the section 2 6 before using it E122 Dispersal capacity 7 Latitudinal dispersion only for samples in DataMa nager ie Longitudinal dispersion only for samples Mean distance only for samples To apply data cleaning in DataManager A ja o Bathymetry you can just select the tree branch from ae which you want to apply it and select o Chla Cloud cover Mapping Apply data cleaning to this i branch menu option or the Mapping E a features Apply data cleaning to this E Nitrate ae PAR branch option in the contextual menu of pH the tree node A dialog box will be shown Salinity In this dialog box you can select on the Temperature tree the variables you want to use in the restrial data cleaning Then click on the Continue button to go to the next step In the next step you can see on the left the 21 list of selected variables Before 21 As you can see unlike in Mapmaker data cleaning see secti
30. All cells are took into account to calculate the mean even if they have a richness of zero e SD Species Richness standard deviation of the richness of the cells of the latitudinal band calculated in the same way than Mean Species Richness e Mean AOO Index mean of the AOO Area Of Occupancy index metrics calculated for each one of the cells of the latitudinal band taking cells of the longitude width in degrees indicated in the dialog box described above That is the AOO index of each cell of the longitude width and latitude height in degrees indicated is calculated for a latitudinal band and then the mean of all those values is calculated Be aware that only cells with a richness value bigger than zero that is where there at least one species 165 ModestR Software Quick start tutorial present are took into account to calculate the mean Details about AOO index metric can be found in section 6 17 above e SD AOO Index standard deviation of the AOO index of the cells of the latitudinal band calculated in the same way than Mean AOO Index e Mean EOO Index mean of the EOO Extent Of Occurence index metrics calculated for each one of the cells of the latitudinal band taking cells of the longitude width in degrees indicated in the dialog box described above That is the EOO index of each cell of the longitude width and latitude height in degrees indicated is calculated for a latitudinal band and then the mean of all those values is
31. C Small Drains Wetlands E Small rivers E Large Channels Large Ditches C Large Drains C Reservoirs E Large rivers The options of this dialog box are the same than the shown when importing samples from CSV or GBIF You can find more details in subsection 2 3 If the Shapefile contains polygons this dialog box will be shown where just the valid habitats for the species have to be selected If an area is not located in the habitats selected as valid it will not be shown in the map or only the valid portion if any will be shown 178 ModestR Software Quick start tutorial Select valid habitats for new data Select valid habitats for the species El Sea E Land All freshwaters x Teee E Lentic habitats Small Channels Small Ditches E Small Drains Wetlands E Small rivers E Large Channels O Large Ditches E Large Drains Reservoirs E Large rivers Accept 7 5 Importing from KML files You can import areas and samples from files in KML format which is a widely used format in GIS software Currently only polygon and point elements from a KML file can be imported Polygons will be converted to areas whereas points will be converted to samples Besides this as MapMaker parses KML files primarily as XML data only KML files that comply with well formed XML documents rules are currently supported as KML files are XML specialized files If the imported KML file contains points which will be converte
32. Discard ag Save To clear visual templates from the map you can go to menu Layers Visual templates Clear all visual templates or use the corresponding button of the toolbar You can convert a visual template to a presence area going to Layers Visual templates Convert to presence areas A dialog box will ask you the valid habitats for the species and the corresponding areas will be added to the map 2 14 1 Using visual templates to unfill or intersect You can use visual templates as patterns to unfill a portion of a presence area or to calculate the intersection with a presence area For example in this map a presence area and next a visual template have been added File Edit Samples View Layers Mapping ModestR tools Options Help ADMIN Y PRUEBAS BOJA HHHOO p aoa el M Sb r FALA A Map MEM aker R w F ED 2 HF CT Samples V Valid V Invalid Freshwater habitats Coordinates Decimal Degrees Detail Level 1 Viewing from 24 58081 6 040792 to 58 18497 39 95609 Ready 61 ModestR Software Quick start tutorial Then going to Layers Visual templates Unfill using visual template the result will be File Edit Samples View Layers Mapping ModestRtools Options Help ADMIN Y PRUEBAS BOSG BG4 9R a Oo 26 8 9 4 Bs k FALA Detail Level 1 Viewing from 24 58081 6 040792 to 58 18497 39 95609 Ready In turn if we used Layers Visual te
33. Export Export maps of the selected 30 Futher information about Maxent software can be found in Steven J Phillips Miroslav Dudik 2008 Modeling of species distributions with Maxent new extensions and a comprehensive evaluation Ecography 31 2 161 175 DOI 10 1111 j 0906 7590 2008 5203 x 167 ModestR Software Quick start tutorial branch To Maxent in main menu or equivalent option in the tree contextual menu A dialog box will be shown Map exportation to MaxEnt Pseudosamples coordinates Select data export style Longitude Center Right Latitude Center Top Valid samples only for samples map data Presence pseudosamples data Pseudosamples exportation options Select samples precision 5 minutes cells Add sample is species is present in one cell Add sample if species occupies atleast 22 1x1 minute blocks in cell Xx Cancel Options are quite similar to the ones explained in section 6 14 excepted for the absence of some options such as environmental variables or full taxonomy exportation as those options are not suitable for Maxent Once accepted DataManager will generate and export a CSV file with selected species data Consult the Maxent documentation for more details about how to import and use them in Maxent software 6 22 Exporting species data to RWizard applications DataManager can export species presence data in a format specifically designed to be imported by particular RWizard a
34. ModestR Software Quick start tutorial On the left side there is a tree where you can explore the taxonomy ranks by expanding the branches You can also select any branch using the corresponding checkbox All selected branches will be exported when clicking on the Export button located on the bottom right corner The Export button will only be enabled if there is at least one branch selected to be exported On the right size of the dialog there are two tabs The first one is the Export options tab in this tab you can select the levels to be included when exporting data By default only levels supported by ModestR are selected You can select other levels but in this case exported data would not be suitable to be imported to a ModestR database In this tab you can also change the field separator to be used when exporting data to CSV and require that only taxonomic ranks that meet Taxonomic Work Group standard will be shown and exported Finally you can enabled the option for the exported data to be imported to currently opened ModestR database In this case after exporting data from ITIS database to a CSV file DataManager will import this same file to the current ModestR database The other tab is the Search tool tab In this tab you can enter a text in a textbox and all ranks from the ITIS database that start with this text will be shown on the list below At least 3 characters are required to start searching You can filter results by kingdoms u
35. Presence the minimum detected value of this variable where the species is present according to the used distribution data o Max Presence the maximum detected value of this variable where the species is present according to the used distribution data o Mean Presence the mean value of this variable where the species is present according to the used distribution data o Min Absence the minimum detected value of this variable where the species is absent according to the used distribution data Remember that absence is determined as the areas of the EOO or full extent of the species where it is not present o Max Absence the maximum detected value of this variable where the species is absent according to the used distribution data o Mean Absence the mean detected value of this variable where the species is absent according to the used distribution data 6 19 Exporting clipped rasters In section 2 9 4 we described the raster clipping feature in MapMaker This feature is useful when having to cut off some rasters using some single pattern But sometimes you may want to cut off rasters using as pattern the specific EOO of a set of species It should be too tedious having to do it species by species Therefore you can use DataManager raster clipping feature to do it in a single operation To do that the raster files have to be previously integrated in ModestR typically as environmental vatiables Details about how to integrate
36. Sosa isssnstic eicasisotdcanon ane e E EAEE Ri 36 2133 Rastercolor scale setting S searreinere rnea EE 36 ZN Rer Cd ba ClO NS secs N 38 2 13 5 Adding a kernel density Map as raSter cccccescccccsssccecesseccceeseceeeeeceeeaeseeeeeuaeess 39 2 14 Working with visual TEMDIACES sccwsiccnissssnvesduchavececseceeaiwenedsiasueussstusassaanesedaaaweieteteesonnneds 59 2 14 1 Using visual templates to unfill OF iNntersSect essseeeeseensesreresrressrrrresrrrrerrrrssene 61 2 15 Other useful features cccccccsesssssseeeccccceeeesseecccccesaueesseeeecceesaeeusseeececeessaganseeeeeeeesaaas 66 Llr og 0 9 72 OS elemen eee ne een ee 66 2 15 2 Querying distance between TWO POINTS ccccccesseccccessececeesececeenecceseeeeeeeeuaeees 67 ModestR Software Quick start tutorial 2 15 3 Querying a point in OpenstreetMaps or GOORIEMADPS cscccccssseceeeeseeeceeneees 67 Zoey EMC IPC IIMS presence Al Oa Seca ctecentoccacenccuisencsstcnoateiainenaascarosseusennnsduneeaoatensunsenceoaiece 67 2 15 5 Showing environmental data at MOUSE CUISOF ccccccssseccceeseceeeeeceeeeeseeeeeeneess 68 2 156 Raster transformation TOO I istensernevaedcesesvesaduestnncrswausnatescinenavensucseeuacieieuecens 69 BAS Me ergmg FADS sesira e S e 71 2 16 Exporting data and reports sccscsssincosiececsiszesiiacisiacosiacninatidadanaasaandoaiaieesnidesnsaeoecaazent 71 217 SavneaMapMaker MaDe E E 72 ZAG Retrieving a Map nccecrcesscevccevrcestvarr
37. The output will be a CSV file with this format CoordLastModified column indicates the date when each sample coordinate has been modified see section 3 14 for some explanations Taxonomy columns are optional depending of selected settings As well as the last column of this example which here is the Bathymetry variable Class Order Family Genus Species Longitude Latitude CoordLastModified Bathymetry Batoids Batoids Batoids Batoids Batoids Batoids Batoids Batoids Batoids Batoids Batoids Batoids Batoids Pristiformes Pristiformes Pristiformes Pristiformes Pristiformes Pristiformes Pristiformes Pristiformes Pristiformes Pristiformes Pristiformes Pristiformes Pristiformes Pristidae Pristidae Pristidae Pristidae Pristidae Pristidae Pristidae Pristidae Pristidae Pristidae Pristidae Pristidae Pristidae Anoxypristis Anoxypristis Anoxypristis Anoxypristis Anoxypristis Anoxypristis Anoxypristis Anoxypristis Anoxypristis Anoxypristis Anoxypristis Anoxypristis Anoxypristis Anoxypristis cuspidata Anoxypristis cuspidata Anoxypristis cuspidata Anoxypristis cuspidata Anoxypristis cuspidata Anoxypristis cuspidata Anoxypristis cuspidata Anoxypristis cuspidata Anoxypristis cuspidata Anoxypristis cuspidata Anoxypristis cuspidata Anoxypristis cuspidata Anoxypristis cuspidata 153 100 095833 75 149 600006 149 600006 75 146 83
38. This can be useful to use species distribution presence areas as a template to add intersect or just visualize them over another species map You can use the View Show visual templates menu item or the corresponding button of the toolbar to show hide a visual template In the option Layers Visual templates Set visual template transparency you can change the transparency degree of the visual templates From ModestR version 2 0 a collection of predefined visual templates is provided with ModestR that are displayed under the ModestR Preselections node of the tree but you can also add your own visual templates that will appear under the User selections node of the tree To do that go to Add visual templates option Initially you will meet an empty list To import your own templates from KML or shapefiles you can go to Layers Manage visual templates A dialog box will be shown where you can add new templates and organize them in a tree You can see more detail in section 4 11 about predefined selections in MRFinder which support the same feature When a predefined visual template is added to the map e g a country a river basin its name is displayed on the mouse cursor when you place the mouse over it 60 ModestR Software Quick start tutorial o i Stored selections a Countries 5 Europe ee Albania met Austria C Select childs of this node when selecting it Selection data a Import E Clear
39. XX for MapMaker to select automatically the variables with the higher contribution to reach the indicated that you can modify Selected variables will be highlighted in the list Similarly to the Layer extent option described in the previous step variable contribution can be calculated for the full extent for a visual template or for the EOO given that a visual template or occurrence data are present on the map as explained before Take into account that extent used to calculate variable contribution could be different from the extent selected for the environmental layer ModestR does not establish any limitation in this sense so the convenience of using one or another option is left to the user Click on Continue button to go to next step In this step definitely selected variables are shown on the list and on the right panel a representation of how they will be ordered to calculate polar coordinated is displayed Variables are automatically ordered according to their relative correlations the next variable to another is the one which as the higher correlation with it You can eventually manually change order by selecting a variable in the list and using the buttons located on the right of the list 52 ModestR Software Quick start tutorial Environmental layer generation Select Variables Analysis Variable analysis Order Processing Scale Options Variable ordering in polar space Polar space Corel mat
40. a short emerging explanation will be shown Data Cleaning calculation Select Variables Processing a ee ey Validation mode combo box Selected Variables Cover Variable settings a 0 44 REV Name Althymetry Bathymetry 99 56 OK Calcite 100 00 OK Validation mode Chlorophyll a 100 00 OK Autoselect best larger n of accepted values Sea surface temperature 100 00 OK Automatically selected outliers mode Apply Quartile outliers A to All Consider extreme outliers as invalid Min accepted value 376 Max accepted value 705 5 Missing value options Missing value options C invalidate an area if the value for this vanable is missing abo to Don t take into account this variable when its value is missing Select the variable on the list to see its outlier determination a l Main variable settings settings and basic information Allowed invalid variables 0 Allowed missing variables 5 i Cancel 4 Previous Continue gt Then you can select how outliers will be detected for each variable To do that you must select a variable on the left listbox The corresponding settings for this variables will be shown on the right up panel The available settings are e Validation mode this is the way the values for this variable on the presence zones whether samples or areas will be evaluated to determine
41. appear where you can change the color For presence areas range maps the color editor will include the possibility of changing the fill pattern the foreground color and the background color as well as the transparency for each one It may be convenient to use a more or less high transparency for a better visualization of overlappings between several map items e g several species distributions 137 ModestR Software Quick start tutorial Select fill brush properties Brush fill style selection Selected brush Color settings E E EE EEEE E EErEE f E oe reir E ME E E EME Foi enn id color REEERE EEEE R E SY om a x Transparency 0 Background color Transparency 61 It is worth to mention that any modifications done in the Map list editor can easily be undone Just close the Map list editor and use the Undo button or the Edit Undo menu option in the main window 5 3 Adding new elements to the map Even if the main usage of MRMapping is adding already existing distribution maps you can eventually add presence areas or samples directly to the world map the same way you can do it in MapMaker see 2 2 and 2 3 Those elements will appear in the Map list editor seen above under the item name User add operations You can also add arrows text or placemarks to the map the same way you can do it in MapMaker see 2 16 1 Finally you can show in the map rasters e g environmental data and visual temp
42. area 7 10 Export occupied areas summary report This option generates a report in CSV format with the areas in km of each type of habitat where the species is present A similar report but for any set of species not just of one can be obtained using DataManager Moreover in MRMapping a similar report is available for any rank or arbitrary group of species families orders etc MRFinder offers a similar feature to calculate the area of any arbitrary selection in the map In MapMaker this options is located in the menu File Export Areas summary report MapName Total AOO Sea Area Land Area Large rivers Small rivers Lentic water Small channi Large channe Small ditche Large ModestR Map 698894 584 O 698894 584 0 0 0 0 0 0 The output format is a CSV file with the following columns e Total Area Of Occupancy of the species Total AOO e Total area for each habitat type occupied by the species Sea Area Land Area Large Rivers Area Small Rivers Area Lentic waters Area etc e Minimum and maximum coordinates where the species is present Min Longitude Max Longitude Min Latitude Max Latitude 7 11 Export environmental layer report As explained in 2 11 when creating an environmental layer you can export a report that contains several files about the created layer You can export this report any time later going to menu Mapping Niche of occurrence Manage environmental layers Select the wanted layer in the list that will appear and
43. assume we have a map with the samples shown below 11 For more information on kernel smoothing you can see Wand M P amp Jones M C 1995 Kernel Smoothing Chapman and Hall London 32 ModestR Software Quick start tutorial To calculate density estimation hull just go to Mapping Hull transformation Kernel Density Distribution Map menu option A dialog box will be shown where you can set the parameters and select the wanted feature Kernel density estimation Kemel density estimation options Parameters Cell width 5 minutes 7 Dont use duplicates Lower Normal Higher Smoothing X Perform Density hull visual simulation Add as presence area HK Grose gf Appi e Cell width in minutes allows you to set the cell size to be used to calculate density Density will be calculated for each cell and assumed to be the same in all the cell So the smaller the cell size the more precise is the density calculation But take into account that the time to perform the calculations grows geometrically as cell size diminishes e Don t use duplicates if enabled only distinct samples usually considered until the 5 decimal will be used to calculate kernel density This avoids biasing density because there are many duplicates of some samples e Smoothing smoothing factor determines how smooth the density matrix will be The greater it is the more the density will soread out far around presence ar
44. can return several separated polygons and it may not contains all the samples depending on the alpha value and the distances between the samples You can easily test alpha shape with different alpha values to see the differences and select the value you consider more accurate e Add as presence area this option will add a presence area to the map corresponding to the alpha shape hull Existing data will not be deleted but this adds a new presence area to the map The habitats assigned as valid to this new area will be inferred from the already existing presence data samples and areas You can undo changes using Edit Undo or modify this new area using Unfill feature see section 2 2 2 8 3 Using density based hull with samples The density estimation algorithm calculates one or more polygons that contain all the samples on a map depending on a parameter usually called the bandwidth The density is estimated using a kernel smoothing normal distribution algorithm As the bandwidth is increased the estimated hull is broader while it tends to the initial set of points when it is decreased Density hull in ModestR is calculated using as cut off threshold the minimal density value for the Samples present on the map This way all samples will always be included in the calculated hull At least three samples are required to calculate density This feature cannot be used with areas so it is mainly useful in sample maps As an example we ll
45. click on Edit details button A panel will be displayed on the right where you can click on the Export report button The exported report contains the following files e Name of the layer Axes JPG an image with just the axes used to define the polar coordinates 182 ModestR Software Quick start tutorial Name of the layer _ColorMap ASC an ASC raster where each cell contains the color value of each cell according to the environmental layer as a 32 bits integer that corresponds to an ARGB color Name of the layer _ColorScale JPG an image with the axes used to define the polar coordinates and the full rectangle that represents the color scale assigned to the rectangular area where there are data in the layer Name of the layer _DataScale JPG an image with the axes used to define the polar coordinates and a point for each cell of the world map or the region used to calculate the environmental layer in its corresponding location in the polar coordinates system and with its corresponding color Name of the layer _X ASC an ASC raster where each cell contains the X coordinate of the cell in the polar coordinates system of the environmental layer Name of the layer _Y ASC an ASC raster where each cell contains the Y coordinate of the cell in the polar coordinates system of the environmental layer 183 ModestR Software Quick start tutorial 8 MRFinder import export files format In this section we briefly explain
46. csvercsvensusercussrcncaversencusurencuvsresvarsrrercusarensans 135 5 3 Adding new elements to the Map cccccccsssccccessececeesececeeesececeeseceeseaeceeeeeseeeeseneess 138 5 4 Importing file of visual template NAMES cceeseccceeseccccessececeeseceeeeeececeeeceeeeeeeeetas 138 5 5 EXDOrUN aL INAS CHIE vciichixvestavaessatesdnciabiiaevnniesdawecteniedinioavdroieiltaleamcianGiesiaves 138 5 6 Exporting environmental data Raster data ClIPPING cccceesecccesseceeeeeeeeeeeeeeeeees 139 5 QUANTIFYING occupied ALCAS ccccccssseccccesscccceesecccceeceecesececeuseceseugeceeeeuecetseneceeeuees 140 5 8 Quantifying overlapping areaS ccecccccsssccccesecccceeceeceeseceeeuececeeeeceeseusecetseneceesuees 140 6 DataManager import export files format ccccssccssscsscssccssscescssscesssesensees 141 6 1 Importing taxonomy from a CSV file ou eecccccsssececeesececeeeecceeeeseceeeeaecetseeeceeseneeeetas 141 6 2 Importing taxonomy from another ModestR database cccccccssseceeeeseeeeeeeeeeeees 141 6 3 Importing taxonomy from PhylOXML files cccccceeseccceeseececeesececeeeceeeeneceeeeneeeeeas 141 6 4 Importing taxonomy from ITIS database ceeccccessecccceseececeesececeeeceeseneceeeeeeeeetas 141 6 5 Importing Map Files from MapMaker map files cc sseccccesseccceeseceeeeeeceeeeeeeeeees 142 ModestR Software Quick start tutorial 6 6 Importing Map Files from another ModestR
47. database ccccccssccccsessceeeceeeneeeeenses 142 6 7 Importing samples from GBIF online database ccccesecccssesccesecceececeueceseeeeeenees 143 6 8 Importing Samples from CSV files cccccceseccccessececeeececceeseceeeeseceeeeecesseaeceesegseeetas 146 6 9 Importing samples from Darwin Core Archives cccccesecccesescceeeseeececeueceneeseeeuess 147 6 10 Importing data from distribution models ccc ceeeccceeeceeeeecceeececeeeceseueceeeneceeeeeens 148 6 11 Importing distribution Maps from shapefiles ccccceecccssececesceseeececeeeceeeeeeeeneeees 149 612 Exporting taxonomy to a CSV TG wcsvessencercoc ctavecaciducesnocesesancadetembeienmcadunemmenaten 151 6 13 Exporting maps to standalone map files seseeuseseessrenssrreresrrressreresrrrrerreresrrresseere 152 6 14 Exporting presence data to CSV data files eeeneesesseeneernserresrrrssrrserersrrresrreereseeee 152 6 15 Exporting presence data to raster files sseeeedienesrersrrserrnssrrrsrrnssrersrersrreesreeerereeeee 155 6 16 Exporting samples to Darwin Core Archive Style c cccccceeecccescsceeececeeceeeeseeeneeees 156 6 17 Exporting metrics and environmental data ccccccesececssescceseeceeeceeeeceeeeseeeneeees 157 6 18 Exporting variables contribution report seseeeseseesesrrrsssrrrosrtessserresererssrereserersseeee 161 6 19 Exporting clipped rasters cccccc NE aeeoe eeo A cececscecseresauere
48. depending on the number of maps to be exported 6 25 Exporting JPEG BMP density map images DataManager can generate and export JPEG BMP images from density maps calculated for each species An example of those maps is explained in 2 9 5 When selecting Export Export maps of the selected branch To JPEG BMP density maps in main menu or equivalent option in the tree contextual menu a first dialog box to select kernel density calculation setting The settings here are quite the same than explained in 2 9 5 Density based Hulling Options Density based hull options Parameters Maps to include Include only sample maps Cell width 5 minutes J Dont use duplicates Include all maps Density map options Lower Normal Higher w Show only significant densities lo Visual filtering Smoothing X 1 00 By habitat pin Transparency 39 Kenca of OK Then another dialog box to select the output folder will be shown Next an exportation settings dialog with several tabs is shown that is the same than explained in 6 24 excepted for raster and template settings that are not available here The exported image is by default a full world map view If you want to export a specific zoomed view you should set the wanted boundaries in the first tab Dimensions and format Remember that in the last tab Display options you can select which elements from valid invalid samples text arrows or placemarks will be shown on th
49. e Precision the dimensions of the cells that will be used to calculate gradients in degrees from 12 to 102 Latitude precision indicates the height of the latitudinal bands for which gradients will be calculated Longitude indicates the width of the cells that latitudinal bands will be split in to calculate some of the metrics into the latitudinal bands Other metrics will be calculated globally for all the latitudinal band without taking into account longitudinal cells e You can also select which habitats have to be included in metrics calculus By default all habitats are took into account If you exclude one habitat all samples or zones with this associated habitat will be excluded from the calculus e You can define the zone boundaries to be examined in degrees with a minimum of a 12x12 zone Output will be generated as a CSV file with the following columns e Latitude top limit of the latitudinal band e Total Species Richness total richness of the latitudinal band This metric is calculated globally for all the latitudinal band without taking into account longitudinal cells e Mean Species Richness mean of the richness of the cells of the latitudinal band taking cells of the longitude width in degrees indicated in the dialog box described above That is the richness of each cell of the longitude width and latitude height in degrees indicated is calculated for a latitudinal band and then the mean of all those values is calculated
50. each species present in this cell n l Xari n cell and P is the Patch distribution index taking into account all the world of Patch index for each cell as CPI where n is the richness of the each species present in this cell Patch index of each species has been previously calculated when processing maps In subsection 6 23 you can find and explanation of patch index for each species is calculated yi A00 n of the cell and AOO is the Area Of Occupancy taking into account all the world o AOO index for each cell as CAI where n is the richness of each species present in this cell n yin FOO n of the cell and EOO is the Extent Of Occurrence taking into account all the o EOO index for each cell as CAI where n is the richness world and using convex hull method of each species i present in this cell 158 ModestR Software Quick start tutorial n 1 i 1LR n richness of the cell and LR is the latitudinal range that is the higher latitude o Latitudinal range index for each cell as LRI where n is the minus the lower latitude taking into account all the world of each species i present in this cell o Habitats area the area in Km for each kind of habitat in this cell Take into account that this value is calculated using a raster world map of 1 x1 precision making results only roughly approximate particularly for rivers and small freshwater areas Except for the CSV lis
51. environmental data in ModestR are explained in section 6 26 First select the wanted group order family of species to use as patterns in the DataManager taxonomy tree Then go to Export Export maps of the selected branch To clipped environmental data in the main menu or the equivalent option in the tree contextual menu A dialog box will appear where you will have to select the destination folder As existing files with the same name will be overwritten we recommend to select an empty folder Next a dialog box will appear where you have to set the exportation options e Select the variables raster data you want to export in the left tree e Select which maps you want to export only sample maps only area range maps or both e Select if you want to create a subfolder where clipped raster files for each species will be stored Those folders will be named as the corresponding species 163 ModestR Software Quick start tutorial e Select how EOO will be calculated for each species This EOO will be the pattern used to cut off selected rasters for each species More details about each EOO calculation mode can be found in section 3 6 Once those settings set click on the OK button and exportation will start Take into account that this process can require quite some time depending on the number of selected species Environmental clipping options Environmental variables to clip and export S Environmental Variables
52. for a latitudinal band and then the mean of all those values is calculated Be aware that only cells with a richness value bigger than zero that is where there at least one species present are took into account to calculate the mean Details about patch index metric can be found in section 6 17 above e SD Patch Index standard deviation of the area index of the cells of the latitudinal band calculated in the same way than Mean Patch Index e Mean Latitudinal Range Index mean of the latitudinal range index metrics calculated for each one of the cells of the latitudinal band taking cells of the longitude width in degrees indicated in the dialog box described above That is the latitudinal range index of each cell of the longitude width and latitude height in degrees indicated is calculated for a latitudinal band and then the mean of all those values is calculated Be aware that only cells with a richness value bigger than zero that is where there at least one species present are took into account to calculate the mean Details about latitudinal range index metric can be found in section 6 17 above e SD Latitudinal Range Index standard deviation of the area index of the cells of the latitudinal band calculated in the same way than Mean Latitudinal Range Index 166 ModestR Software Quick start tutorial e Mean AOO mean of the AOO of all species present in the latitudinal band taking into account the AOO that each species occupies i
53. for each selected environmental variable Be careful because any existing file with the same name will be overwritten A report in CSV format is also generated with data about clipped areas in km and simple Statistical measures max min mean std and quartiles for the environmental data in the clipped areas see 7 9 about the similar report in MapMaker for more details 5 7 Quantifying occupied areas Similarly to MapMaker you can quantify and export a report about the presence areas of each map item dataset in the world map The difference being that in MapMaker this feature allows you to measure the presence areas of a single species while in MRMapping as in the world map you could have added several map items datasets from several species families orders etc you can measure the presence areas of each one of those map items To do that go to File Export Areas summary report This generates a report in CSV format with the areas in km of each type of habitat where each map item is present See 7 10 for details about the exported report 5 8 Quantifying overlapping areas MRMapping can quantify the areas where several map items overlap That is the areas where two or more species or any other rank you added to the map such as families orders are present To do that go to File Export Overlapping report You can choose between a short report and a full report The short report contains data about total overlapping areas and p
54. from origin database 6 7 Importing samples from GBIF online database You can import samples and create maps downloading data from GBIF database Global Biodiversity Information Facility http www gbif org This can be done using the Import Import presence data From GBIF samples for selected branch menu item in the main menu or the Import presence data for this branch From GBIF samples option that will appear in the contextual menu of the taxonomy tree clicking with left mouse button on the desired element of the tree GBIF samples importation options GBIF download options Download data only for species without map in the selected branch Merging method Ei Download data only for species with map in the selected branch i a Download data for all the species of the selected branch See Kind of records to download 7 All Select region boundaries L3 Observation Preserved Specimen E Human Observation E Fossil O Machine Observati E Living specimen From longitude 180 0 to 180 04 Material Sample E Literature E Unknown From latitude 90 0 to 90 0 Check if species is a synonym according to GBIF Temporal bracket Opronaily enter start andlor end dates using Cran oe n format YYYYMM DD a aM Occurrences modified since a date borona enter a date using the iomat YYYY MALDO Modified since poe o Samples conversion Make habitat auto checked Skip samples with same longitude and latitude Skip samples in 0
55. in one superior level for example they have a different family two species will be considered as different during importation Next two options affect overwriting maps during importation e Import only new maps from origin database if selected only maps for species that don t have maps in the currently opened database will be imported Existing maps will not be overwritten Of course maps for species that don t exist in the currently opened database will be imported or not regarding the option selected regarding taxonomic data importation previously described e Overwrite existing maps in current database with maps from origin database if selected existing maps in the currently opened database could be overwritten if there is a map for the same species in the origin database 142 ModestR Software Quick start tutorial You have to take care of the fact that different combinations of the selection options will affect maps importation in different ways Import maps from another ModestR database CAJModestR Mapas Pezong DB Select DE file Taxonomy importation options Import only maps for species already existing in the curent database Import maps from all species of the origin database new taxonomies will be added to curent database if needed Maps importation options Import only new maps from ongin database edsting maps will not be 7 overwntten 9 Overwrite existing maps in curent database with maps
56. listed and so on Total Species Column will contain the total number of species in the current taxonomic level class order family Here is an example Class Order Genus Species Total Species Map exists Mammalia Carnivora Canidae Canis adustus Canis aureus Canis latrans Canis mesomelas Canis rufus Canis simensis 6 13 Exporting maps to standalone map files You can export maps of any branch of a DataManager database to standalone map files files with PMMAC extension using the Export Export maps of selected branch To Standalone map files option The exported files can be opened with MapMaker This option will ask the user for selecting a folder and it will export all maps from the currently selected branch of the database to this folder Maps exported will contain full taxonomic information 6 14 Exporting presence data to CSV data files You can export maps of any branch of a DataManager database to CSV using the Export Export maps of selected branch To presence data To presence data and variables option This feature furthermore allows including environmental variables in the exported data This option will show a dialog box with several selections A brief explanation of each option of this dialog box will be shown in an emerging tooltip if you place the mouse on it On the left groupbox you can select if the exported data will be exported to one separated file for each species of the selected 152 ModestR
57. maps that contain polygons e g range maps This operation implies geometrical calculations that can take some time depending on the complexity of the polygons to merge Once completed you ll see that the resulting intersection areas will be added as a new single item in the list which name is by default the concatenation of the names of the intersecting items Finally you can edit the name and color settings of any map item by selecting it not checking it just selecting it in the list and clicking the button Edit A dialog box will be displayed where you can change the name and the color settings of the map item You can change individually the color assigned to the presence areas for each type of habitat as well as for samples This allows for example to assign a different color to presence areas located in the sea and to those located in the land Edit submap settings Map name Pristis pectinata Samples colors Habitat auto User rule validated Marker size 100 validated sample sample ees Samples Habitat auto User rule invalidated z 50 invalidated sample E sample E Transparency Presence areas colors and GZ E sa PZZ o Large rivers LZ Large Channels LZ Large Drains ie Small rivers Small Ditches Lentic habitats D Wetlands Large Ditches Reservoirs LZ Small Drains Small Channels nce To change any color just double click on the corresponding color rectangle A color editor dialog will
58. match a pattern that can be the presence areas of a map or a visual template see 2 14 for visual templates features To do that the raster file has to be previously integrated in ModestR Details about how to integrate environmental data in ModestR are explained in section 6 26 For example let s suppose we have this map with two presence areas in the sea File Edit Samples View Process Tools Options Help BOSQBG4 9C aoc 20 8 I wo BX ul VLLao rin jr A aia Ro 7 er a Lat 16 16982 Lon 19 61023 Detail Level 0 Viewing from 84 07377 27 98652 to 56 15112 49 94312 Ready Now we want to export Bathymetry data from the corresponding raster just for those areas We ll go to File Export Environmental data For presence areas A dialog box will show to you the available variables those previously integrated in ModestR We ll select the wanted one it could be more than one to generate several clipped files Next we ll have to selected the target folder where the file will be saved in ESRI ASC format Be careful because any existing file with the same name will be overwritten A report in CSV format is also generated with data about clipped areas in km and simple statistical measures max min mean std and quartiles for the environmental data in the clipped areas see 7 9 Here we can see the resulting raster which only contains data for the selected areas 38 ModestR Software Quic
59. of occurrence of a species In this process the areas where a species can potentially be present are determined basing on their proximity to the environmental conditions where the species is present in the polar coordinates system You can create environmental layers for the entire world or for a selected area Environmental data needed to use this features are not included in ModestR so they have to be provided by the user as data files in ESRI ASCII or CSV format There exist free datasets available in Internet such as Bi Oracle for example that are fully compatible with ModestR Therefore the first step will be to integrate those data in ModestR to allow it to use them when needed To do that you can use the menu Layers Manage environmental variables either in MapMaker or in DataManager Details about how to integrate environmental data in ModestR are explained in section 6 26 i Tyberghein L Verbruggen H Pauly K Troupin C Minur F de Clerck O 2012 Bio ORACLE a global environmental dataset for marine species distribution modelling Global Ecology and Biogeography 21 272 281 49 ModestR Software Quick start tutorial 2 11 1 Step by step environmental layer Environmental layer generation creation Select Variables Analysis Order Processing Scale Options To create a new environmental layer go to the Purseen as menu Mapping Niche of occurrence Create new gris i v Bathymetry environmen
60. of one can be obtained using DataManager Moreover in MRMapping a similar report is available for any rank or arbitrary group of species families orders etc MRFinder offers a similar feature to calculate the area of any arbitrary selection in the map 2 18 Saving a MapMaker map A map can be mainly saved in two ways e Toa standalone map file this option allows you to save a map in a standalone file with extension IPMMAC which will only contain this map in a specific format based on XML In this case taxonomic information about the map is not mandatory but it will be saved if you provide it To enter this information before saving a map you can use the menu item Edit Assign taxonomy for current map or the corresponding button of the tool bar A dialog box will allow entering taxonomic data or selecting it from a ModestR database if you have configured it previously Select taxonomy for current map meal Introduce taxonomy data Class Elasmobranchii a Select from a database Order Carcharhiniformes Family Carcharhinidae Genus Carcharhinus Species Carcharhinus acronotus e Toa ModestR database using File Save To ModestR maps database option menu that allows you to save the map associated to a species previously existing in a ModestR database In this case taxonomic information about the map is mandatory and you will be asked to provide it before saving the map eventually selecting it from a t
61. parts of this zone will be filled in to indicate the presence of the species Filling colors as well as map element colors can be modified in the Options Preferences menu File Edit Samples View Process Tools Options Help s E oo ite Detail Level 0 Viewing from 70 79903 50 44567 to 73 05214 59 33085 Ready You can unfill part of a selection just selecting a zone and using Unfill button 13 ModestR Software Quick start tutorial File Edit Samples View Process Tools Options Help B2O8E8Gn 9R 490 26 8 9 S Map a if Gia G y Detail Level Auto Low Med High Highest L Daana Select the area to unfill and press the Unfill button FreeHand Rectangle sa Spare oo ST 5 Tet His p Del te pee jobjects Sample Valid habitats Sea F I and File Edit Samples View Process Tools Options Help BOSE BG 9F amwage sE Samples Valid V Invalid Freshwater habitats 7 Al Select gt If you want to fully undo an operation you would rather use the Undo button of the toolbar or the Edit Undo option in the main menu or the Ctrl Z key combination Operations that can be undone in MapMaker are those that affect the map distribution data such as adding or removing samples presence areas etc Operations that only visualize data such as displaying environmental data or visual templates
62. quartiles for the environmental data in the clipped areas The format of this report is like that when clipping using visual templates the report will contain a section for each visual template 181 ModestR Software Quick start tutorial Species _1 Total Area Sea Area Land Area __Large rivers Small rivers Lentic water Small chann Large channeSmall ditche Large ditche Small drains Large drains Reservoirs A Wetlands Ari Species 1 698894 584 O 698894 584 0 0 0 0 0 0 0 0 0 0 0 Species 1 Species 1 Variable Num Values Min Max Mean Std Sum Quartile 1 Quartile 2 Quartile 3 Species 1 Altitude Clip 11077 1 2731 597 31868 410 90834 6616499 254 567 851 Species 1 BlO1Clippec 11321 0 7 19 2 13 22012 2 77992 149665 11 6 13 1 15 4 Species 1 BIlO10Clippe 11321 7 9 28 20 72597 2 97527 234638 7 18 8 20 4 23 2 Species 1 BlO11Clippe 11321 5 3 12 9 6 30609 2 97016 71391 3 4 4 6 8 6 The columns are e Total Area in km of the area used to clip the rasters e Total area for each habitat type of the area used to clip the rasters Sea Area Land Area Large Rivers Area Small Rivers Area Lentic waters Area etc e For each variable clipped Number of not null values cells in the clipped area Minimum and maximum value of the variable in the clipped area Mean and standard deviation of the values of the variable in the clipped area Sum of the values of the variable in the clipped area O O O O Quartiles of the variable in the clipped
63. rr Once accepted raster will be loaded and shown on the map like this I Tyberghein L Verbruggen H Pauly K Troupin C Minur F de Clerck O 2012 Bio ORACLE a global environmental dataset for marine species distribution modelling Global Ecology and Biogeography 21 272 281 35 ModestR Software Quick start tutorial ModestR MapMaker New Map1 RASTER Bathymetry File Edit Samples View Process Tools Options Help BOsGH H4 OR A REPI Bly ui FLLeo Map s Ful 9 Detail Level Auto Low Med High Highest od Map Tools Zoom Select gt Drag map Show distance FreeHand gt Rectangle Add sample gt Edit sample Samples V Valid 7 Invalid gt Lat 73 08307 Lon 74 60564 4 Detail Level 0 Viewing from 180 0009 108 7787 to 180 0009 108 7787 Ready A color scale will be shown on the right of the map but it can be hidden using the gt gt butto You can change the raster to be shown just by doing the same steps and selecting another variable To temporally hide show this raster you can use the menu item View Show selected rasters or the corresponding button of the toolbar To definitely clear the raster from the map you can use the menu item Layers Raster templates Clear raster template or the corresponding button of the toolbar 2 9 2 Loading raster file
64. sea habitats 18 ModestR Software Quick start tutorial Delete a group of samples to delete several simply select an area that contains the samples you want to delete using the Freehand or the Rectangle tools from the left tool panel and press the Delete samples button on the Fill Selection groupbox Or use the context menu item Selected samples Delete samples pressing the right mouse button to show it Take into account that only samples that are currently visible in the selected area will be deleted If for example you set display selections to only show invalid samples only those samples will be affected by a delete operation samples can be shown hidden using View Map Show Options Show Samples menu or in Show options in the left tool panel ModestR MapMaker FILE C ModestRProject BD Carcharhinus leucas IPMMAC Carcharhiniformes Carcharhinidae Carcharhinus Carcharhinus leucas eller File Edit Samples View Process Tools Options Z2aesa hGH 9 4 RG Map __ DE a _ Detail Level af Map Tools Zoom Select Drag map Show distance FreeHand Rectangle Add sample Edit sample Large rivers Small drains Auto Low Med High Highest Select an area that contains samples to be deleted using the Freehand or the Rectangle tools Press Delete Samples button Z Large channels Small ditches Large drains in the current selection y currentl
65. selected value is displayed after importation e Valid habitats you have to select which habitats at least one are valid for the species data you are importing Only areas corresponding to those habitats will be accepted and shown in the map Import from ESRI ASC probability distribution data Set probability cutoff for data to be imported Probability cutoff 0 7500 4 Select valid habitats for the species E Sea Z Land All freshwaters Lentic habitats Small Channels Small Ditches x oes Small rivers Large Channels Large Ditches Large rivers Small Drains O Wetlands Reservoirs Large Drains 33 Futher information about Maxent software can be found in Steven J Phillips Miroslav Dud k 2008 Modeling of species distributions with Maxent new extensions and a comprehensive evaluation Ecography 31 2 161 175 DOI 10 1111 j 0906 7590 2008 5203 x 176 ModestR Software Quick start tutorial Once accepted this dialog box the importation process will start MapMaker will transform each cell with a probability greater or equal than the selected cutoff value to an occupied area in the map applying the selected habitats This way if a cell or some portion of it is not located in the habitats selected as valid it will not be shown in the map or only the valid portion will be shown It is important to take into account than some imported areas can be very small therefore not visible in a full world map view To a
66. the bounds of the selected area Mean Max Latitude this column summarizes the mean of the previous column for each higher taxonomic level from genus to subclass within the bounds of the selected area SD Max Latitude this column summarizes the standard deviation of the maximum latitude where species are present for each higher taxonomic level from genus to subclass within the bounds of the selected area If there is only one species in a higher level for example in a genus this value will be obviously empty Minimum Latitude Mean Min Latitude SD Min Latitude those columns contain similar result than the three previous ones but for the minimum latitude where species are present Maximum Longitude Mean Max Longitude SD Max Longitude those columns contain similar result than the three previous ones but for the maximum longitude where species are present Minimum Longitude Mean Min Longitude SD Min Longitude those columns contain similar result than the three previous ones but for the minimum longitude where species are present Real Area Reference Area this column is the ratio between the real area occupied by a species within the bounds of the selected area and the reference or potential area that this species could take up in this selected area taking into account the valid habitats for this species For example is a species is only present in marine habitats only sea areas will be took into account to calculate refere
67. two options to export data e To clipboard this option will copy the coordinates longitude latitude of the vertexes of the selected region to the clipboard e Toa CSV file this option will export the coordinates longitude latitude of the vertexes of the selected region to a CSV file using the default delimiter and decimal point settings The resulting file will look like this Longitude Latitude 64 40827 37 33813 66 89748 38 27158 72 4982 39 5162 77 16547 40 1385 81 21043 40 1385 8 10 Export map view to an image file You can export the map view you are currently seeing in MRFinder to a JPEG or BMP file using the Export current map view button in the toolbar or the File Export Current map view as image menu option Next a dialog box will appear with several tabs The settings and steps are the same than in MapMaker see 7 6 8 11 Export selections to shapefile or KML You can export current selections in the map to a shapefile or a KML file using the File Export Current selection menu option and then selecting the wanted suboption All selections will be exported to the file in the selected format 189 ModestR Software Quick start tutorial 8 12 Export to ASC rasters This option generates a raster in ASC format with the selected precision where the cells corresponding to the selections in the map have a value not null usually 1 but can be selected by the used This option is located in the menu File
68. used as filter when importing You can also directly write a condition in the textbox The syntax of the conditions is similar to the syntax of a WHERE clause in SQL Papert ShageFile Options See hide fieldlist Yahm ee red y Eonian im iha file Import file C ModeetAProecfbiehspesiepeces_97O0 eho mpiiication tolerances m mrada 020 Optional teing citea jet back bc moor ai 4 LEGEND E E E 4 5 Using predefined selections To avoid having to make or to import a selection each time we want to use it to perform a search MRFinder can store predefined selections then you can easily reuse them All predefined selections can be shown going to Edit Add predefined selections menu or the corresponding button of the toolbar A dialog box will be shown where predefined selections are shown in a tree Those provided with ModestR are displayed under the ModestR Preselections node of the tree but you can also add your own predefined selections that will appear under the User selections node of the tree later in this chapter we explain how to store your own selections in this tree 113 ModestR Software Quick start tutorial Add a stored selection 3 ModestR preselections f World Basins 5 A World Countries Q Africa lt lt fi Antarctica fi Asia fi Central America fi Europe fi North America 4 Oceania Ei South America m i User selections FE FE FR
69. w Full Zoom Selections editor Current selections v World Countries South America Argentina World Countries South America Bolivia World Countries South America Brazil World Countries South America Chile v World Countries South America Colombia World Countries South America Ecuador World Countries South America Falkland Islands Malvinas World Countries South America French Guiana World Countries South America French Southern Territories World Countries South America Guyana World Countries South America Paraguay World Countries South America Peru World Countries South America South Georgia and the South Sandwich Islands World Countries South America Suriname World Countries South America Trinidad and Tobago World Countries South America Uruguay World Countries South America Venezuela Boe Detail Level 0 Viewing from 128 16 84 14703 to 96 30226 40 59737 Ready 4 11 Managing user predefined selections User predefined selections are a useful tool of MRFinder that allows users to store the areas they select on the map to perform searches for later usages as well as to import areas from existing shapefiles or KML for example As described before ModestR also includes other predefined selections such as world administrative areas but the user cannot modify those selections because they are regularly updated when installing new ModestR versions Here we are talkin
70. without taking into account longitudinal cells e SD Latitudinal Range standard deviation of the latitudinal range occupied by all species present in the latitudinal band taking into account the area that each species occupies in all the world independently from the range selected for the analysis This metric is calculated globally for all the latitudinal band without taking into account longitudinal cells e Mean Patch Distrib mean of the patch value of all species present in the latitudinal band taking into account the area that each species occupies in all the world independently from the range selected for the analysis In subsection 6 23 you can find and explanation of patch index for each species is calculated This metric is calculated globally for all the latitudinal band without taking into account longitudinal cells e SD Patch Distrib standard deviation of the patch value of all species present in the latitudinal band taking into account the area that each species occupies in all the world independently from the range selected for the analysis This metric is calculated globally for all the latitudinal band without taking into account longitudinal cells 6 21 Exporting species data to Maxent DataManager can export species presence data in a format directly importable by Maxent Maxent is able to import data in form of occurrences from one or more species To export this data select the wanted node in the tree then go to
71. 2993 140 166 80 3000031 80 3000031 80 3000031 80 3000031 136 75 136 75 9 58749962 10 22 2830009 22 2830009 10 19 25 17 4160004 13 0830002 13 0830002 13 0830002 13 0830002 12 1499996 12 1333303 11 05 2015 0 00 11 05 2015 0 00 11 05 2015 0 00 11 05 2015 0 00 11 05 2015 0 00 11 05 2015 0 00 11 05 2015 0 00 11 05 2015 0 00 11 05 2015 0 00 11 05 2015 0 00 11 05 2015 0 00 11 05 2015 0 00 11 05 2015 0 00 2204 7244 0 0 2204 7244 ModestR Software Quick start tutorial Batoids Pristiformes Pristidae Anoxypristis Anoxypristis cuspidata 141 516663 12 4333296 11 05 2015 0 00 Batoids Pristiformes Pristidae Anoxypristis Anoxypristis cuspidata 136 75 12 03333 11 05 2015 0 00 Batoids Pristiformes Pristidae Anoxypristis Anoxypristis cuspidata 141 5 12 75 11 05 2015 0 00 e Presence pseudosamples data this option generates pseudosamples from rasterized species map so basing on a 1 x1 cells precision This requires that the maps are already rasterized see 3 6 This option is useful to generate sample data from range maps where species presence is stored as polygonal zones If the maps you have stored in the database already are based on samples or occurrence records i e downloaded from GBIF it s probably preferable to directly export those samples see option above Valid samples in turn of generating pseudosamples When selecting this option Pseudosamples exportation options group
72. 80 to 180 From latitude 99 to 90 x Cancel e You can set the precision of the output adjusting the width in minutes of the cells that will be used If for example you select 5 cell width one metric value for each 5 x5 minutes cell on the world map will be generated By default it is 1 degree 155 ModestR Software Quick start tutorial e Youcan also set presence count method count a species if it is just present in the output cell default or in turn set a threshold of 1 x1 minutes cells occupation that has to be exceeded to count a species in this cell For example if you set a cell output of 5 x5 you could want that only if a species occupies at least 20 of this cell that is 20 of 5x5 5 so 5 cells of 1 x1 minutes the species has to be counted so the value for this cell incremented e You can also select which habitats have to be included in presence detection By default all habitats are took into account If you exclude one habitat all samples or zones with this associated habitat will be excluded from the presence detection e You can define the zone boundaries to be examined in degrees with a minimum of a 12x12 zone e The Export zero as NODATA checkbox allows to select if a zero value absence for a cell will be exported as NODATA usually will not appear when showing the raster in a viewer or as zero will be shown as a zero value A single ASC raster file will be exported fo
73. DataManager Details about how to integrate environmental data in ModestR are explained in section 6 26 To apply Environmental Occurrence to a distribution map you should go to the Mapping Environmental Occurrence menu option ModestR will guide you across several steps to perform this task 13 Environmental Occurrence was formerly called Niche of Occurrence in previous versions of ModestR But from version 2 1 Niche of Occurrence names a different feature explained later in this manual 14 Tyberghein L Verbruggen H Pauly K Troupin C Minur F de Clerck O 2012 Bio ORACLE a global environmental dataset for marine species distribution modelling Global Ecology and Biogeography 21 272 281 43 ModestR Software Quick start tutorial The first step is selecting the range calculation Environmental Qccurrence calculation a for the environmental occurrence and the EOO Hull Select Variables Comelations Variable analysis Setri mode There are two options for the range Range calculation Full Extent E00 e Full extent the environmental l Potential EOO calculation occurrence will be calculated for all Hul cakun mmie available environmental data For Convex hull example if you use environmental Parameters 7 ha shane epe a A variables that contain data for all the Aphashape Alpha value 6 0 degrees world the environmental occurrence will be calculated for all the wor
74. DataManager cannot be aware of them or if some unexpected error happened that could have corrupted data 3 7 Exporting data The utility of DataManager besides creating and managing taxonomy and maps databases resides in the calculation and data exportation features it offers which are gathered in the 82 ModestR Software Quick start tutorial Export menu option They are also accessible from the context menu when clicking on any tree node with the right mouse button you can select the root tree node to select the whole database tcp ModestR DataManager C ModestRProject BD Terrestrial carntvores DB File Edit Import Export Process Options Tools Help 28 HRiPEHe ryLeaou Database Taxonomy Classification ff3 Terrestrial carnivores S i Mammalia Carnivora H Ailuridae H Canidae H To Standalone Map Files 4 7 Export taxonomy of this branch To presence data and variables BAr bp Import presence data to this branch To metrics and variables Hg f Z To summary data H N Set samples from maps of this branch aan o To variables contribution report Delete areas from maps of this branch To clipped environmental data L Apply map transformation to this branch H J To JPEG BMP images Vi Process maps for this branch To Darwin Core Archive data Insert node in this branch To latitudinal gradients Change node name To Maxent Cut node To RWizard applications Delete this node The
75. Export Current selections To ASC raster Export ASC raster options Select precision Precision 5 minutes ESRI ASCII options Value for selected areas 1 00000 x 8 13 Export environmental data This option allows exporting environmental data clipped to the selections currently added to the map It s explained in section 4 12 3 The exportation format is an ASC raster It is located in the menu File Export Environmental data for selections Besides clipped rasters a report is generated as a CSV file More details can be found in section 7 9 8 14 Export selection areas summary report This option generates a report in CSV format with the areas in km of each selection currently added to the map This option is located in the menu _ File Export Selection area summary report Area Total Area Sea Area Land Area __Large rivers Small rivers Lentic water Small channi Large channeSmall ditche Large ditche Small dr Region 1 12486850 2 7357684 37 5009050 18 12037 9188 13418 0881 40556 1719 641 505403 28 2510168 545 991673 1 24475277 104 004 Region 2 210154 301 205277 693 4359 11177 39 7605351 1 98068858 449 092818 0 0 0 0 Region 3 7294616 21 1989837 92 5216552 31 49795 0012 4815 26997 18173 362 93 115466 2 43716662 24 3640554 O 14 8686 Region 4 1429657 68 1429657 68 0 0 0 0 0 0 0 0 The output format is a CSV file with the following columns e Area name of the selection e Total Area of the selection e Total area for ea
76. F B012 F B013 F Bio14 MIA RN x Cancel lt r Cover 100 00 OK 100 00 OK 100 00 OK 100 00 OK 100 00 OK 100 00 OK 100 00 OK VIF 4 96 3 43 3 32 2 52 1 85 1 64 1 39 variable such as Bathymetry will have a f Preselected vars Default quite null coverage for a terrestrial phosphate Sea surface temperature species Silicate Chlorophyll a Salinity In the next step you can perform a cacte 5 P 7 A Bathymet statistical analysis for selecting those variables that are more affecting the most the distribution of the species The environmental variables selected can be checked either for the full extent where environmental data are available or just Colinearity analysis within the EOO of the species the EOO is calculated using the settings you entered in an earlier step Then an el index of instability is calculated using Press this button to calculate VIF Variance Inflation Factor of each variable You may consider removing variables with an VIF gt 30 as it is commonly considered an indicador of high collinearity af Calculate a VIF Delete A ereriovs contie I gt the fluctuation index of Dubois 1973 modified by Guisande et al 2006 Once the instability index is calculated is possible to estimate the percentage of contribution of each variable to the index Those environmental variables with a higher percentage
77. Gh facctrtine cote D ee eee Writing part of a species name a list of matching names will be il Canine serie IE padal elo E Curtis shiga E danh aE Calabria tariei shown in the Results Just select one to find it in the tree 77 ModestR Software Quick start tutorial 3 4 Adding and managing maps in a database Once a ModestR database created and populated with taxonomy the purpose of the database is of course to store distribution maps associated to the species You will have different options to do that e You can simply create new maps in MapMaker and directly save them in the database To do that you have to configure the database as the default database in MapMaker and use the Save To ModestR maps database menu item in MapMaker to store a map in the database as explained in sections 2 18 and 2 20 e You can import already existing maps made with MapMaker either saved in standalone files see section 6 5 or from another existing ModestR database see section 6 6 e You can create new maps by downloading data from GBIF database Global Biodiversity Information Facility http www gbif org or importing them from CSV files see section 6 7 e You can import maps from ESRI ASC probability distribution models such as the maps generated with Maxent software see section 6 10 e You can import distribution maps from shapefiles DataManager is able to import a collection of maps from
78. O Area Of Occupancy This option is the recommended in most of the cases for area maps because unlike sample maps in area maps we can often assume that the presence data AOO already define the EOO Convex hull EOO is calculated as the convex hull area of the areas plus samples if any If there aren t not enough samples to calculate convex hull it is assumed that EOO AOO More details about convex hull can be found in 2 8 Regarding the possible inaccuracy of convex hulling with areas pointed out in section 2 8 1 it should be made clear that this problem will only appear in MapMaker when the user applies this feature manually When processing maps in DataManager the maps are rasterized and only real presence area is took into account Therefore in DataManager convex hull area will be accurately calculated This option can be useful for mixt maps or for maps which we know that presence areas don t represent the EOO so we want and estimation of the EOO to be made but it should be used with caution and understanding well its operation e Other options besides the options described above there are other options for map processing O Force full map reprocessing this option forces ModestR to fully reprocess maps This option is not usually required as ModestR automatically check which data has to be recalculated and which one has not been modified when processing maps But if some external modification has been done on a map or s
79. O O 0 0 0 0 0 0 4 0 0 0 0 As the CSV format does not support several pages if you select this output format and several metrics to be outputted you will be warned that one single CSV file for each selected metric will be generated e CSV list in columns this format outputs a list with several columns latitude and longitude for each cell and a column for each selected metric Here we see an example where a zone with longitude from 110 to 120 and latitude from O to 2 with a precision of 30 Small Rivers Large Rivers Lentic Waters Latitude Longitude Species Richness Sea Area Land Area Area Area Area 1 3090 04356 1806 41211 968 580384 315 99288 2291 28846 800 403343 2418 5789 6 73 4048384 2339 91575 752 482526 As this format requires loading all data to be outputted at the same time if you select several variables it can require a long time When exporting environmental data in this format if a value is missing for a cell an empty value will appear on the output e Excel worksheet 2007 or higher this format will produce an XML file directly recognized and readable by Microsoft Excel 2007 or higher This format has the advantage of being multipage so one worksheet is generated for each metric to be outputted e ESRI ASCII Raster matrix this format outputs the ESRI ASCII format widely accepted by GIS software Here we see an example where a zone with longitude from 120 to 125 and latitude from 0 to 2 wi
80. PANISH Poetic e Inthis example we ll suppose we choose the Name of the country field and we accepted ModestR will import all data from the shapefile As in this case this shapefile contains several shapes one by country ModestR will ask you if you want to import them as a whole so they will be a single stored selection or you want to split them to make each shape to be a single selection Of course this last one is probable the most used choice and the one we do in this example 127 ModestR Software Quick start tutorial Warning i Imported selection data contains several selections Do you want to split and store each selection in a single node Press No to store imported selection as a whole e Asa result ModestR will import each country shape as a different node under the Countries node ag Selections Manager a th Stored selections Selection settings Hame Afghanistan A inanan d eke Cabegons Counties Albania gt Akana Descriptor Amarican Samos Andorra Angola Anguilla Anarca Antigua amd Barbuda Selecion data Argentina z Armenia This eslertios contains tata Arubes 4 Ashmore and Carter island sala Spit ria g Ararbaijan Bahamas g Bahrain g Baker bland Baker landt i Bangladesh By Barbados Belarus Belgium 4 Belize Benin F Diii eats ii 2 set This simple example showed how to import selections to ModestR They could be used either as
81. RITE existing one it may be recommendable to accept doing a backup to avoid data losing in case of an unexpected modification or error e Next a dialog box will allow you to select one or more shapefiles to import As in Windows Explorer you can select several files just by using the Ctrl or Shift get more information in Windows help e Then a dialog box allows you to select if you want to import data for species that don t still have a map in the database or for those that already have it or for all in the last two cases you can decide if imported data will overwrite or will be added to existing maps You shall also select which habitats will be considered as valid for all the species 149 ModestR Software Quick start tutorial to be imported when importing several species in a batch you have to assign the same valid habitats to all species Select valid habitats and merge mode for the species to be imported Importation options Import data only for species without map in the selected branch Import data only for species with map in the selected branch Import data for all the species of the selected branch Select valid habitats for the species E Sea fF Land All freshwaters Lentic habitats Small Channels C Small Ditches Small Drains E Wetlands Small ivers Large Channels C Large Ditches Large Drains Reservoirs Large rivers e DataManager will read the first shapefile to be imported
82. Reset samples last modified date ModestR stores a date associated to the addition time or the last modification done for each sample of a distribution map Even if this cannot be considered a reliable audit data this can just help finding last changes made in samples of a map particularly when several people work on the same database When exporting samples from maps e g exporting presence data as explained in 6 14 this date is added to sample data To reset this date for all the samples of several maps to a specific date you can use the option Edit Set samples of the selected branch Reset samples last modified date 3 15 Searching maps with no data Sometimes it is useful to check if there are maps in our database that do not contain any valid data This can happens for example if we download maps from GBIF or we import them from CSV files and none of the sample records is classified as valid by ModestR e g because they are outside of the habitats of the species Or if by mistake we save an empty map in the database Even if an empty map or a map with no valid samples don t produce any problem to DataManager or MapMaker it can be useful to be able to find them easily To do that use Process Search maps with no data menu item in DataManager After a moment a list of maps with no data will be displayed in the right panel You can even click on any species of this list to directly select it in the tree 105 ModestR Software Quick start
83. Software Quick start tutorial branch or to a single file where all species data will be consecutively stored In the first case you will be asked to select on file name to output whereas in the second one you will have to select a folder where exported files will be saved You can also set characters used as field delimiter and decimal separator Maps exportation to CSV options select file export format Select data export style Select variables to output clean a cal aia Valid samples only for samples map data z Environmental Variables ee ee ee Presence pseudosamples data EH a3 awe CSV Exportation options Se EEE E eof G Bathy Decimal Field 2 separator f separator 5 J Add headers 7 Add species taxonomy to each sample tm in The available exportation format options are e Valid samples this option will export only valid sample data from maps Therefore it will only be useful if the maps contain sample data because range data polygonal area of presence will be skipped This option exports only samples checked as valid either automatically or manually without any extrapolation on the contrary of pseudosamples exportation described above You can add environmental variables from the right tree if there are variables available see section 6 26 In this case a column will be added for each selected variable with the value if it exists of this variable at the coordinates of the samples
84. _ World Basins Basins of Africa 0 __ World Basins Basins of Africa 1 _ World Basins Basins of Africa 1 World Basins Basins of Africa 2 World Basins Basins of Africa 3 World Basins Basins of Africa 4 World Basins Basins of Africa 5 World Basins Basins of Africa 6 World Basins Basins of Africa 7 __ World Basins Basins of Africa 8 World Basins Basins of Africa 9 64 ModestR Software Quick start tutorial On the left side a list of the visual templates corresponding to geographical areas currently added to the map appears On the right side a graph will initially show the polar coordinates graph of the whole environmental layer If we select a particular visual template on the left list after some seconds the corresponding data map of the region will be shown on the right side The areas of the environmental layer that correspond to this geographical area will appear in color on this graph while the rest of the areas appear in grey Areas Visual templates Region data map Region density Map S World Basins Basins of Africa 0 World Basins Basins of Africa 1 World Basins Basins of Africa 1 World Basins Basins of Africa 2 World Basins Basins of Africa 3 World Basins Basins of Africa 4 World Basins Basins of Africa 5 World Basins Basins of Africa 6 World Basins Basins of Africa 7 World Basins Basins of Africa 8 World Basins Basins of Africa 9 GE e
85. a CSV file On the main menu select File Import Sample data from CSV You will have to select the file where the CSV data is located Expected format is a list of samples in the form Species Longitude Latitude where Species field is optional or Species Latitude Longitude where Species field is optional Data can optionally contain a headers row Details of the expected format are explained in 7 1 Anyway you can select the right options regarding the format of the source file in the importation dialog box OO aa Select coord columns order in CSV file First row contains headers Longitude Latitude First column contains species name Latitude Longitude Sample point size Skip samples in 0 0 coordinates Skip samples with same longitude and latitude coordinates Make the sample habitat auto checked Consider and remove duplicated samples if they are equal until 4 a th decimal 15 ModestR Software Quick start tutorial 3 Importing samples from the GBIF online database On the main menu select File Import Samples from online GBIF database or the equivalent button of the toolbar You will have to write the desired species name Alternatively you can select it from a ModestR database if you already have one populated with taxonomic data this will be explained later on this tutorial You can also enter an LSID that identifies a species then MapMaker will try to resolve it Select species name E
86. a O no if the original species of the input file is an accepted species according to GBIF e OriginalName is the original species name of the input file that can be different from the name returned by GBIF in case of synonyms or corrections e Corrected indicates using a 1 yes or a O no if GBIF returned a correction the original species of the input file is an accepted species according to GBIF e Confidence when a correction has been suggested this indicates its confidence according to GBIF or 100 for another case e lIsSynonym indicates using a 1 yes or a O no if GBIF considered that the original species name was a synonym of the returned species name e Observations other observations if any A B C D E F G H I J K Class Order Family Accepted OriginalNam Corrected Confidence IsSynonym Observations Actinopteryg Anguilliform Anguillidae Anguilla 1 Anguilla ang 100 Actinoptery Anguilliform Anguillidae Anguilla 1 Anguilla rost 100 Genus Species Anguilla ang Anguilla rost O OO N OUAU Ne Actinopteryg Perciformes Blenniidae Entomacrod Entomacrodi Actinopteryg Perciformes Cichlidae Limbochrom Limbochrom Actinoptery Perciformes Haemulidae Anisotremus Anisotremus Actinopteryg Perciformes Scombridae Thunnus Thunnus thy Actinopteryg Perciformes Serranidae Epinephelus Epinephelus Actinopteryg Perciformes Serranidae Epinephelus Epinephelus Actinopteryg Perciformes Serranidae Mycteroperc Mycteroperc Actinoptery
87. a set of shapefiles or from a single shapefile which may contain several maps such as shapefiles available in IUCN website for example More details about this feature can be found in section 6 11 Of course those options can be also used to overwrite existing distribution data with new data depending on the importation options you use in each case You can optionally use some of those options for adding new data to already existing maps in the database The difference between some of those importation options and the similar ones in MapMaker is that in DataManager they can be used to import a collection of maps at once for example from GBIF or CSV files whereas in MapMaker they can only used to import one single map After importing maps usually a report will be shown on the right tab panel of DataManager where imported maps and eventual errors will be reported Maps can be individually deleted simply by selecting them in the tree and using Edit Erase selected map menu option or Erase map option in the context menu Be aware that if you delete a node of any level for example if you delete a family all maps directly or indirectly descending of this node will also be deleted In a ModestR database a map created and linked to a species A cannot be directly moved to a different species B If eventually you want to do that you should have to open the map in MapMaker assign it to another species B see 2 18 and save it to the database
88. aManager see section 6 12 o Total Species this column will count the number of species for each higher taxonomic level in a structured way similar to the used when exporting taxonomy to a CSV structured file in DataManager see section 6 12 o Total Rare Species this column is similar to the previous one but it will only count the number of rare species for each higher taxonomic level 187 ModestR Software Quick start tutorial Rare Species this column contains a 1 value for the rare species otherwise it will be empty AOO km2 this column summarizes the total AOO in Km occupied by each taxonomic level from species to subclass but only within the bounds of the selected area That is if you selected an area of 4 Km the maximum value of this column will be 4 This column is calculated with a precision of 1 x1 Mean AOO this column summarizes the mean AOO occupied by the species of each higher taxonomic level from genus to subclass within the bounds of the selected area SD AOO this column summarizes the standard deviation of the area occupied by the species of each higher taxonomic level from genus to subclass within the bounds of the selected area If there is only one species in a higher level for example in a genus this value will be obviously empty Maximum Latitude this column summarizes the maximum latitude where a species is present for each taxonomic level from species to subclass within
89. able and allows you to browse them in an intuitive way For example you can select World countries and a world map will be shown on the right preview panel You can then double click on Africa in this preview to go into Africa branch and see details such as African countries A context menu allows you to select any element in the preview to add it to the map You can also select it in the left tree 59 ModestR Software Quick start tutorial a Add a stored selection ModestR preselections ig World Basins f Basins of Africa 17 44 27 North 20 20 10 East re 9 Ef Basins of Asia Ef Basins of Australasia Ei Basins of Europe Ei Basins of North America Ef Basins of South America fig World Countries Lm Some buttons on the bottom left corner provide other features such as searching by name or color settings To add your owner drawn visual templates just use the Freehand or the Rectangle tool to draw any shape on the map then click with the right mouse button and select Add as visual template You can add as many visual templates as you want You can also import a shapefile as a visual template going to Layers Visual templates Import from shapefile Another option is copying a species distribution map using Edit Copy as ModestR map and pasting it latter using Edit Paste map as visual template In this way the areas of the copied map will be pasted as a visual template over the current map
90. ables with missing values are not individually configured as directly invalidating an area when their value is missing as explained above That is this rule will be applied only if after applying the rules for each individual variable the sample area has not already been considered as invalid e Samples tab in this tab page you have to select which samples apply to all only already valid ones only already invalid ones or none You can also select to add placemarks to validated invalidated samples to make easier localizing them on the map This tab will only be shown if the map contains samples e Areas tab in this tab page you can select to validate or not validate areas of presence To visualize the zones that don t comply with the rule you can add a visual template usually using a semitransparent showy color see section 2 14 for more information about visual templates The visual template doesn t modify map presence data as it s just a visual helping element This tab will only be shown if the map contains areas Once all those settings configured press the Continue button to perform data cleaning ModestR will apply validation rule for each variable on each sample and on each 1 x1 cell of each presence area 24 ModestR Software Quick start tutorial For example in this map after the validation a red placemark indicates the samples located in points that don t comply with the validation rule Green ones indicate sa
91. ager allows creating taxonomic databases where maps should be stored associated to a species It also performs calculations and exports data like presence or richness matrices that can be processed with other software tools Most of the features available in MapMaker to analize and transform maps are also available in DataManager with the crucial difference that while in MapMaker they will be applied to one single map in DataManager they could be applied to a whole collection of maps launching a sort of batch task e MRFinder allows to find in the distribution maps stored in a ModestR database which species are present in an area of the world simply by selecting this area in the map Then it can generate several statistical and summary data output e MRMapping is a tool to easily make maps grouping several species data by any rank and presenting several datasets in the same map This makes easy to represent de distribution of any group of species of genus a family etc or to show where two or more species or groups of species overlap MRMapping can also calculate overlapping areas In the next sections we introduce those tools We also describe the different importation and exportation options and formats supported by ModestR applications in the sections 6 7 and 8 respectively 1 1 ModestR assumptions Before all it is interesting to point out some assumptions and facts about ModestR that can be important to correctly understand how it
92. alled mixt maps and are treated as area maps Once all those settings configured press the Continue button The Environmental Occurrence calculation processing will start and process each one of the selected species The resulting estimated presence areas will be added to each distribution map Take into account that this process can take a long time depending on the number of maps to process and their complexity Once ended a report of the whole process will be shown on the right side of DataManager showing processed maps and not processed maps commonly because they don t comply with conditions to apply Environmental Occurrence If you choose to use variable contribution index to selected variables to be applied to each species a Report button will be shown on the right panel allowing to export a CSV report where the contribution index for each variable and selected variables are listed It must be said that independently from Environmental Occurrence feature a report about variable contribution for each species can also be exported using an exportation option of DataManager see section 6 18 3 12 Calculating niche of occurrence with an existing environmental layer Niche Of Occurrence NOO from now has been explained in section 2 13 As for other features such as data cleaning or hull calculation DataManager can easily calculate NOO for a set of maps in a single step while MapMaker will only do it for one As explained in se
93. alue in this location in this case an area sample will be cleaned considered invalid as soon as there is no value for the variable for this area sample no matter the values for the other variables 7 It must be pointed out that for mean distance variable included in the Dispersal capacity group the minimum value of the acceptance range is always set to zero to avoid eventual elimination of samples with small mean distances to the other ones 8 Chapman A D 2005 Principles and Methods of Data Cleaning Primary Species and Species Occurrence Data version 1 0 Report for the Global Biodiversity Information Facility Copenhagen Available online at http www gbif org orc doc_id 1262 23 ModestR Software Quick start tutorial o Don t take into account this variable when its value is missing in this case if there is no value for the variable for this area sample this variable will be just not considered to make a decision ModestR will check the values took by the other variables to decide about the validity of the area sample Take into account that those options are per variable That is you can set different options for each variable A missing value for a variable can lead to immediately invalidate an area sample while for another variable it will not be took into account You should decide in a per variable basis the most adequate option e Apply to all buttons either in the tabbed box that displays the options for the curr
94. an make an approximate selection in the map using the Rectangle tool and then select to manually enter a region and just adjust the desired region with more precision Manually enter a region Set zone boundaries From longitude 180 0000 to longitude 180 0000 From latitude 90 0000 to latitude 90 0000 You can select several areas to perform a search So you can add several areas to the map MRFinder allows selections that totally or partly overlap To clear them click on the Clear all button on the left tool panel S ModestR MRFinder DB aaaaaa DB File Edit View Options Tools Help Z e a2 4 a 6 0 APr rk AO aLa Map E a Zor g Detail Level Auto Low Med High Highest Map Tools Drag map Zoom Select FreeHand Rectangle Enter a region Arow Text 112 ModestR Software Quick start tutorial It is important to indicate that MRFinder can search species in several selections at the same time but that a single selection in MRFinder can contain several polygons i e several areas When the user adds selections using the Rectangle or the Freehand tools each selection i e each polygon he she adds is considered a different selection But this can be changed using the Selections editor explained later in this chapter to merge several selections in one for example Moreover when you add a predefined selection see later in this chapter this select
95. ant to point out that map processing can require a large amount of time particularly for range maps usually less time for sample based maps In addition we recommend to avoid using any other ModestR application MapMaker or MRFinder while processing maps to avoid resources conflicts During map processing a dialog box will appear showing the process progression You can cancel the process in any moment without losing the work done until this moment This way you can continue processing remaining maps later Processing maps Curent map processing When the processing task has ended or has been canceled a list of processed and not processed maps will be displayed on the right panel of DataManager If there are not processed maps it can be due just to a user cancelation or to another kind of error that will be shown in the list aside the species map name Even if usually DataManager checks for the necessity of processing maps and only process those who need it the option exists of forcing maps reprocessing using Process Reprocess all maps menu item or Process maps for this branch All option in the contextual menu that will appear clicking with the right mouse button on any branch of the taxonomic tree This can be useful if for some reason you manually made modifications in map data such as forcing maps to be considered as updated see section 3 15 or in the world reference map data which of course is not recommended the way that
96. ape hull area of the samples If there aren t not enough samples to calculate alpha shape hull it is assumed that EOO AOO More details about alpha shape hull can be found in 2 8 Density estimation EOO is calculated as a hull area based on the density estimation kernel smoothing of the samples If there aren t not enough samples to calculate density estimation hull it is assumed that EOO AOO More details about density estimation hull can be found in 2 8 EOO options for area and mixt maps are Areas Convex hull of samples EOO is calculated as the presence areas already existing plus the convex hull of the samples if any Convex of areas samples EOO is calculated as the convex hull area of the areas plus samples if any Areas Alpha shape of samples EOO is calculated as the presence areas already existing plus the alpha shape of the samples if any Areas Kernel density estimation of samples EOO is calculated as the presence areas already existing plus the kernel density estimation shape of the samples if any 97 ModestR Software Quick start tutorial In this step you can also select here if you want to make a copy of the database and apply Environmental Occurrence on this copy This avoids modifying current database and then prevents from losing data You can select here to apply Environmental Occurrence to all types of maps only to sample maps or only to area mixt maps maps that contain both samples and areas area c
97. as samples and other elements of the map but it is not directly usable to calculate some results such as presence matrix occupied area or metrics such as richness That is why it is necessary to process those maps in order to rasterize them That is to convert those declarative data to a matrix of presence DataManager can only process maps that are stored in a ModestR database but not those saved as standalone files in this case you have to import them to a ModestR database Processing feature converts each map to a presence matrix of 1 x1 cells and stores it in the database to avoid doing that conversion each time you need to calculate some data Anyway if you modify a map or if you update the reference world map for example when installing some ModestR updates you should reprocess maps In any case DataManager will warn you about that when required To perform this processing you should use Process Process pending maps menu option That will checks and process all maps from the database that need to be processed You can also use Process maps for this branch option in the contextual menu that will appear clicking with the right mouse button on any branch of the taxonomic tree to process only the maps for a specific taxonomic group 79 ModestR Software Quick start tutorial ModestR DataManager C ModestRProject BD Terrestrial carnivores DB File Edit Import Export Process Options Tools Help 23B 2 2R PEO FLeou Data
98. asAreas set to 1 if the map contains presence areas samples are not took into account only range areas zero otherwise Remember that characters used as field delimiter and decimal separator can be selected in the preferences Options Preferences menu 6 24 Exporting JPEG BMP images DataManager can generate and export JPEG BMP images from maps When selecting Export Export maps of the selected branch To JPEG BMP image in main menu or equivalent option in the tree contextual menu a dialog box to select the output folder will be shown Next an exportation settings dialog with several tabs is shown The exported image is by default a full world map view If you want to export a specific zoomed view you should set the wanted boundaries in the first tab Dimensions and format 31 It is important to point out that patch index calculation has been modified after version 1 3 2 of ModestR The current calculation used is the one described here 169 ModestR Software Quick start tutorial Set map display options Set zone boundaries From longitude 180 0000 to longitude 180 0000 Resize image 5 20 2j ag Resulting map dimensions 1638 XxX 819 Image quality J 100 Image format JPEG D Bitmap BMP x Cancel oK You can also modify resulting image size and quality By default the image size is set to be slightly bigger than your screen resolution which may be enough to use the image in a presentation a
99. ataManager as Ateleopus indicus species Import from ESRI ASC probability distribution data Set probability cutoff for data to be imported Merging method Default probability cutoff 0 7500 G Ovenwnte existing maps Add data to existing maps Use minimum probability at presence if exists Dont modify existing maps Select valid habitats for the species Sea Land Lentic habitats Small Channels Small Ditches Small Drains Wetlands Small rivers Large Channels Large Ditches Large Drains Reservoirs Large rivers Accept When using this importation option you first have to select the folder where probability ESRI ASC files are stored Then a dialog box will allow you to set several settings e Default probability cutoff the minimal probability under which presence data will not be imported If for example you select 0 75 only cells with a probability gt 0 75 will be imported to the map e Use minimal probability at presence this option is only useful if you are importing data from species that already have a sample based map on the current database In this case this option allows you to use as probability cutoff the lowest probability value where a sample exists in the existing map For example you can have several maps with samples in the database for several species then import probability distribution data files for those species to the database Then DataManager will automatically find the probability values in the points wher
100. ayer will be calculated only within the bounds of the EOO Extent of Occurrence of the species e Occupied river basins selecting this option a right panel will appear where you ll have to select a river basin level O higher 5 lower The layer will be calculated only within the bounds of the river basins of this level where there are samples of the species See 2 14 2 for more details of how ModestR determines the river basins occupied by a species It has to be noted that the options explained above define the extent or bounds of the environmental layer to be calculated for each species that is not the same than the bounds for the NOO to be calculated for the species You can for example calculate the environmental layer using as bounds a continent and next calculate the NOO of the species using as bounds a specific country of this continent Obviously the extent of the environmental layer inherently limits the potential NOO of the species If you limit the environmental layer to a country for example the NOO of the species will be inherently limited to this country independently of the bounding options you use for the NOO Seeing explanations about environmental layer creation see 2 11 and NOO calculation see 2 13 in MapMaker can help correctly understanding difference between options affecting environmental layers and those for NOO calculation Once those options set click on Continue button to go to next step In the next step
101. base Taxonomy Classification tis Terrestrial carnivores 3 A Mammalia Carnivora C3 Export all maps of this branch gt Ey Export taxonomy of this branch b Hi Import presence data to this branch gt Set samples from maps of this branch gt Delete areas from maps of this branch Ni Apply map transformation to this branch Pr pi Process maps for this branch gt Ge Only not processed Ut Insert node in this branch EA All EE 0 0OA0AA0AA0AAAAA A E CEEE EEEE EEE TE Change node name Cut node Delete this node A dialog box will appear showing the processing options that we describe below Map processing options Extent Of Occurence calculation mode EOQ for sample based maps Options 0 None EOO A00 9 Convex hull i Farameters Alpha shape Alpha value 6 0 degrees Force rechecking all samples T Kemel density C Stop on errors estimation W Calculate patch area EQO for area based or med maps None EOO A00 Convexhul Wcance e Extent of Occurrence calculation mode during map processing ModestR estimates and calculates Extent of Occurrence area of each species from its current distribution map Here you can configure how this area is calculated There are different options for sample maps and for area maps range maps Maps that contain both samples and areas area called mixt maps and are treated as area maps EOO options for sample maps a
102. based on RWizard environment and the statistical package R and Those applications will be available online in the ModestR or the RWizard websites 83 ModestR Software Quick start tutorial 3 8 Applying convex concave hull transformation As seen in section 2 8 MapMaker is able to calculate the convex hull or the alpha shape area from the presence data in a species distribution map But if you want to apply this transformation to numerous maps it may be easier to do it in a single operation from DataManager in turn of doing it for each map in MapMaker You can just select the tree branch from which you want to apply it and select Mapping Apply hull transformation to this branch Convex Alpha shape hull menu option or the Mapping features Apply hull transformation to this branch Convex Alpha shape hull option in the contextual menu of the tree node A dialog box will be shown Hull options Hull application options Hull calculation mode Data to include in hull calculation Convex hull Include only samples Alpha shape Parameters Alpha value degrees Maps to include Include only sample maps Include all maps Create a copy of the database cancel The available options are e Hull calculation mode you can choose between convex hull or alpha shape For alpha shape you can select the alpha value More details about those hull modes can be found in 2 8 e Data to include in hull calculation this option a
103. baty 1minuto Baty0 50 Calcite CDOM Chlorophyll a Cloud cover Diffuse attenuation Dissolved oxygen Nitrate PAR pH Phosphate POC Salinity Sea surface temperature Silicate BOO calculation mode for environmental clipping 6 20 Exporting latitudinal gradients DataManager can calculate and export several latitudinal gradients for several metrics from maps When selecting Export Export maps of the selected branch To latitudinal gradients in main menu or the equivalent option in the tree contextual menu a dialog box to select exportation settings is shown 164 Alpha shape Maps to export Export sample based maps Export ar a based or mixed maps Folder C ModestRProject PRUEBAS tmp Create a folder for each species EOQ for sample based maps O None E0O A00 O Convex hull Parameters Alpha value 6 0 degrees a Kemel density estimation ell width 5 EQO for area based or med maps None EOO A00 Memes oo ModestR Software Quick start tutorial Export latitudinal gradients options Select precision Select habitats to include Precision i gt degrees of latitude J Sea J Small rivers x iT degrees of longitude Land v Lange rivers Lentic habitats Set exportation zone boundaries From longitude 180 lt to longitude 180 From latitude w to lattude 50 CSV Expertation options Decimal separator F In this dialog box you can set
104. be evaluated to determine if some sample area has to be removed from estimated EOO or not There are two validation modes o Tolerance the default validation mode is Tolerance It consists of using the range minimum and maximum of valid values for the variable increased by a tolerance percent by default 1 but you can modify it so any value that fall outside this range will be considered invalid and the corresponding area removed from the EOO o Custom in this case it is the user that will manually set the minimum and maximum values of the range of valid values for a variable Any value that fall outside this range will be considered invalid e Missing value options under the tabbed box that show the information for the variable two radiobuttons allow you to select what to do when there is no value for the variable in a particular area sample You can select between two possibilities o Invalidate an area sample if the value for the variable is missing that is if the variable have a null value in this location in this case an area sample will be cleaned considered invalid as soon as there is no value for the variable for this area sample no matter the values for the other variables o Don t take into account this variable when its value is missing in this case if there is no value for the variable for this area sample this variable will be just not considered to make a decision ModestR will check the values took by the oth
105. bles Indicates how many variables can take invalid values that is outliers according to their validation rule before considering an area or sample as invalid for the species The default value is 0 and the maximum is N 1 where N is the number of selected variables Usually this field will be 0 because typically you will want to clean a sample areas as soon as one of the selected variables takes an outlier value But this setting provides a way to be more flexible For example you can select 10 variables and allow that up to two variables of these take outlier values before considering a sample area as invalid e Allowed missing variables Indicates how many variables can be missing have a null value before considering an area or sample as invalid for the species By default it will be set to N where N is the number of selected variables That is if all variables have null values for a sample area the area will be considered as valid Take into account that this parameter will be applied only if the variables with missing values are not individually configured as directly invalidating an area when their value is missing as explained above That is this rule will be applied only if after applying the rules for each individual variable the sample area has not already been considered as invalid Once all those settings configured press the Continue button to perform Environmental Occurrence calculation Once ended the resulting estimated presen
106. box on the bottom will activate to allow configuring pseudosamples generation You can also set the precision or density of the samples adjusting the width in minutes of the cells that will be used If for example you select 5 cell width at most one sample for each 5 x5 minutes cell on the world map will be generated if the species is present in any point of this cell You can also set if the sample will be generated with the coordinates of one corner or center of the cell The smaller cell you select the more numerous samples you have and with the higher accuracy But for large zones this can result if a too large number of samples You can also set if a sample has to be generated if the species is just present in the output cell or in turn set a threshold of 1 x1 minutes cells occupation that has to be exceeded to generate a sample for this cell For example if you set a cell output of 5 x5 you could want that only if a species occupies at least 20 of this cell that is 20 of 5x5 5 so 5 cells of 1 x1 minutes a pseudo sample has to be generated for this 5 x5 cell You can also set how the pseudosamples coordinates will be exported regarding the cell they correspond to using the longitudinal coordinate of the center right or left corner of the cell and so on for the latitudinal coordinate You can also add environmental variables from the right tree In this case a column will be added for each selected variable
107. calculated Be aware that only cells with a richness value bigger than zero that is where there at least one species present are took into account to calculate the mean Details about EOO index metric can be found in section 6 17 above e SD EOO Index standard deviation of the EOO index of the cells of the latitudinal band calculated in the same way than Mean EOO Index e Mean Rarity Index mean of the rarity index metrics calculated for each one of the cells of the latitudinal band taking cells of the longitude width in degrees indicated in the dialog box described above That is the rarity index of each cell of the longitude width and latitude height in degrees indicated is calculated for a latitudinal band and then the mean of all those values is calculated Be aware that only cells with a richness value bigger than zero that is where there at least one species present are took into account to calculate the mean Details about rarity index metric can be found in section 6 17 above e SD Rarity Index standard deviation of the area index of the cells of the latitudinal band calculated in the same way than Mean Rarity Index e Mean Patch Index mean of the patch index metrics calculated for each one of the cells of the latitudinal band taking cells of the longitude width in degrees indicated in the dialog box described above That is the patch index of each cell of the longitude width and latitude height in degrees indicated is calculated
108. ce areas will be added to the distribution map In the figures below you can see an example of applying Environmental Occurrence to a sample map compared to just the EOO using the alpha shape for example As you can see here Environmental Occurrence used the EOO estimated by the alpha shape but removed several areas that didn t complied with the environmental conditions estimated for the species from its initial presence data 48 ModestR Software Quick start tutorial Environmental Occurrence using alpha E i 2 11 Creating environmental layers An environmental layer in ModestR is a data layer somewhat similar to a raster But it is not to be confused with raster environmental data or environmental variables which can be imported from ASC files see section 2 9 While a raster usually contains information about a single variable e g altitude temperature ModestR environmental layers are a compound of several variables using an approach basing on a polar coordinates system In a large sense this can be compared to a sort of multidimensional scaling approach where multiple variables that can be somewhat considered as dimensions are scaled in a two dimensional polar coordinates system Environmental layers can have two applications in ModestR e To visualize the different environments that are present according to a set of environmental variables in a single graph e To calculate the niche
109. ch habitat type in the selection Sea Area Land Area Large Rivers Area Small Rivers Area Lentic waters Area etc e Minimum and maximum coordinates of the selection Min Longitude Max Longitude Min Latitude Max Latitude 190 ModestR Software 9 MRMapping import export files format 9 1 Exporting overlapping areas report Extract of a short report Distribution1 Anoxypristis cuspidata Anoxypristis cuspidata Anoxypristis cuspidata Anoxypristis cuspidata Anoxypristis cuspidata Anoxypristis cuspidata Pristis clavata Pristis clavata Pristis clavata Pristis clavata Distribution2 Pristis clavata Pristis pristis Pristis zijsron Pristis microdon Pristis pectinata Pristis perotteti Pristis pristis Extract of a full report MapName Total AQO Sea Area Anoxypristis 527298237 Pristis clava 2438180 Pristis micro 4607241 58 Pristis pecti 155594891 Pristis perot 3894366 15 Pristis pristi 6981606 656 Pristis zijsro 5269368 51 Land Area 527298237 2458180 4607241 58 13359489 1 3894366 15 6981606 66 526936851 Pristis microdon Pristis pectinata Pristis perotteti 0 Total Overlap Km2 1583507 109 2293411 291 2311801 787 O 259147 6932 3089963 245 1423604 954 814865 4331 0 533412 4817 0 0 Spatial overlapping report between Anoxypristis cuspidata and Pristis clavata Total spatia 1585507 11 Overlapping 1585507 11 Total spatia 0 30031 Total spatia 0 e4946 Overlapping
110. ch one of the species to be processed If you select this second option This analysis will be performed 94 ModestR Software Quick start tutorial for each species the environmental variables selected are checked within the EOO of the species or for the full the extent where environmental data are available according to the selected option Then an index of instability is calculated using the fluctuation index of Dubois 1973 modified by Guisande et al 2006 73 Once the instability index is calculated the percentage of contribution of each variable to the index is calculated Those environmental variables with a higher percentage contribution to the instability index can be considered as those more affecting the most the distribution of the species In order to include only the variables with higher contribution you have to select a threshold percentage with the accumulative percentages of the variables This feature has already been explained in 2 9 for MapMaker where this analysis can be done interactively for a species It can be a good idea to do it first in MapMaker for a single species to better understand how it works Independently from Environmental Occurrence feature a report about variable contribution for each species can also be exported using a specific exportation option of DataManager see section 6 18 e Validation mode this is the way the values for this variable on the presence zones whether samples or areas will
111. ch with more than 1 minute of precision and in turn a slight simplification can dramatically improve search performance However in order to really understand we recommend you to manually test the effects of simplifying selections using the Simplify tool on a selection before performing a search see section 4 12 1 If you need a very accurate search you can disable this option Moreover MRFinder also automatically disable it when selections are simple usually selections made using Freehand Rectangle or Enter a region tools described above as simplification will not provide significant performance increase for those selections Anyway if you use this option you can set the tolerance or level of simplification in minutes that will be applied Again we refer you to section 4 12 1 to manually test the effects of simplifying selections using the Simplify tool on a selection 4 7 Performing search Once search options set in the Search options dialog box and the Search button clicked in this dialog MRFinder will perform the search which can require from few minutes to much more time if the selections are complex and there are many species in the database 117 ModestR Software Quick start tutorial If there are more than one search area during and after the search a color scale will appear at the right side representing the richness or number of found species of each selected area Each search area will take the corresponding color during t
112. cies Then on the bottom of the dialog box you can select the mode the distribution data from the selected species will be added to the world map e Add as individual maps each one of the distribution maps of the selected species will be added to the world map as single separated datasets This allows managing each one of those species maps individually for example to change their color delete it etc e Add as single map all the distribution maps of the selected species will be merged and added to the world map as a single dataset That is it will be identified as a single dataset with a single name and color settings etc You would be able to discriminate between the species included in this dataset later on e Group by class order family genus all the distribution maps of the selected species will be grouped by the rank you select and added to the world map as a datasets one 132 ModestR Software Quick start tutorial dataset for each different rank You would be able to discriminate between the species included in those datasets later on Select species from Elasmobranchii DE Classification fs Elasmobranchi fi Batoids HC Pristiformes a Rajiformes a El Torpediniformes Eiig Sharks Check any ranks to select the species you want to add to the map a e Carcharhiniformes a Wl Carcharhinidae nERI 1 Hemigaleidae Ele Leptochariidae species are currently selected cimi Leptocharias
113. cleaning using automatic range based rules cccccceeeceeessseeeececeeceeeneseeeeeeees 20 2 7 Data cleaning USING CUSTOM validation FUIES ccccccceccccssseccccseceeceueecesseeceeseneceeseees 26 2 8 Using hull transformations tools ccccccsseccccessccccesececcesececcensceeseeseeeseuaecesseeceeseges 28 2 8 1 Using convex hull Withee qoa MMMM cesrseresssrcncsssrenvesrsereusureneuserensans 30 2 8 2 Using alpha shape hull With samples ccccceeeeecesescceeccceeececeecsceueceeeeeeeeuess 30 2 8 3 Using density based hull with samples ccccccceccccesecccesscceeececeeeceeeueceeeneeeeeuess 32 2 9 Calculating Environmental OCCUrENCE cscccccssseccccesececcesececeuseceeeuaeceeeaeseeetauseses 34 2 10 Creating ENVironMental lAYESS cccceesecccsseccccesscccceesececeeececseuseeeseesecessueeceeseneeeetas 49 2 10 1 Step by step environmental layer Creation cccccccsssecccesseceeeeseceeseseceeeeseess 50 2 11 Managing environmental layers cccccccssseccccsseccccesececseececceeeccesseeceseeeeceeseneeeetas 54 2 12 Calculating niche of occurrence cceeeccccesseccccesscccceesececeuececeeaeeceseuecessueeceeseneeeetas 55 2 13 Workingiith rasters BE ccccscssssssessevsrscresserencuvsrenvensrsercusarencaversapesrrencuvarensaversens 34 2 13 1 Adding environmental data as raster seseesesseesssreresrrrsrreressrerssrrresrrrrererresene 35 2 13 2 Loading ras CRM OS
114. contribution to the instability index can be considered as those more affecting the most the distribution of the species In order to include only the variables with higher contribution in ModestR is possible to select a 1 gt Dubois D M 1973 An index of fluctuations Do connected with diversity and stability of ecosystems applications in the Lotka Volterra model and in an experimental distribution of species Rapport de syth se III Programme National sur l environment Physique et Biologique Project Mer Commision Interminist rielle de la Politique Scientifique Li ge Guisande C Barreiro A Maneiro I Riveiro I Vergara A R Vaamonde A 2006 Tratamiento de datos Ediciones Diaz de Santos 367 pp 45 ModestR Software Quick start tutorial threshold percentage with the accumulative percentages of the variables But this is an optional step If you just want to include all variables you can simply continue Same as when calculating VIF you can also see the coverage percent of each environmental variable into the EOO 7100 00 OK 700 007 OK 100 00 OK Vanable contribution analysis Variable contribution calculation mode Select best variables for a 6 Full Extent Extent of Occurrence 2 contribution of a H In the next step ModestR will first determine the range of values took by each one of the selected variables in the estimated EOO Before continuing it is interesting to point out tha
115. ction 2 13 NOO relies on the concept of environmental layers NOO is intended to be applied on sample based maps as range maps already include presence areas MapMaker allows calculating and storing environmental layers see section 2 11 that can be latter used to calculate NOO of a set of species in DataManager It is very important to point out that as seen before an environmental layer is built upon several environmental variables And to perform niche of occurrence those original environmental variables are needed besides the environmental layer itself Consequently to obtain accurate results those original environmental variables must still exist with the same names and data than when the environmental layer was created Errors or inaccurate results can be obtained if some variable has been modified since the environmental layer creation To avoid those problems as much as possible from ModestR v 3 1 when you delete or modify an environmental variable any environmental layer that used this variable will be deleted To apply NOO using an already created and stored environmental layer in DataManager select the tree branch from which you want to apply it and select Wapping Apply Niche of Occurrence to this branch Using a stored layer menu option or the Mapping features Apply Niche of Occurrence to this branch Using a stored layer option in the contextual menu of the tree node 98 ModestR Software Quick start tutorial A dialog bo
116. d ASC file for each one will be generated and saved on the selected target folder 2 16 7 Merging maps You can merge several species maps in MapMaker but take into account that MapMaker doesn t keep information of the different species you merge That is MapMaker will consider all merged data as a single species map To make maps that allow several species data to be managed and visualized as distinct datasets you should use MRMapping instead see chapter 5 However this option can be useful to merge several data from a same species or related species such as all the species maps of a family for example visualize and export the results and apply any of the transformations allowed by ModestR such as EOO estimation NOO etc To merge several species maps there are several options e You can use menu File Merge Standalone map file to load a map saved as a standalone map file and merge it with the current map e You can use menu File Merge Maps from database to select one or more maps from the default database and merge them with the current map default database can be changed going to File Select database or to Options Preferences e Another option is copying a species distribution map using Edit Copy as ModestR map and pasting it latter using Edit Paste ModestR map 2 17 Exporting dataand reports MapMaker importation and exportation formats and settings are detailed in section 7 Here we ll just point out some of the most relevant
117. d file and will do a copy of the database and apply NOO on this copy preserving the Original database Click on the Start button to go to next step NOO calculation processing will start and process each one of the selected species The resulting estimated presence areas will be added to each distribution map Take into account that this process can take a long time depending on the number of maps to process and their complexity Once ended a report of the whole process will be shown on the right side of DataManager showing processed maps and not processed maps commonly because they don t comply with conditions to calculate EOO or they don t have data in the selected range 3 14 Batch map areas or samples modification DataManager has some features that can be useful when we want to modify a set of maps ina single operation For example to delete areas from maps or to reassign valid habitats to occurrences of several maps They are located in the Edit option of the main menu but they can also be found on the contextual menu that appears when right clicking on any element of the taxonomic tree 104 ModestR Software Quick start tutorial e Edit Delete areas of the maps in the selected branch delete presence areas of all the maps of the selected branch Occurrences are preserved e Edit Delete samples of the maps in the selected branch delete occurrences of all the maps of the selected branch Presence areas polygons from range maps
118. d party LIMITATION OF LIABILITY In no event shall This document be liable for any damages including without limitation lost profits business interruption or lost information rising out of Authorized Users use of or inability to use This document even if advised of the possibility of such damages In no event will This document be liable for inaccurate results software errors loss of data or for indirect special incidental consequential including lost profit or other damages based in contract tort or otherwise This document shall have no liability with respect to the content of this document or any part thereof including but not limited to errors or omissions contained therein libel infringements of rights of publicity privacy trademark rights business interruption personal injury loss of privacy moral rights or the disclosure of confidential information ModestR Software Quick start tutorial ModestR Software Quick start tutorial 1 Introduction ModestR software is a software package to help academic community managing species distribution information It is currently composed of three applications e MapMaker aimed to build distribution maps in a simple way either by selected the zones where the species is found range maps or by adding samples or occurrences in the map from CSV files o GBIF database It also provides several tools to analize and transform a map such as data cleaning hulling etc e DataMan
119. d to samples a dialog box will be shown Set importation options for samples data Samples conversion Sample point size 100 Skip samples in 0 0 coordinates 7 Make the sample habitat auto checked Skip samples with same longitude F w and latitude coordinates Consider duplicated samples f they are equal until 4 th decimal T Select valid habitats for the species X Cancel E Sea Land All freshwaters Accept E Lentic habitats Small Channels Small Ditches C Small Drains E Wetlands Small rivers E Large Channels Large Ditches Large Drains O Reservoirs E Large rivers The options of this dialog box are the same than the shown when importing samples from CSV or GBIF You can find more details in subsection 2 3 If the KML file only contains areas this dialog box will be shown where just the valid habitats for the species have to be selected If an area is not located in the habitats selected as valid it will not be shown in the map or only the valid portion if any will be shown Select valid habitats for new data Select valid habitats for the species E Sea E Land All freshwaters x ad Lentic habitats E Small Channels C Small Ditches Small Drains Wetlands E Small rivers Large Channels C Large Ditches C Lange Drains Reservoirs E Large rivers Accept 179 ModestR Software Quick start tutorial 7 6 Export map view to an image file You can export the map vi
120. data folder Warming don t modify this parameter unless you are aware of fhe comsequences C ModestRProyect Data V Check for updates from ModestR website Ge x Cancel 3 3 Creating a new database To create a new ModestR database you just have to use File New Taxonomy database menu option Then select the name and folder to create the database file The ModestR database will be stored in a single file with the name you entered So if you want to copy send or delete a ModestR database you just have to do it on that file DataManager will not allow to create a database overwriting an existing file this is to avoid accidentally overwriting files The new database will be created with an empty taxonomic tree The taxonomic levels of a ModestR database begin at the Class level then Order Family Genus and Species That is there are 5 levels without taking into account the root node To populate the database with taxonomic data you have several options a Manually create each node To do that EF PSEA Dass Ease CWT o a Manager C Mo select a node in the tree initially the root file Edit Impor Export Process Options Tools Help node and use Edit Insert node in this Database Taxonomy Classification branch menu option or the analog Hm context menu item context menu can be e Change node name displayed clicking on the node with the A Insert a new taxon in this branch of the taxonomic tree E
121. destR Software Quick start tutorial Environmental layer generation Select Variables Analysis Variable analysis Order Scale Options Options Layer identification Layername Enteral ayer name to export report or save Layer description Enter a layer description x Cancel Close g d Load layer Finally you can close this dialog box or load the layer in the current work session even if you not saved it to be able to use it just during the current work session As pointed out before it is highly recommended to use environmental variables with the same cell size 5 minutes for example when creating an environmental layer to obtain more accurate results Another important issue is that environmental layers don t store environmental data that was used to generate it they just store a link to those data So it is important that you don t delete neither modify environmental variables used to generate a layer because this will make environmental layer unusable 2 12 Managing environmental layers You can manage the environmental layers you have stored going to the menu Mapping Niche of occurrence Manage environmental layers A dialog box will appear showing the currently stored layers an error message will be shown in case there is no stored layers You can select any layer of the list and e Show it in the map a
122. dialog box that allows adding importation criteria when importing shapefiles will not appear when importing KML files If the imported KML contains several shapes which is quite usual you will be able to select if you want to import them as a single selection or to split them the same way as described for shapefiles see 8 1 185 ModestR Software 8 3 Importing from CSV In MRFinder you can import selections to search for species from a CSV file To import a CSV file go to File Import selection From CSV file menu The expected format consists of two columns longitude and latitude or vice versa that can be selected by the user during importation Each row should correspond to a point of the shape 8 4 Exporting metrics data Quick start tutorial Latitude 47 8150215 47 8150215 47 8150215 47 5225754 46 3527908 45 4754486 44 3056641 Longitude 44 3056641 44 8905563 45 1830025 45 7678986 46 9376831 47 8150253 49 277256 MRFinder can calculate and export several metrics from maps from selected species such as richness data rarity index etc When selecting Export metrics in the exportation tools of the search result window see section 4 8 a dialog box to select exportation settings is shown with the same options and operation as the corresponding option inDataManager You can find more details about metrics exportation in section 6 17 Export metrics options Select format style Precision 5 gt
123. document etc If you need more resolution for example to allow zooming on the image you can increment this size In the next tab Grid and scale you can add a grid and a numeric scale to the map In the last tab Display options you can select which elements from valid invalid samples text arrows or placemarks will be shown on the exported map Presence areas will be always shown You can also add a raster to the exported maps Rasters will typically correspond to environmental data To add a raster you have to have previously integrated it in ModestR as described in section 6 26 You can find more information about raster display settings in section 2 9 1 You can also add visual templates to the maps to be exported You can find more information about visual templates in section 2 14 and 4 5 Set map display options Dimensions and format Grd and scale Show map elements W Show valid samples EC Show text Show placemarks Show invalid samples Show arows Rasters and templates ro Curently selected raster Add raster Add Curmenth selected templates E templates Aone E x cancel E ok 170 ModestR Software Quick start tutorial Once set and accepted those options exportation will start showing a dialog box where each exported map is shown As this requires loading all the world map data and recreating each species map it can take a long time to be completed
124. don t need to be reprocessed For example if the modifications in the reference world map only involved freshwater the maps of marine species are supposed not to be concerned As map processing can be a very time consuming task particularly for expert drawn maps in those cases you can avoid having to reprocess maps by selecting the branch you want to avoid having to reprocess and using the menu item Tools Force set maps from current branch as updated This option only has to be used very carefully and only if you clearly understand its effects Existing processed maps will be just marked as updated even if they were not processed using the current world reference map This way DataManager will then consider them as already processed with the current reference world map Anyway if you incorrectly used this option you can always reprocess all maps to come back to a correct and updated state as explained in section 3 6 above but forcing full map reprocessing and samples rechecking to make sure that all map information is rechecked 106 ModestR Software Quick start tutorial Map processing options Extent Of Occurrence calculation mode EOQ for sample based maps E None E0O A00 7 Force full map reprocessing E Convex hull Farameters E Alpha shape Alpha value 6 0 degrees Force rechecking all samples i Kemel density Si E Stop on emors estimation EQO for area based or med maps None EOO A00 O Convex hull
125. e Basins of North America Basins of South America World Countries f User selections But you can also make MapMaker to automatically search and add the river basins where the species is present Please note that this feature only works with sample data but not with area data To do that go to Layers Visual templates Add river basins with samples and select the basin level you want to add O higher 5 lower MapMaker will add to the map the visual templates corresponding to the basins of the selected level where there are samples of the current species ModestR MapMaker New Map1 Ser File Edit Samples View Layers Mapping ModestR tools Options Help BOS EG dl OG a lt oo ge BI eo Bru FILLOA E oe Zoom P s j gt _ gt o e f l i gt O a oe E X Gal Map ful r Detail Level Auto Low Med High Highest Map Tools Show distance FreeHand Rectangle Add sample Edit sample gt Coordinates Degrees Besides visual purposes this feature can be useful to calculate NOO for a species limiting the potential area to the river basins where the species is present for example see 2 13 2 15 Showing environmental layer data for a visual template In section 2 11 environmental layers have been explained Has seen there an environmental layer combines data from several environmental variables in a single polar coo
126. e 7 Make the sample habitat auto checked i E coordinates Consider and remove duplicated samples if they are equal until 4 th decimal Select valid habitats for the species x Cancel Sea Land Lentic habitats Small Channels Small Ditches Small Drains Wetlands Small rivers Large Channels Large Ditches Large Drains D Reservoirs Large rivers e Sample point size select the size of the visual point that will indicate a sample in the map This size has no importance when processing map It is only a visual parameter e Skip samples in 0 0 coordinates don t process samples whose coordinates are 02 longitude and 02 latitude as those samples are usually erroneous data e Skip samples whose longitude and latitude coordinates have the same value as those Samples are usually erroneous data e Consider and remove duplicated samples if they are equal until the Xth decimal this allows setting when two samples will be considered as duplicated thus avoiding adding them twice If for example we configure this option to take into account until the 2th decimal samples like 122 4567 9 4568 and 122 4598 9 4560 will be considered duplicated If you don t check this option all samples will be imported and added to the map even if they are duplicated e Make the sample habitat auto checked using this option a sample will be automatically checked by MapMaker to determine if it is situated in a valid or invalid habitat and therefore
127. e map item can eventually hide another that this painted below it You can change the order the map items are painted by selecting any map item not checking it just selecting it in the list and moving it using the buttons Top Up Down and Bottom You can delete any map item by checking it not selecting it but checking it using the checkbox on the right of the map item name and clicking on the De button You can also merge two or more map items to join them in a single item with a single name and single color settings To merge items check them not selecting it but checking it using the checkbox on the right of the map item name and click on the Merge button If map items to be merged contains polygons e g range maps this operation implies geometrical calculations that can take some time depending on the complexity of the polygons to merge Once completed you ll see that the merged items are replaced by a new single item in the list which name is by default the concatenation of the names of the items merged In a similar way you can calculate the intersection of two or more map items The intersecting areas will be added as a new item with its own name and color settings To intersect items check them not selecting it but checking it using the checkbox on the right of the map item 136 ModestR Software Quick start tutorial name and click on the Intersect button Obviously this operation it s only useful when applied to
128. e tati Neotoma palatina i i island Monachus monachus When importing several wien s ata season Emballonura semicaudata shapefiles where each one Z e oOUurce ere ecus scat contains a single species map dist com Sao Gas _ cal Aepeomys reigi you can alternatively use the subpop Brachytarsomys villosa Hylopetes sipora filename as species name by Use same option for the next files x Defaut Accept clicking on the Default button In this dialog you can see in the left side a list of the data fields contained in the shapefile to be imported Selecting one of those fields in the right list you can see the values took by this field This can help you to select the right field that contains species names You can decide to use this same field as species name for all remaining files to be imported if there is only one file to be imported this option will have no effect This option is checked by default so it will only be shown for the first file to be imported But if you want to use different fields for each file to be imported you can unchecked it then DataManager will show this dialog box for each file to be imported After that last step importation will start You can cancel it in any moment but species already imported until this moment will be added to the database At the end of the task information about imported species not imported and warnings will be shown on the right panel 6 12 E
129. e available settings are e Validation mode this is the way the values for this variable on the presence zones whether samples or areas will be evaluated to determine if some sample area has to be removed from estimated EOO or not There are two validation modes o Tolerance the default validation mode is Tolerance It consists of using the range minimum and maximum of valid values for the variable increased by a tolerance percent by default 1 but you can modify it so any value that fall outside this range will be considered invalid and the corresponding area removed from the EOO o Custom in this case it is the user that will manually set the minimum and maximum values of the range of valid values for a variable Any value that fall outside this range will be considered invalid e Info tab under the validation mode combo box a tabbed b ere information and options for the currently selected validation mode ere is also a Info tab where you can consult basic statistics for the curren dle such as maximum and minimum values that this variable has on the current presence areas samples mean value quartiles and jackknife ranges e Missing value options under the tabbed box that show the information for the variable two radiobuttons allow you to select what to do when there is no value for the variable in a particular area sample You can select between two possibilities o Invalidate an area sample if the value for the variab
130. e been processed but allows you to continue anyway In this case only processed maps will be took into account to do the search Before performing the search MRFinder will display a dialog to configure search options 115 ModestR Software Quick start tutorial Search options You can select only the habitats in the selected areas where you want to search for speces This increases performance as spesies that ive outade those habitats won t have to be considered Select habitats to include Sea Land Lentic habitats Small Channels Small Ditches Small Drains Wetlands Small rivers Large Channels Large Ditches Large Drains Reservoirs Large rivers In this dialog box there are 3 tabs The first one is Habitats tab There you can select the habitats that will be took into account in the search For example if you select sea only species that are present in sea will be checked Besides increasing performance as some species will be early excluded from search this allows to focus on specific species Moreover it makes unnecessary to do very precise selections to perform search in specific habitats Babed HEFoen TT adds eee Hh GC Craw T ki lie Si of mee i e FRB 4 e 7 We can do an imprecise selection that includes for example land portions but if posteriorly we only select to search in sea habitats only species that are present in the sea portion included in the area selected will be found S
131. e example map shown below and using the default parameters the result will be Lat 3 693209 Lon 110 7164 If you select the visual filtering by habitat MapMaker will only show density map on the habitats allowed for the species For example for a marine species this could be the result a very high smoothing value has been used for visual purposes 41 ModestR Software Quick start tutorial ModestR MapMaker New Map1 RASTER KernelSmoothingTemplate l oy Ea File Edit Samples View Process Tools Options Help BOJA Beh OG a Oc Ze BA AE k FALA E Ga _ Detail Level U Auto Low Med High Highest od Map Tools Zoom Select D Drag map Show distance FreeHand gt Rectangle D Add sample Edit sample Placemark 3 Show V Borders Samples V Valid V Invalid Freshwater habitats E All Select p gt Coordinates Decimal Degrees Lat 12 2909 Lon 22 96278 Detail Level 2 Viewing from 58 08445 18 047 to 14 41355 6 223 Ready The visual filtering by habitat is well fitted for sample maps But it can be less adequate for maps that also contain areas as density map will be always shown OVER the presence areas hiding them For example if in the folowing map we have samples and also a presence area Therefore the density map will be calculated using only samples and shown over presence areas hiding them totally or partially l
132. e exported map Below there is an example of a map exported using this feature where samples have been hidden to only show density information 171 ModestR Software Quick start tutorial 6 26 Managing environmental variables ModestR allows adding environmental variables coming as data in CSV or ESRI ASC files i e Bi Oracle to metrics exportation options see section 6 17 This option is needed to obtain integrated outputs where metrics and environmental variables for a specific zone are included to perform data cleaning using environmental data to calculate niche of occurrence to show environmental data in a map etc To Add modify delete environmental variables you can use the Layers Manage environmental variables menu in DataManager or also in MapMaker the same variables will be available from any ModestR application no matter if you added them from MapMaker or DataManager Then a dialog box will be shown In this dialog box a tree shows the currently configured variables ordered using their assigned type On the bottom left side you can see two groups of buttons one for variables and the other for types If you select a variable in the tree its settings will be shown in the right panel in read only mode You can delete a variable by selecting it in the tree and using De ete button for variables or the equivalent option of the contextual menu clicking the right mouse button on the tree You can edit a va
133. e for this area sample this variable will be just not considered to make a decision ModestR will check the values took by the other variables to decide about the validity of the area sample Take into account that those options are per variable That is you can set different options for each variable A missing value for a variable can lead to immediately invalidate an area sample while for another variable it will not be took into account You should decide in a per variable basis the most adequate option e Apply to all buttons either in the tabbed box that displays the options for the currently selected validation mode or in the missing value options you can see a button Apply to All This button can be used to replicate the corresponding settings for the current variable to all variables in an easy way Finally on the right bottom side of the dialog box you can see a tabbed box with main settings While settings described above are for each variable those main settings have global effects They are e Allowed invalid variables Indicates how many variables can take invalid values that is outliers according to their validation rule before considering an area or sample as invalid for the species The default value is 0 and the maximum is N 1 where N is the number of selected variables Usually this field will be 0 because typically you will want to clean a sample areas as soon as one of the selected variables takes an outlier value B
134. e in minutes each element of theCSV matrix stores the value of the variable for a square cell of a certain size in minutes Indicate the minutes in this field o No Data value indicate in this field the value used to indicate that there is no value for the variable for a certain cell It is typically 9999 o Top corner longitude and latitude indicates the coordinates that correspond to the first value of the file Usually there are 1802 longitude and 902 latitude o First row contains headers First column contains headers check uncheck those options to set if the CSV file contains a first row column of headers that has to be skipped when reading variable data o Decimal separator indicates the character used as decimal part separator in the CSV file It can be point or comma o Field separator indicates the character used as field part separator in the CSV file It can be comma or semicolon If you want to add several variables which data is contained in several files in a same folder and that have the same format you can use the mport button In this case you will only have to enter a descriptive type for the variables that will be imported select the kind of format ASC or CSV and select all the files to import A variable will be added linked to each one of the selected 173 ModestR Software Quick start tutorial files The name will be set by default to the filename You can later edit those variables to modify or com
135. e species included in the database are searched Clear Squatiniformes Taxonomy Prefilter i i a Class Order Family Genus Species Plad Sharks Carcharhiniformes r Sharks Heterodontiformes Rd ei BA J 2 a s W Show V Borda y Coordinates Decimal Degrees Selected species 290 B Select 4 Zoom Detail Level 0 Viewing from 180 0009 100 0351 to 180 0009 100 0351 Ready The last tab is the Grouping and simplify tab There are here the group options If you selected more than one area to search for you can choose between a separated or a grouped search In the first case MRFinder will perform a search in each area and you will be able to obtain a list of species found in each area separately In the second one MRFinder will perform a search in all areas at the same time so results will contain all species present in any of the areas The second options is obviously faster so if you do not need the information provided by the first option we recommend you to select this second one In this tab there is also the simplify option this option will makes MRFinder preprocess selected searching areas to simplify them This is particularly useful when using complex selections such as some selections that can be imported from very detailed shapefiles or complex predefined selections see section 4 4 for more details about predefined selections In most of the cases we don t need to perform a sear
136. e there are samples in the corresponding map for 28 Futher information about Maxent software can be found in Steven J Phillips Miroslav Dudik 2008 Modeling of species distributions with Maxent new extensions and a comprehensive evaluation Ecography 31 2 161 175 DOI 10 1111 j 0906 7590 2008 5203 x 148 ModestR Software Quick start tutorial each species and use the minimum of these values as probability cutoff to import probability data The selected values for each species are displayed after importation If you import data from species that don t have a sample based map on the current database default probability cutoff will be used even if you activate the use minimal probability at presence option e Valid habitats you have to select which habitats at least one are valid for the species data you are importing Only areas corresponding to those habitats will be accepted and add to the map e Merging method you can select to overwrite existing maps if any with new maps created using imported data to add new data to existing maps or to not modify existing maps so importing only data for species that still don t have a map in the database Once accepted this dialog the importation process will start This can be time consuming if you import a lot of maps or they are complex When the process will be completed a report showing imported maps and possible errors will be show in the right panel 6 11 Importing dis
137. ea Land Area Large Rivers Area Small Rivers Area Lentic waters Area etc e Total Extent Of Occurrence of the species Total EOO e Minimum and maximum coordinates where the species is present Min Longitude Max Longitude Min Latitude Max Latitude e Patch index t Patch Index This index is calculated as Patch Index total EOO of species total convex hull area of species where EOO is the Extent of Occurrence calculated according to user settings see 3 6 and convex hull area is the area of the convex hull calculated from all the presence data for the species both samples and areas but taking into account only habitats valid for the species For example is a species is only present in marine habitats only sea areas will be took into account to calculate EOO and the convex hull area of the species e EOO Mode indicates the way the EOO has been calculated for this map EOO mode is selected when processing maps see section 3 6 and can be none EOO AO0 ConvexHull ConcaveHull alpha shape or DensityEstimation kernel density e Alpha Value when the EOO mode is alpha shape this value indicates the value of the alpha parameter used to calculate the EOO e ConvexHull Area area of the convex hull of the map This value is independent from the chosen EOO mode and it is ised to calculate the patch index value as explained above e NumSamples number of valid samples contained in the map must be O for pure range maps e H
138. ean countries as selections to the map That depends on how the tree is organized You can add one or more selections in this way Then click on the Close button to go back to the main window By default MRFinder will zoom on the area where the current selections are located this can be modified in the Options menu of the predefined selection dialog box 114 ModestR Software Quick start tutorial 4 5 1 Querying for selections in a point of the map When having several selections on the world map moreover if they overlap it can be sometimes difficult to know which are the selections in a specific point To query that you have just to place the mouse in the map If one or more selections are currently present at this point of the map this information will appear under the information of longitude and latitude Lat 42 99096 Lon 8 284961 Word Countries Europe Spain iby Autonomous community Galicia Word Countries Europe Spain 4 6 Search options Once one ormore search areas selections have been added to the map you can click on the Search button that will be enabled at the left tool panel MRFinder will use rasterized that is processed maps from the currently selected ModestR database to perform the search so it is necessary that all maps have been previously processed using DataManager to obtain accurate results see section 3 6 MRFinder will warn you if you try to make a search using a database where not all maps hav
139. eas Default factor x1 has been adjusted to return a density area with a standard deviation of the distances between presence areas near the original standard deviation of the distances between samples e Density hull visual simulation this option shows a visual template of the hull calculated using the density estimation with the set parameters For the example below this will be the result 33 ModestR Software Quick start tutorial nome density estimation Kemel density estimation options Parameters Cell width 5 minutes 7 Dont use duplicates Lower Normal Higher l Perform Density hull visual simulation D Add as presence area RK aose ef oi AK aose f OK As you can see density hull usually return several separated polygons but it will contains all the samples even if the polygons can be very small for some samples You can easily test density hull with different parameters to see the differences and select the value you consider more accurate Anyway remember that default smoothing value x1 has been adjusted to return a density area with a standard deviation of the distances between presence areas near the original standard deviation of the distances between samples e Add as presence area this option will add a presence area to the map corresponding to the density hull Existing data will not be deleted but this adds a new presence area to the map The habitats assigned as valid to this
140. ect Data ModestR taxonomy and maps database umm CAModestRFryect BED Elasmobrancha DB Default database MapMaker Extemal utilities GDAL ogr2ogr exe path Warning don t modif this parameter unless you are aware of fhe consequences C ModestRProyectiData GDAL bin Ogr2ogr exe Select coords registering mode for pixel 6 Show coords of pixel start Show coords of pixel center O Show coords of pixel end CSV Exportation options Decimal separator 7 Field separator 7 Check for updates from ModestR website Save as default values Accept 74 for ModestR Software Quick start tutorial 3 First steps in DataManager DataManager is another application of ModestR software It is aimed to create and manage ModestR databases which are databases containing taxonomic data and associated distribution maps You can create a new database or just use existing ModestR databases like the Ipez database you can find in the ModestR website Many of the features available in MapMaker are also available in DataManager The main difference is that while MapMaker is designed to work with a single species distribution map DataManager is meant to work with many maps at the same time For example in DataManager you can download data from GBIF or apply a data cleaning for a whole class of species in a single operation while in MapMaker you can only do it species by species Furthermore DataManager can perform analyses and generate repor
141. ection 3 6 or that it doesn t contains data enough to calculate hull At least three samples are required to calculate convex hull and at least four for alpha shape but depending on their relative distances it can be impossible to calculate alpha shape Maps excluded because they are not of the selected kind will also be listed For example range maps will be listed as excluded if we selected to apply alpha shape hull which can only be applied on maps with samples m Convex hulling Map convex hulling transformation Correctly hulled maps Notoraja alisae Notoraja fjiensis Squalus bucephalus Squalus crassispinus Squalus edmundsi Squalus grahami Squalus notocaudatus Incorrectly hulled maps Species Problem Bic Anoxypristis cuspidata Map is not processed Cannot apply conv E Pristis clavata Map is not processed Cannot apply conv Pristis microdon Map is not processed Cannot apply conv _ Pristis pectinata Map is not processed Cannot apply conv Remember that you can copy the contents of those lists to the clipboard by clicking on them with the right button and selecting the Copy to clipboard option that will appear on a contextual menu After applying hull transformation you should process the transformed maps as hull transformation involves a modification of the map presence data see section 3 6 86 ModestR Software Quick start tutorial 3 9 Apply
142. ed out that it is also possible to only select environmental variables to output without including any metrics To manage environmental variables see section 6 26 e When exporting metrics such as richness in ESRI ASC format using the Export zero as NODATA checkbox you can select if a zero value for a cell will be exported as NODATA usually will not appear when showing the raster in a viewer or as zero will be shown as a zero value Finally you can select the output format for presence richness data among the following ones e CSV matrix longitude X latitude this format outputs a matrix with coordinates of each cell at row longitude column latitude headers and metrics data as values for each cell of the matrix Here we see an example of richness output for a zone with longitude from 109 to 120 and latitude from O to 11 and with a cell precision of 60 Values of longitude and latitude correspond here to the right down corner of each cell The zero value in the first position of the first row has no signification it is used to avoid 159 ModestR Software Quick start tutorial importation problems with some applications like R When exporting environmental data in this format if a value is missing for a cell an empty value will appear on the output O 110 111 112 113 114 115 116 117 118 119 120 10 1 1 0 0 4 3 0 0 5 0 7 0 3 2 0 9 9 8 7 6 5 4 3 2 0 0 0 0 0 0 0 0 0 0 O O O O O O O O O
143. ed to show how much species are currently selected If no species comply with the filters it will indicate zero and exportation tools will be disabled As said before you can also go to Filtered results page to see the species that currently comply with all the filters including the taxonomic one You can remove a filter o clear all using the Remove or Clear filter buttons respectively 119 ModestR Software Select the filters to apply to the nails found cloner filter F Rare species filter Categories filter F Filtered results E Export data Quick start tutorial agel Elasmobranchii GBIF Class Sarcopterygii J Boa Order Coelacanthiformes W Batoids 3 Sarcopterygii Family amp Coelacanthiformes Genus EY Taxonomic tree of the species found in the selected area Buttons to add or delete filters Batoids Torpediniformes Sarcopterygii Coelacanthiformes J PEP Search button Species matching criteria 32 Total species in region 222 Species matching criteria 32 Region Bounds Long 86 19 to 77 48 Lat 0 31 to 73 43 Clear all 4 8 2 Rare species filter page The second page is the Rare species filter page Here you can set a filter regarding the area occupied by the species which is particularly aimed to select endemic or rare species This can be done checking the Filter only rare species checkbox to activate the filter
144. eeeceecececenseseenceseueceseueseeeeeeeeeeeeees 189 8 11 Export selections to shapefile OF KML ccccceeececeeececeeesceeeseceeecseeeeseeeeeseeeeeeeees 189 8 12 Export to ASC raster ccccecer es QIMMMMMs cosccscceccercercererserserss AQ ssscsccsscercersersersersens 190 8 13 Export environmental data O annees e AQIS cacscsenerenaareres 190 8 14 Export selection areas summary FEPOMt cccccseccceeeccceseccceseccceeceeeeeceteneceeeeeseeneeeees 190 9 MRMapping import export files fortmat cccccsssccsssssccssccescsescnsscessseseneces 191 9 1 Exporting Overlapping areas report ccccceeececcsssccccessececnessccceeescceceeecessuaeceesaneeeets 191 9 2 Importing file Of visual template NAMES cccceseccceeecececccescseeueceseuecseeueeseeneeeeenss 191 10 Checking for updated d eee Ne cescnsscscccccessssscasceccnssssccescessnsscescescess 192 NO WARRANTIES This document expressly disclaims any warranty for its contents The document is provided As Is without any express or implied warranty of any kind including but not limited to any warranties of merchantability noninfringement or fitness of a particular purpose This document does not warrant or assume responsibility for the accuracy or completeness of any information text graphics links or other items contained within the document This document further expressly disclaims any warranty or representation to Authorized Users or to any thir
145. elds contained in the shapefile A shapefile can contain several fields with values assigned to each shape contained in the file This dialog box allows you to see those fields and the values they take by clicking in the wanted field This is to help you to select which field you want to use to split and group the shapes contained in the shapefile in several selections For example in the dialog box shown here as example Select field to use as name The file you are importing contains data fields for each selection You can select the field to be used to name the selections or select Default to use default names Fields contained in the file Values AREA PERIMETER AU BAS U BAS ID LEVEL1 LEVEL LEVEL3 LEVEL4 LEVELS LEVEL6 DEM_MEAN DEM STDEV ASPECT _MEA ASPECT STD SLOPE_MEAN SLOPE_STDE a If we select as field the one that is highlighted AU BAS ID the shapes contained in the shapefile will be grouped using this field So all shapes with the value 1 in the field AU_BAS_ID will be grouped and added as a single selection to MRFinder Then all shapes with the value 2 and so on 8 2 Importing selections from KML In MRFinder you can import selections to search for species from KML files This is introduced in 4 4 To import a KML file go to File Import selection From KML file menu The steps are quite the same than the described above for shapefiles see 8 1 with the difference that the first
146. elections editor When you have added several selections to a map you may want to remove one of them change its name or merge several selections in one single logical selection Or even pinpoint one selection among many others in the map To do that you go to Edit Selections Editor The Selections Editor will be displayed In this editor you can 123 ModestR Software Quick start tutorial e Check any selection to highlight it in the map use the checkbox on the left side of a selection to do that e Delete one or more selections use the checkbox on the left side of the selections to select the selections to be deleted and click on the Delete button e Rename a selection just select the wanted selection you don t have to use the checkbox for that just click over the selection and click on the Delete or the Rename button e Merge several selections on one single logical selection use the checkbox on the left side of the selections to select the selections to be merged and click on the Merge button Remember that as explained in 4 3 this feature allows to logically merge several selections to make MRFinder to consider them a single one regarding searching and display But this merging does not imply any geometric union of several areas in a single one To do this type of merging see section 4 12 2 ModestR MRFinder DB Elasmobranchii GBIF DB o amp s File Edit View Options Tools Help ADMIN Y PRUEBAS
147. ene ago 1 o sea lactinopterygiacipenseriformeslacipenseridaehcipenserlAcipenser brevirostrum PETER EEE E ee a a ear 5613 5479 1 o sea _ ActinopterygiiAcipenseriformesAcipenseridae Acipenser Acipenser brevirostrum 77 98 33 94 1 1 _fillSample ActinopterygifAcipenseriformesAcipenseridaelAcipenserAcipenser brevirostrum 76 71 3597 1 2 _fillsamplelActinopterygiiAcipenseriformes AcipenseridaelAcipenser Acipenser brevirostrum 7 af 1 3 _ fillsamptelActinopterygiiAcipenseriformesAcipenseridae Acipenser Acipenser brevirostrum 74 73 40 17 1 4 FillSemplejactinopterygilAcipenseriformesAcipenseridaecipenserlAcipenser brevirostrum 6 15 Exporting presence data to raster files You can export maps of any branch of a DataManager database to individual rasters in ASC format using the Export Export maps of selected branch To presence data To ASC raster maps option Export ASC raster options from Canis Select format style ESRI ASCII options Precision 1 degree Export zero as NODATA Select presence count method Count if species is present in one cell Count if species occupies at least 25 11 minute blocks in cell Select habitats to include W Sea W Land RE All freshwaters W Lentic habitats Small Channels W Small Ditches W Small Drains W Small rivers Large Channels W Large Ditches W Large Drains Fj W Large rivers Wetlands W Reservoirs Set exportation zone boundaries From longitude 1
148. ent ESRI shapefiles or KML files Each one of those importation features is explained in more detail in chapter 7 2 6 Data cleaning using automatic range based rules MapMaker incorporates the possibility of using automatic validation rules basing on outliers detection to determine the validity of samples as well as areas of presence according to environmental variables This allows for example to invalidate samples located in places that have some environmental conditions such as temperature or altitude values outside a certain range Or to delete from an area of presence the parts where some environmental conditions are not respected To do that ModestR will firstly determine the range of values took by those variables on the current presence data and allow the user to select how to determine outliers To determine current ranges for variables in sample maps one single value for each variable is took in the coordinates of the sample For range maps with areas of presence in turn of samples a value for each variable is took for each occupied cell of 1 x1 so for example for a presence area of 10 x4 40 values will be took for each variable Data cleaning will be done for each individual sample and in case of areas for each 1 x1 cell of the presence areas So in case of areas the minimal resolution supported when cleaning is of 1 x1 Environmental data needed to use this features are not included in ModestR so they have
149. ently selected validation mode or in the missing value options you can see a button Apply to All This button can be used to replicate the corresponding settings for the current variable to all variables in an easy way Finally on the right bottom side of the dialog box you can see a tabbed box with main settings While settings described above are for each variable those main settings have global effects They are e Allowed invalid variables Indicates how many variables can take invalid values that is outliers according to their validation rule before considering an area or sample as invalid for the species The default value is 0 and the maximum is N 1 where N is the number of selected variables Usually this field will be 0 because typically you will want to clean a sample areas as soon as one of the selected variables takes an outlier value But this setting provides a way to be more flexible For example you can select 10 variables and allow that up to two variables of these take outlier values before considering a sample area as invalid e Allowed missing variables Indicates how many variables can be missing have a null value before considering an area or sample as invalid for the species By default it will be set to N where N is the number of selected variables That is if all variables have null values for a sample area the area will be considered as valid Take into account that this parameter will be applied only if the vari
150. environmental layer creation process Briefly a visual template is an area that is added to the map just for visual purposes see section 2 14 for more details about visual templates For example if you added a visual template that demarcates a specific country and you select the Visual template layer extent mode in this dialog box the environmental layer to be created will only covers this specific country supposing that environmental data are also available for this area of course e Extent of Occurrence this option will only be available if there exists occurrence data in the map before starting the environmental layer creation process In this case you can select the Extent of Occurrence layer extent mode in this dialog box to delimitate the environmental layer to be created to the Extent of Occurrence EOO that can be calculated from the current occurrence data in the map If you select this option a panel will appear on the right side for you to select how EOO should be calculated see section 2 8 for more details about the different ways of calculating EOO Once those options set click on Continue button to go to next step 50 ModestR Software Quick start tutorial In the next step selected variables are shown in a list You can optionally calculate Variance Inflation Factor by clicking on the Calculate VIF button But this is just optional You can skip this step and click on Continue button to go to next step
151. er oxyrinchus desotoi e decimalLatitude decimalLongitude coordinates of the samples The exported CSV file will be easily opened with a worksheet application like Excel and copied to the Excel template provided by GBIF in http tools gbif org spreadsheet processor to subsequently generate a Darwin Core Archive 6 17 Exporting metrics and environmental data DataManager can calculate and export several metrics from maps like richness data rarity index etc If you have files containing environmental variables data you can incorporate them to DataManager to make that they can be exported at the same time that metrics The way to manage environmental variables is explained in section 6 26 When selecting Export Export maps of the selected branch To metrics and variables in main menu or the equivalent option in the tree contextual menu a dialog box to select exportation settings is shown 157 ModestR Software Quick start tutorial Export metrics options from Select format style Select metrics and variables to output Precision 1 degree g Metrics CSV listin colum 5 Excel worksheet 2007 or high ist in ns cel worksheet 2007 or higher 2 Fo Rarity i gt CSV matrix longitude X latitude ESRI ASCII Raster matrix FJA A00 index Select richness count method 4 Patch index Count if species is present in one cell Of Latitudinal range io i ATU nge index Count if species occupies a
152. er variables to decide about the validity of the area sample 23 Dubois D M 1973 An index of fluctuations Do connected with diversity and stability of ecosystems applications in the Lotka Volterra model and in an experimental distribution of species Rapport de syth se III Programme National sur l environment Physique et Biologique Project Mer Commision Interminist rielle de la Politique Scientifique Li ge Guisande C Barreiro A Maneiro I Riveiro I Vergara A R Vaamonde A 2006 Tratamiento de datos Ediciones D az de Santos 367 pp 95 ModestR Software Quick start tutorial Take into account that those options are per variable That is you can set different options for each variable A missing value for a variable can lead to immediately invalidate an area sample while for another variable it will not be took into account You should decide in a per variable basis the most adequate option e Apply to all buttons either in the tabbed box that displays the options for the currently selected validation mode or in the missing value options you can see a button Apply to All This button can be used to replicate the corresponding settings for the current variable to all variables in an easy way Finally on the right bottom side of the dialog box you can see a tabbed box with main settings While settings described above are for each variable those main settings have global effects They are e Allowed inval
153. ercents between each pair of map items The full report contains the same information but broke down by type of habitat e g land sea lentic waters See 9 1 for details about the exported report 140 ModestR Software Quick start tutorial 6 DataManager import export files format In this section we briefly explain the main file formats used by ModestR DataManager to import export data from to a ModestR database Remember that some exportation defaults concerning CSV format can be set in the DataManager default settings see 3 2 6 1 Importing taxonomy from a CSV file You can import taxonomic data in CSV to a ModestR database using the mport Import Taxonomy From CSV file menu option Data to be imported have to be in CSV format either separated by comma or semicolon They can contain headers You should indicate those options in the dialog box that will appear before importation Each row must correspond to a species to be imported Each row must contain the class order family genus and species in this order Importation process is not case sensitive For example those data will be valid to be imported Elasmobranchii Torpediniformes Narkidae Typhlonarke Typhlonarke aysoni Elasmobranchii Torpediniformes Narkidae Typhlonarke Typhlonarke tarakea Actinopterygii Zeiformes Oreosomatidae Allocyttus Allocyttus folletti Actinopterygii Zeiformes Oreosomatidae Allocyttus Allocyttus guineensis Actinopterygii Zeiformes Zenionidae Cap
154. es Decimal Degrees Lat 16 25636 Lon 22 42552 4 Detail Level 1 Viewing from 66 85538 22 403 to 1 90863 13 691 Ready When you want to make density maps like the explained above but for many species in turn of doing it one by one in MapMaker it could be more useful to do it in DataManager that has a feature for that see section 6 25 2 10 Calculating Environmental Occurrence MapMaker can estimate the Environmental Occurrence of a species that can be defined as all the available areas for the species within a specific range typically the EOO but it can also be all the world but excluding the habitats not occupied by the species and considering only those areas within the range of environmental conditions suitable for the presence of the species This option is intended to be applied on sample based maps as range maps already include presence areas but it can be also applied to those type of maps with some restrictions Environmental data needed to use this features are not included in ModestR so they have to be provided by the user as data files in ESRI ASCII or CSV format There exist free datasets available in Internet such as Bi Oracle for example that are fully compatible with ModestR Therefore the first step will be to integrate those data in ModestR to allow it to use them when needed To do that you can use the menu Layers Manage environmental variables either in MapMaker or in
155. es only species found in the current search that also are included in one of the selected categories will be included in any posterior exportation As said before you can go to Filtered results page to see the species that currently comply with all the current filter settings remember that all filters are applied to obtain those filtered results 121 ModestR Software Quick start tutorial Taxonomy filter Rare species filter Categories filter Filtered results Expor data Import categories file H File has headers Field separator gt os Species in selected categories Lynx pardinus Mustela lutreola Procyon pygmaeus Urocyon littoralis Viverra civettina G Load file CAModestRProject BD C digos carnivoros csv V Enable filter by category F Near Threatened F Not evaluated F Vulnerable Total species in region 222 Species matching criteria 0 Region Bounds Long 86 19 to 77 48 Lat 0 31 to 73 43 4 8 4 Color map and filter clearing Once you have set the filters you want you can just click on the Close button and you will see that the colors of the areas in the map as well as the color scale will be updated to take into account only the filtered results This is also indicated on the top of the right color scale where a Filter ON label will be shown You can go back to the filtering window clicking on the Filter Export button on the F Fiter left tool panel modify the filter and accept i
156. es with maps or only branches were there are species with maps for examples You can also use the search box than can be displayed using the magnifying glass button on the bottom left corner In the search box you can write some part of the species you are looking for and coinciding names will be shown in the Results list Once selected a species with a map in the tree press Select button to load it in MapMaker Select species for map from prueba DE 28 Foe Ex The world icon indicates Classification c i prueba Actinopterygii 1 Elasmobranchii E Carcharhiniformes i Ele Carcharhinidae amp Carcharhinus that this species have a map saved in the database e Carcharhinus acronotug Carcharhinus albirnargianrg Carcharhinus altimus Carcharhinus amblyrhynchoides g Filter E Filter options Show only branches with maps Show only species with maps Show only branches without maps 5 Show only species without maps Writing part of a species name Search Scientific name i gm a list of coincident names will be B c shown in the Results Just select E Genus on to find it in the three Button to show hide A Carcharhinus brachyurus Carcharhinus brevipinna Carcharhinus cautus Carcharhinus cerdale search box Results 37 elements found x Once loaded you can for example modify a map in MapMaker and save it again This way you can wor
157. euscoeincvorseiatiavensact lt topiateedoniatnenipientedasaestinieanesiebsatentes 73 2 19 Setting the default ModestR database and other preferences in MapMaker 74 3 First steps in DataManager essessescecceecoesceeceecoeccoeccesceccoecoescesceccoescecceeceesceccee 75 3 1 DataManager user interface ccc ccrcsees AM 000s AQMD cco csrencassrenvensrserensureneusarensans 75 3 2 Default settings in DataManager cccccccessccccssecccesecccauseseccescceeeuseeesseeceseunecetsenes 76 3 3 Creating a new database MMMM rccsssrescessresresssrercssere D nonnene neneeese rererere 76 3 4 Adding and managing maps in a Catabase cccceccccsescccsescccsececevececeuecsseeceeeneseeeusss 78 3 5 Opening a map from DataManager 0 MQMMMMD sccseuvecussrcsvevsrsereseurencavarenvensrsareusars 78 3 6 Processing MADPS cccccoecce CA O O ccesctescrescrescsescsesccesccesscesceeeceseces 79 3 7 Saha gt A ee 82 3 8 Applying convex concave hull transformation cccccccecccccccccseeeeeeceeeesseeeseeeeeeeeeess 84 3 9 Applying density based hull transformation cccccescccccsseccecessececeeseceeeeeceeeeeeeeees 87 3 10 Demeeeaing in De SID csccscsssssresvessrsercusercncassrsevensusencussrenvansreens 89 3 11 Applying Environmental Occurrence cccecccceesscccceesececceeceeceeecceseeseceeeueeceeseneeeeeas 93 3 12 Calculating niche of occurrence with an existing environ
158. ever visual templates are not saved with the map For the example map above this will be the result File Edit Samples View Process Tools Options Help BOS8G BSUMOS a Oo ZO BI we Br ui FLLeBo i G it Samples Valid V Invalid Freshwater habitats aa Lat 52 72576 Lon 118 116 i Detail Level 1 Viewing from 178 5878 35 4137 to 98 94543 79 67474 Ready Add as presence area this option will add a presence area to the map corresponding to the convex hull Existing data will not be deleted but this adds a new presence area to the map The habitats assigned as valid to this new area will be inferred from the already existing presence data samples and areas You can undo changes using Edit undo or modify this new area as any other area using Unfill feature see section 2 2 For the example map above this will be the result File Edit Samples View Process Tools Options Help BOSE BGh OC a Dage ee Br ul FALLA i oi 3 7 Borders Samples 7 Vaid 7 Invalid Lat 56 16752 F x ENE Lon 110 1312 Freshwater habitats E _ p a Di ii TN i Decimi Degrees Detail Level 1 Viewing from 178 5878 35 4137 to 98 94543 79 67474 Ready 29 ModestR Software Quick start tutorial 2 8 1 Using convex hull with areas Convex hull is mainly intended to be used with sample data But it can also be used with area data as ModestR can use the p
159. ew 5 1 1 Querying for species in a point When having several species distribution maps that overlap on the world map it can be sometimes difficult to know which species are really present in a specific point To query that you have just to double click with the mouse in the map If one or more species are currently present at this point of the map a little tool tip will appear with this information Lat 14 54319 Lon 51 96864 Pristis pectinata Pristis zijsron Anoxypristis cuspidata 5 2 Changing map settings Once one or more distribution maps we can also name them datasets or map items to the world map you can edit them and modify their settings going to the menu Edit Map list editor 135 ModestR Software Quick start tutorial A dialog box is displayed with the list of all distribution maps map items currently added to the world map Current map items Order Pristis zijsron S Pristis pristis FY Pristis perotteti al FY Pristis pectinata Pristis microdon E FY Pristis clavata a a Anoxypristis cuspidata Options Encircle checked items in map In this list the map items are shown by default regarding the order they are painted in the map That is the last map item of the list is the one that is painted the first while the first one of the list is the last painted so it is painted above all the others That can be important because on
160. ew you are currently seeing in MapMaker to a JPEG or BMP file using the Export current map view button in the toolbar or the File Export Current map view as image menu option Next a dialog box will appear with several tabs In the Grid and scale tab you can set if you want to see a grid scale in the exported image every degress minutes you want this grid scale etc In the Dimensions and format tab you can directly modify the coordinates of the portion of the map that will be exported By default the same view currently displayed in MapMaker will be exported You can also select the size of the exported image By default MapMaker sets the image size as slightly bigger than your screen resolution This is usually a good resolution to use the image in another document presentation etc But if you want a more precise image that can be zoomed correctly you can increase the image size Finally you can select between JPG or BMP format Set map display options Set zone boundaries From longitude 180 0000 to longitude 180 0000 From latitude 90 0000 to latitude 90 0000 Set image size and quality for exportation Resize image J Resulting map dimensions 1638 Image quality Image format JPEG Bitmap BMP amp Preview Cancel Accept 7 7 Exportpresence areas and samples You can export presence areas and samples from the map to a file
161. explained later in this chapter cannot be undone because they do not really imply a modification of the map just a change in display options 2 5 Making an occurrence based distribution map in MapMaker To make a distribution map basing on samples or occurrences of a species you should simply have to add the samples on the map using one of three options manually adding samples importing them from a CSV file or downloading them from online GBIF portal Each one of those options is explained below 1 Manually selecting the Add sample tool in the left tool panel Then select the type of sample in the Sample settings groupbox this is explained later in the section and the valid habitats in the Valid Habitats groupbox that will be displayed in the left tool panel And finally click on the position in the map where the sample has to be added You can drag the sample to the exact target location while you have the left mouse button 14 ModestR Software Quick start tutorial pressed Once you release the button the sample will be placed on the map Obviously this option is only useful when having to add few samples File Edit Samples View Process Tools Options Help BOsGBGH oga sagt Bl e gt Map A D Eda Zoom Detail Level Be a Sample settings groupbox 24 Valid habitats gt groupbox Ol Detail Level 0 Viewing from 63 8577 45 14619 to 66 1041 54 03101 Ready 2 Another option is to import samples from
162. exportation featres of MapMaker e Export map as image in File Export Current map view as image you can export the current map view you have in the screen to an image in JPEG or BMP format Options such as adding a grid scale or quality adjust will be shown e Export map to KML or Shapefile File Export To KML or To Shapefile you can export current species map to KML or Shapefile formats Take into account that presence areas in range maps are internally stored the way the user has drawn them To clip those area to coastline when exporting you should enable this option Export options KML export options Areas export options Clip to coastline Medium precision Samples to include Include only valid samples Include all samples xX Cancel la 71 ModestR Software Quick start tutorial e File Export To CSV usually used to export sample coordinates to a CSV file e File Export To ASC raster generates a raster in ASC format with the selected precision where the cells where the species is present have a value not null usually 1 e File Export Environmental data this option allows exporting environmental data clipped to presence areas or visual templates It s explained in section 2 9 4 e File Export Areas summary report generates a report in CSV format with the areas in km of each type of habitat where the species is present A similar report but for any set of species not just
163. f Occurrence names a different feature based on environmental layers described in section 2 11 55 ModestR Software Quick start tutorial than when the environmental layer was created Errors or inaccurate results can be obtained if some variable has been modified since the environmental layer creation To avoid those problems as much as possible from ModestR v 3 1 when you delete or modify an environmental variable any environmental layer that used this variable will be deleted The first step to calculate the NOO of a species in MapMaker is loading the wanted species data for example downloading data from GBIF or from an existing ModestR database Next you have to select the environmental layer that will be used to calculate the NOO This determines the polar coordinates system and the environmental data to be used To select an environmental layer go to menu option Mapping Niche of occurrence Load environmental layer Select the wanted layer in the dialog box that will appear and click on Accept button 4 Select an environmental layer Layer name Creation time Africa 04 10 2014 ejemplo manual 15 01 2015 Espana 05 10 2014 Mar vars gwi 2014 Sudamerica 2 vars oo 0a 2014 G Terrestrial layer os0g2014 Terrestrial layer P 03 05 2014 Once loaded an environmental layer can be used during all the current work session The currently loaded environmental layer is displayed in the right bottom corner of the MapMa
164. fault 68 ModestR Software Quick start tutorial Once selected the wanted variables they will be loaded and you can see their corresponding value on the mouse cursor when moving it on the map If the value of one variable is missing for the current coordinates of the map as it is usual that some variables have only data for sea areas for example the value will be empty File Edit Samples View Process Tools Options Help Bese B8eH 9R 4 Oo 26 8 9 ae Mag A Detail Level Auto Low Med High Highest a Map Tools Drag map FreeHand Rectangle Add sample 7 Lat 29 24821 Arow Lon 135 6619 Tet Flacemark Valid Invalid Freshwater habitats al 2 16 6 Raster transformation tool MapMaker includes a simple tool to rescale clip filter and transform rasters in ASC format To run this tool go to menu Layers Raster transformation tool it is also available from DataManager in the same menu A dialog box like the following one will be shown Cell size minutes Longitude range Latitude range Output Raster settings Rescale cell size C Clip data to selected region C Filter data L Transform raster values L Create merged raster 69 ModestR Software Quick start tutorial You can add the ASC files to be transformed just by dragging and dropping them on the central area or clicking on the Select files button and selecting them Take into account that every
165. for species that already have maps in the selected branch This option is useful to add new data to already existing maps or to overwrite them with new data e Merging method can be gt Overwriting existing maps with new data in this case if a map already exists for a species that will be downloaded from GBIF this map is deleted and a new map is stored only with new data downloaded from GBIF gt Adding new data to existing maps in this case if a map already exists for a species that will be downloaded from GBIF new data downloaded from GBIF are added to this map Therefore no previously existing data is deleted e Check if species isa synonym according to GBIF indicates if you want DataManager to look for synonyms in GBIF database In this case if GBIF indicates that a species is a synonym of the species you are downloading DataManager will use the main species name provided by GBIF to download data For example if DataManager is downloading data for species Isurus alatus and this option is enabled GBIF will indicate that this species is a synonym of Isurus paucus and then DataManager will use surus paucus to download data and add them to the surus alatus map If this option is disabled only the name that appears in the ModestR database will be used but no synonyms in this case only Isurus alatus will be used to download data from GBIF e Kind of records to download allows you to select the type of records you want to download fr
166. g about the predefined selections that you can create or import and store in the user predefined selections database to reuse them later The first way to store a selection is to do it on the map and store it You can select or import several areas Then when all the areas you want to store as a selection are selected in the map click on the Store selection as predefined button in the toolbar or go to File Store as a predefined selection menu option A dialog box will be shown where you have to enter a name and a description for the selection and select under which node of the selections tree the selection will be stored 124 ModestR Software You can also enter other settings such as Quick start tutorial e Description a description about the selection e Select childs of this node when selecting it enabling this option and if you later add selection into this selection child nodes to this node those selections will be automatically selected when you select this node You can see an example of that behavior when adding predefined selections included with ModestR When for example you select the node Africa all countries subnodes of Africa will be selected e mport Export Clear buttons let you import export data for a selection from to an external shapefile or clear this selection data selection is not deleted but it won t contain geographical data Once settings entered just click on Save button to save the select
167. he search process baba oe THA aR OP Th Cd Cpisu Toa Hip Sie aginrsat AB ate BS Ep ha Daal oral tala oe Bes Hij haa Dna ra dmn ikd bE hr ai Ti Riris Dis a g This color scale as well as the selected areas with their corresponding color will be exported if you export the map as a JPEG image File Export Current map view as image Scale and colors will be cleared when modifying search areas As it is explained below you can filter search results to select only some of the species found it this case the color scale and the colors of the areas will be automatically updated to take into account only filtered results It is important to remember as said before see 1 1 that ModestR is intended to work with a resolution of 1 arcminute 1 As a consequence MRFinder is not designed to accurately perform searchings in areas smaller than a 1 width or a 1 height Moreover searching performed by MRFinder is done with a precision of 1 And as said above see 1 1 ModestR assumes that the area of a sample is equal to the area of the cell of 1 x1 where it is located subsequently MRFinder can return in the search results a species with a sample located in a 1 x1 cell even partially included in the search area defined for the searching 4 8 Filtering seach result Once the search completed if species have been found in the selected area a new window will be shown where two ba
168. he shown density map is just a visual template that doesn t modify the map As it is calculated and displayed as a raster it will clear any other raster template you have previously activated To calculate and show this map go to Mapping Hull transformation Kernel Density Density Map In the dialog box you can select the resolution 5 is a good balance between precision and calculation speed You can also select to show only significant densities and to filter density map by habitat by presence area or to show in over the map 39 ModestR Software Quick start tutorial arnal dence marn martire REITE L Ei EiL aG Gr i C LI is Kemel density map options Cell width 5 minutes Dont use duplicates Show only significant densities Visual filtering Transparency By habitat Transparency 35 By presence areas 6 Show over map For example if you use the Show over map option the result can be something like this To obtain more visually appealing maps but with more blurred density areas you can increase smoothing For example using a x11 factor the result is 40 ModestR Software Quick start tutorial You can also modify transparency to increase decrease visibility of the density map regarding the underlying map You can select to show only areas where the density is equal or greater than minimal density at an occurrence record Areas with lower densities will not be shown For th
169. hing features are strongly affected by selection complexity that is the number of points vertexes that define the selections where to search for Manually made selections are rarely concerned by this problem But it can be the case for selections imported from external files such as shapefiles of KML files whether they are directly imported to the map see 4 4 or as predefined selections see 4 5 In those cases you have the possibility of simplifying those selections Simplification eliminates some vertexes with a given tolerance which can be easily acceptable in most cases but can dramatically improve MRFinder searching performance CJ ModestR MRFinder DB Elasmobranchii GBIF DB J ModestR MRFinder DB Elasmobranchii GBIF DB File Edit Options Tools Help File Edit Options Tools Help GSS8 7G OY 2G a BEB Ss weGioawvi 20 a Beeps te Detail F Example of a i simplication with 2 tolerance Both options are available in the Edit Simplify current selections menu options or in the corresponding button of the toolbar A dialog box like the shown below will be displayed where you can set simplification tolerance 129 ModestR Software Quick start tutorial Simplification options Set the values that will be used to make the selections smoother Simplification tolerance in minutes 1 0 E Accept x Cancel 4 12 2 Merging selections If you have several selections that overlap or that are just contiguou
170. hoose the color of the samples while if the y mainly contain presence areas in sea habitats you should select Sea selection and so on Add legend to map Legend Position Right Up E Down Legend text options Font color Hl GY Anoxypristis cuspidata YG Pristis clavata yy Pristis microdon YG Pristis pectinata FG Pristis perotteti GY Pristis pristis Wy Pristis zijsron 5 6 Exporting environmental data Raster data clipping Similarly to MapMaker you can export environmental data or any raster data in general clipped to the presence areas of each map item dataset in the world map see 2 9 4 The 139 ModestR Software Quick start tutorial difference being that in MapMaker this feature allows you to clip rasters to the presence areas of a single species while in MRMapping as in the world map you could have added several map items datasets from several species families orders etc you can clip rasters to each one of those map items To do that go to File Export Environmental data For each dataset A dialog box will show to you the available variables those previously integrated in ModestR We ll select the wanted one it could be more than one to generate several clipped files Next we ll have to selected the target folder where the file will be saved in ESRI ASC format A clipped raster will be exported for each map item e g each species or family added to the map and
171. hull transformation to a map that contains samples that have sea as valid habitat the corresponding hull area will also have sea as valid habitat As an example below we show a map before and after applying density based hull transformation in DataManager samples have been hidden in the resulting map As it can be seen density hull area is added to the map with the sea as valid habitat so other ones such as land are excluded because the previously existing samples have sea as valid habitat After applying hull transformation a report will be shown in the right panel indicating the correctly transformed maps and the incorrectly processed ones which were not updated A brief message will report the encountered problem that prevent processing each incorrectly processed map The most usual problems are that the map doesn t contains data enough to calculate hull At least three samples are required to calculate density 88 ModestR Software Quick start tutorial Summary data Map hull transformation Correctly transformed maps Abbottina rivularis Ablabys binotatus Ablabys taenianotus Not transformed maps Species Problem Aaptosyax grypus Map has no samples Excluded Abbottina obtusirostris Map has no samples Excluded After applying hull transformation you should process the transformed maps as hull transformation involves a map modification see section 3 6 3 10 Data cleaning in DataManager As seen in section
172. id variables Indicates how many variables can take invalid values that is outliers according to their validation rule before considering an area or sample as invalid for the species The default value is 0 and the maximum is N 1 where N is the number of selected variables Usually this field will be 0 because typically you will want to clean a sample areas as soon as one of the selected variables takes an outlier value But this setting provides a way to be more flexible For example you can select 10 variables and allow that up to two variables of these take outlier values before considering a sample area as invalid e Allowed missing variables Indicates how many variables can be missing have a null value before considering an area or sample as invalid for the species By default it will be set to N where N is the number of selected variables That is if all variables have null values for a sample area the area will be considered as valid Take into account that this parameter will be applied only if the variables with missing values are not individually configured as directly invalidating an area when their value is missing as explained above That is this rule will be applied only if after applying the rules for each individual variable the sample area has not already been considered as invalid Once all those settings configured press the Continue button In the next step you can select how potential EOO will be calculated to each s
173. iers as invalid X 3 if you select to consider only extreme outliers as invalid You can also set a custom value of X in the options shown for this validation mode JackKnife outliers this validation mode to detect outliers is described in Chapman s Principles and Methods of Data Cleaning 2005 and it is considered quite reliable ModestR supports two variants of this method the one proposed by CRIA and the one proposed in DIVA GIS both are described in Chapman s book Custom in this case it is the user that will manually set the minimum and maximum values of the range of valid values for a variable Any value that fall outside this range will be considered an outlier e Info tab under the validation mode combo box a tabbed box is shown where information and options for the currently selected validation mode are displayed There is also a nfo tab where you can consult basic statistics for the currently selected variable such as maximum and minimum values that this variable has on the current presence areas samples mean value quartiles and jackknife ranges e Missing value options under the tabbed box that show the information for the variable two radiobuttons allow you to select what to do when there is no value for the variable in a particular area sample You can select between two possibilities O Invalidate an area sample if the value for the variable is missing that is if the variable have a null v
174. if some sample area has to be cleaning or not Any validation mode will determine the range minimum and maximum of valid values for the variable so any value that fall outside this range will 22 ModestR Software Quick start tutorial be considered an outlier The difference between different validation modes will be in the way they use to determine this range By default the validation mode will be set to Autoselect best But you can manually select between the following modes O O Autoselect best this mode will evaluate which one of the other available validation modes returns the less outliers and uses this mode to clean data That is with this mode you will always obtain the minimal number of outliers The specifically selected mode will be described in the box below under the Automatic mode tab and it will be one of the available modes that are described below Quartile outliers or JackKnife outliers Autoselect best mode will not be available for variables with a coverage of 0 that is without not null values for the current presence areas Quartile outliers this option uses a validation based on the values of the Q1 and Q3 quartiles of the values took by a variable in the current presence areas samples This option will consider any value of this variable as invalid if it is outside the range Q1 X Q3 Q1 Q3 X Q3 Q1 where X will be X 1 5 if you select to consider both mild and extreme outl
175. igh Highest 3 Man Tools Zoom Select Drag map Show distance FreeHand Rectangle Add sample Edit sample Arow Text Placemark Show Samples Valid Invalid Freshwater habitats COM Sex Coordinates Decimal Degrees my _ 4 Zoom Detail Level 2 Viewing from 57 58868 26 96792 to 8 165901 0 4132347 Ready Bf Current Env layer Terrestrial layer v 2 14 Working with visual templates In MapMaker visual templates are just helping elements that don t modify map presence data They are not stored with a map but just shown during a worksession They must not be confused with preselections used in MRFinder even if they are stored together so a visual template in MapMaker can be used as preselection in MRFinder and vice versa The difference is their purpose which is merely informative in MapMaker whereas in MRFinder it indicates a search area In MapMaker visual templates will be commonly used to help the user to locate the boundaries of some specific area such as an administrative region a natural site etc To add predefined visual templates to the map you can go to Layers Visual templates Add visual templates or the corresponding button of the toolbar A dialog box will be shown where you can select the visual templates to add from a tree where they are hierarchically grouped On the right of the tree an active map shows a preview of the visual templates when avail
176. igin IN Aegialomys galapagoensis presence reigi E seasonal Ail irnannada melannleiira source f bd 4 ii p V Use those same options for the next files x Canca a Accept KE lt 4 KE 150 ModestR Software Quick start tutorial Then you can select a field to see the values it takes and add criteria that will be used as filter when importing You can also directly write a condition in the textbox The syntax of the conditions is similar to the syntax of a WHERE clause in SQL Finally you can decide to use those same settings for all remaining files to be imported if there is only one file to be imported this option will have no effect This option is checked by default so it will only be shown for the first file to be imported But if you want to use different settings for each file to be imported for example different filtering criteria you can unchecked it then DataManager will show this dialog box for each file to be imported e Next a dialog will be shown Select field to use as name wh ere you h ave to se ect t h e Select the field that has to be used as species name or click on Default to use filename as species name shapefile field that will be used to ide ntify the s pecies name Fields contained in the file Values id ni Plecotus sardus This is mandatory when Cryptotis obscura i Notopteris macdonaldi importing a shapefile that orai Pteropus cognatus contains several species maps ez Melanomys zuniga
177. ike Excel that allows exporting to CSV format 17 Gypaetus barbatus 8 Hieraaetus fasciatus 9 Milvus milvus The next step is going to DataManager and select the menu Neophron percnopterus option Import Import taxonomy GBIF taxonomy search tool A l Neoparon ee andion nallaetus dialog box allows us to indicate if the input file contains a header 23 Anser fabalis rossicus in this case the first line will be just skipped and which separator is used in the CSV file Set importation options for CSV file CSV import options Fi First row contains headers Field separator bi After clicking on the Accept button we ll have to select the folder and the filename where the results will be saved Then DataManager will start the searching task looking for taxonomic information for each species in GBIF online database Downloading taxonomic information from GBIF Downloading species data from GBIF 37 722 Downloading data for Tumis sylvatica Once the task completed a CSV file with the results will be saved It can be easily opened with a worksheet like Excel or any other compatible application This file will contain the following columns e Class order family genus species those columns correspond the the taxonomic classification of each original species of the input file that has been found in GBIF 109 ModestR Software Quick start tutorial e Accepted indicates using a 1 yes or
178. ike this ModestR MapMaker New Map1 RASTER KernelSmoothingTemplate a ie x File Edit Samples View Process Tools Options Help BOSZGHRBGUMOS 2 Oc ZO B A wo Br uli FALA Map ys Zoom D lru 9 Detail Level Auto Low Med High Highest a Map Tools D Zoom Select Drag map D Show distance FreeHand Rectangle _ Add sample Edit sample Placemark 3 Show V Borders Samples V Valid V Invalid gt Coordinates Decimal Degrees Lat 17 71583 Lon 23 37979 Detail Level 1 Viewing from 66 85538 22 403 to 1 90863 13 691 Ready The option of visual filtering by presence areas can be very interesting to compare density estimated from samples and presence areas added using hulling or Environmental Occurrence options This option will use the presence areas as stencils to show density map into those areas This makes easy to compare how well those areas fit into the estimated density from samples This should be the result in the previous map 42 ModestR Software Quick start tutorial ModestR MapMaker New Map1 RASTER KernelSmoothingTemplate l gt File Edit Samples View Process Tools Options Help BOSQBSGUM OB a DaRk FALA E Gea B ee _ Detail Level p Auto Low Med High Highest Map Tools Zoom Select Drag map Show distance FreeHand Rectangle Add sample Edit sample Samples V Valid V Invalid gt Coordinat
179. ing density based hull transformation As seen in section 2 8 MapMaker is able to calculate the density based hull area from the presence data in a species distribution map and add the corresponding hull area But if you want to apply this transformation to numerous maps it may be easier to do it Pemsity based Pulling Options in a single operation from DataManager Panen FaR opi f Parameters in turn of doing it for each map in MapMaker You can just select the tree Cell width 5 v minutes 7 Dont use duplicates branch from which you want to apply it and select Mapping Apply hull Lower Normal Higher transformation to this branch Density based hull menu option or the Mapping features Apply hull transformation to this branch Kernel Density based hulling Maps to include option in the contextual menu of the tree Include only sample maps i i Include all maps node A dialog box will be shown p Create a copy of the database enca off OK The available options are e Cell width in minutes allows you to set the cell size to be used to calculate density Density will be calculated for each cell of the selected size So the smaller the cell size the more precise is the density calculation However take into account that the time to perform the calculations grows geometrically as cell size diminishes The recommended cell size for a good balance between rapidity and precision is 5 minutes e Don t use d
180. ion Selections Manager Sm Stored selections gay Almeria a sadsadsa Select in the tree the node below which you want to store the new selection Discard Selection settings Name Select childs of this node when selecting it selection data Show as preview when browsing a Import E Export E Clear This selection contains 2 polygons Preview data Load subelements for preview E Import Export gf Clear No preview in this selection Adding new selection Now we will briefly explain how to manage predefined selections using the menu Options Manage predefined selections This will show the selections manager window that will be empty unless you already stored some selections predefined selections provided with ModestR are not shown here because they cannot be modified neither managed by the user 125 ModestR Software Selections Manager Lr Heardi H sat Quick start tutorial Q Stored selections Selection settings Name Category Root Description Selection data Export amp y No data in this selection Preview data A c gf No preview in this selection Selections have to be organized in a tree So the first step can be adding a selection node To do that just click on the Add Selection button The right panel will change its color to signal that you are in edit mode Let s suppose you want to add a node named Countries unde
181. ion commonly contains several polygons For example if you add a predefined selection of Spain this selection will include several polygons corresponding to all Spanish territories including islands When searching for species MRFinder will treat this selection as a single one even if it is composed of several polygons That is distinction between selections is done by the user and not by the fact that a selection may contain several areas To see which logical selections are currently add to a map and manage them delete rename or merge them you can use the selections editor see section 4 10 4 4 Importing selections Besides manually selecting searching areas MRFinder provides the possibility of importing existing data as selections For example you can import a shapefile or a KML file with one or more administrative areas To do that use File Import selection option from main menu When importing shapefiles a dialog box will be shown where you can enter a simplification tolerance We strongly recommend to use the default value as it avoids some problems with shapefiles such as autointersections and it involves a minimal precision loss If you are familiar with shapefile format you can also add importation criteria to filter which data will be imported To do that use the See hide fieldlist button to see the list of fields contained in the shapefile Then you can select a field to see the values it takes and add criteria that will be
182. ionally calculate the contribution of each variable to the presence of the species by clicking on the Analyze button This is just optional You can skip this step and click on Continue button to go to next step 51 ModestR Software Quick start tutorial Even if the resulting environmental layer can be used as any other layer the aim of this option is to create an environmental layer using the variables more relevant for a specific species possibly to posteriorly use it to calculate Niche of Occurrence of this particular species Environmental layer generation Select Variables Analysis Variable analysis Order Processing Scale Options Vanable contribution analysis Selected Variables Contrib Cower Cloud cover 36 01 100 00 Chla 18 45 100 00 Bathymetry 18 44 100 00 Calcite 18 44 100 00 CDOM 7 36 100 00 Variable contribution analysis ni Extent of occurrence D Analyse Select best variables fora l x Cancel a Previous Continue gt In the case you click on the Analyse button the contribution of each variable will be shown in the list Contributions can be useful to determine which variables seems to be more influential on the species presence absence see section 2 9 for more details Once contributions calculated you can check the option Select best variables for a contribution of
183. it as NOO involves irreversible map modification it can be prudent to make a copy of the database before performing this transformation Checking this option DataManager will ask you for a destination folder and file and will do a copy of the database and apply NOO on this copy preserving the original database Once parameters set click on Continue button NOO calculation processing will start and process each one of the selected species The resulting estimated presence areas will be added to each distribution map Take into account that this process can take a long time depending on the number of maps to process and their complexity Once ended a report of the whole process will be shown on the right side of DataManager showing processed maps and not processed maps commonly because they don t comply with conditions to calculate EOO or they don t have data in the selected range 3 13 Calculating niche of occurrence with a per species environmental layer In the previous section we described how to calculate NOO using a previously generated and stored environmental layer The main drawback of this approach is that the same environmental layer will be used for all the species for which we are calculating NOO This inherently involves using the same environmental variables for all the species If we consider that the environmental variables that influence the most a species distribution can be different from one species to another a more co
184. it will be considered valid or invalid with a precision of aprox 1 seconds You can set 3 This requires installing the last software updates If you want to distinguish freshwaters you also have to install freshwater data in ModestR available in ModestR website Anyway as freshwater habitats are 17 ModestR Software Quick start tutorial different colors for valid an invalid samples to easily distinguish them in the Options Preferences option on the main menu of MapMaker Moreover only valid samples will be used when processing and extracting data from a map like presence or richness data If on the contrary you don t set a sample as dynamic it will be considered as manually validated invalidated By default it will be valid and you have to manually set it as invalid if needed Therefore we recommend you to try the dynamic validation e Select valid habitats for the samples you have to select which habitats are valid for the samples you are importing this option appears on the left tool panel when manually adding samples You can select one or more samples but it is mandatory to select at least one habitat If you selected to make the samples as habitat auto checked those habitats will be used to validate invalidate a sample If you don t selected to make the samples as dynamic this information will NOT be used as samples have to be manually validated invalidated But it will be stored and used in case you later modify a samp
185. k on a map in different sessions 73 ModestR Software Quick start tutorial 2 20 Setting the default ModestR database and other preferences in MapMaker In the previous subsections regarding MapMaker we frequently mentioned ModestR databases MapMaker will usually have one ModestR database configured by default and that will be the database it will use when you select open or save a map in a database This database can be selected in the File Select Database menu item or in the dialog box that is shown selecting Options Preferences menu In this dialog box you can also set the colors for each element of the map each kind of selection each type of sample dynamically manually validated and valid invalid and transparency percentages for some elements like visual templates samples or selections Also the elements that will be visible by default in the map If for example you don t work with freshwater ecosystems you can unselected them to avoid MapMaker having to load and paint them thus making it works faster You also have an option to select the data folder where MapMaker will search world map data It is important that you don t modify this parameter unless you have moved map data to a different folder than the default one proposed in the installation process g Preferences Folders and other options Data folders ModestR map data folder Waming don t modily this parameler unless you are aware of the consequences C ModestRProy
186. k start tutorial ModestR MapMaker New Map1 RASTER C ModestRProject Species 1_Bathymetry Clipped ASC ee fe File Edit Samples View Process Tools Options Help BOJAHH HAORA BO BPBIIJ A Br k FALAN Ma a RET TS Auto Low Med High Highest Map Tools Zoom Select Drag map Show distance FreeHand Rectangle Add sample Edit sample V Valid V Invalid gt Coordinates Decimal Degrees 4 Detail Level 0 Viewing from 74 40404 17 90183 to 31 97234 46 38389 Ready The same process can be done to cut off and export raster data for visual templates We ll just have to add the wanted visual templates to the map see 2 14 and use the File Export Environmental data For each visual template To cut off a raster following an arbitrary pattern you can also use MRFinder as explained in section 4 12 3 To easily cut off rasters using as patterns the corresponding EOO of a set of species you can use DataManager as explained in section 6 19 2 9 5 Adding a Kernel density map as raster In section 2 8 3 we described how to calculate a hull using a kernel density algorithm But you can also show a kernel density map just for informative and presentation purposes Even if MapMaker will allow you to use it in maps that contain areas and samples this option only takes into account samples It calculates density gradients from the samples and shows them as a density map T
187. ker window You can change it by loading another one NO gt l o t Zoom B Current Env layer ejemplo manual ModestR Software Quick start tutorial Once selected the environmental layer to be used to calculate NOO you can go to menu Mapping Niche of occurrence and select between e Density map this option calculates and show the density map corresponding to environmental conditions for the species In this map you can see which areas are near that have high density to the environmental conditions where the species is already present using the selected environmental layer as reference and those which are far that have low density This option does not modify the map it s just for visualization purposes e Distribution map this option calculates the NOO for the species using the selected environmental layer as reference In terms of calculations it s very similar to the density map The difference is that in turn of showing a density map the areas that have a density above the cutoff value described before in this section are added to the map as presence areas So the species map is modified as NOO is added In both cases the displayed dialogs are quite the same As you can see the main difference is just in the display options For density map you can set how density map will be show Visual filtering options while for distribution map you can select to show a simulation or to add NOO t
188. lates the same way you can do it in MapMaker see 2 9 and 2 142 16 1 5 4 Importing a file of visual template names DER CONSTRUCTION 5 5 Exporting map image To export the current map as an image in JPG or BMP format go to File Export Current map view as image A dialog box will appear with several tabs In the Grid and scale tab you can set if you want to see a grid scale in the exported image every degress minutes you want this grid scale etc In the Dimensions and format tab you can directly modify the coordinates of the portion of the map that will be exported By default the same view currently displayed in MapMaker will be exported You can also select the size of the exported image By default MapMaker sets the image size as slightly bigger than your screen resolution This is usually a 138 ModestR Software Quick start tutorial good resolution to use the image in another document presentation etc But if you want a more precise image that can be zoomed correctly you can increase the image size Finally you can select between JPG or BMP format In the Legend tab you can add a legend to the map where each map item dataset name will be shown with the corresponding color You can select the position of the legend and the font The Color to show combo box allows you to select which color will be shown in the legend for each map item If the map items you adiled to the world map contain samples you should c
189. ld If you use environmental variables that Keme s density contain data for a single country the estimation environmental occurrence will be calculated for this country e EOO Extent of occurrence environmental occurrence will be calculated only for the area contained in GS Preview the EOO of the species This EOO willbe calculated according to the settings you x Cancel Continue gt have to enter in this same step Regarding the way the EOO will be estimated you can select any of the methods already available to calculate a hull on a distribution map see section 2 8 before If EOO hull cannot be calculated using the selected option you cannot continue to the next step This can happens if for example there are too few samples in a map see section 2 8 before for more details about each hull method Even if you select Full extent range you have to select a EOO mode because those settings will also be used for variable contribution analysis Next step is selecting the environmental variables that will be used to calculate Environmental Occurrence Of course in the ideal case you should select the variables that affect the most the species distribution Anyway you can always select most variables and ModestR will help you to choose the best ones in the next steps 44 ModestR Software Next step allows you to optionally calculate Variance Inflation Factor VIF A VIF value higher than 30 is commo
190. le Edit Samples View Layers Mapping ModestR tools Options Help ADMIN Y PRUEBAS m Kernel density map options Environmental Kemel density map Information Total coverage 100 00 8101 BIOJ BI014 BIOTS PP Parameters Lower Normal WJ Smoothing factor X 3 70 Allow a tolerance of 1 Visual filtering Range By habitat Full layer Show over map E00 7 Show only significant densities ee Kae y PP BI 19 BION BIO3 BIOI BIC Detail Level 2 Viewing from 57 58868 29778284 to 8 165901 1 228151 Ready Bf Current Env layer Terrestrial layer i For Density map option the data shown in the map correspond to the areas that would be part of the NOO of the species with the color corresponding to the density of each area Areas with higher density are those near from the environmental conditions of the species in the environmental layer as shown in the Density data map shown on the right panel 58 ModestR Software Quick start tutorial For Distribution map if you selected Hull simulation the areas highlighted in the map correspond to the areas that would be part of the NOO of the species If you selected Add Area NOO will be added to the map as presence areas File Edit Samples View Layers Mapping ModestR tools Options p ADMIN Y PRUEBAS BOSQ iBGu OB anoaz 8 9 uc Bw i FALA MUPA Map E 2 Detail Level Auto Low Med H
191. le at the left tool panel You also have contextual menus that will appear when you click with the right button of the mouse on the map Also quite all menus buttons and other elements have a tooltip that briefly explains their usage and that will be shown when you place the mouse over an element CD ModestR MRFinder DB Elasmobranchii DB i i Da s Help aa Map _ Detail Level l EE Emerging tooltip shown when 6 Map Tools S placing the mouse on an element Drag map Zoom Select Detail Level 0 Viewing from 1809 009 100 0351 to 180 0009 100 0351 Ready 4 1 Default settings in MRFinder MRFinder mandatorily has to work using the data of a ModestR database A database can be selected using the File Open database menu option MRFinder will automatically use the last used database when running it again If no database is selected or the default database is not found a dialog box will be shown when you try to work with data allowing you to select a database to be used during this session Warming EI There is not a valid database selected in Preferences Do you want to A select mow a database Los Ls Using the Options Preferences menu a dialog box will be shown where several options can be set such as the colors of the elements and their default visibility status delimiter and decimal separator for CSV exportation format can also be set here 111 ModestR Software Quick s
192. le is missing that is if the variable have a null value in this location in this case an area sample will be 47 ModestR Software Quick start tutorial cleaned considered invalid as soon as there is no value for the variable for this area sample no matter the values for the other variables o Don t take into account this variable when its value is missing in this case if there is no value for the variable for this area sample this variable will be just not considered to make a decision ModestR will check the values took by the other variables to decide about the validity of the area sample Take into account that those options are per variable That is you can set different options for each variable A missing value for a variable can lead to immediately invalidate an area sample while for another variable it will not be took into account You should decide in a per variable basis the most adequate option e Apply to all buttons either in the tabbed box that displays the options for the currently selected validation mode or in the missing value options you can see a button Apply to All This button can be used to replicate the corresponding settings for the current variable to all variables in an easy way Finally on the right bottom side of the dialog box you can see a tabbed box with main settings While settings described above are for each variable those main settings have global effects They are e Allowed invalid varia
193. le to make it as habitat auto checked 2 4 Modifying samples in a map Once samples added to a MapMaker map you may want to modify them MapMaker allows the following possibilities e Move a sample sometimes you can want to relocate a sample to a near location For example to relocate a sample incorrectly placed in the sea for a few meters for a terrestrial species To do that you can use the Edit sample tool from the left tool panel With this tool selected go to the map click on the wanted sample and drag it to the new position then drop it ModestR MapMaker FILE C ModestRProject BD Carcharhinus leucas IPMMAC Carcharhiniformes Carcharhinidae Carcharhinus File Edit Samples View Process Tools Options Help AG8G8GW 9 4 001 2068 9 e Map A van D A _ Detail Level 5 Auto Low Med High Highest Pod Map Tools Zoom Select Drag map Show distance Lat 28 7124 Lon 84 49329 FreeHand Rectangle Select the sample Add sample Edit sample then drag it to the new position Placemark P Show e Delete one single sample To do that you can use the Edit sample tool from the left tool panel With this tool selected go to the map click on the wanted sample and press the Delete key You can also click on the sample with the right mouse button and select the Delete sample option still being reviewed and updated in some areas checking feature may only distinguishes between land and
194. led ModestR software Updates will try to install themselves by default in the default ModestR installation path C ModestR If you have modified this path when installing ModestR for the first time you may have to set the correct path to install updates 192
195. ll determine which ones of the previously selected variables influence the most the species distribution and therefore will be used to generate the environmental layer that will be used to calculate NOO This feature has already been explained in 2 9 for MapMaker where this analysis can be done interactively for a species It can be a good idea to do it first in MapMaker for a single species to better understand how it works It is also cited in 3 11 In a similar way to the Layer extent option described in a previous step variable contribution can be calculated for the full extent for a visual template for the occupied river basins or for the EOO of the species Take into account that extent used to calculate variable contribution could be different from the extent selected for the environmental layer ModestR does not establish any limitation in this sense so the convenience of using one or another option is left to the user You may set the value of the field Select best variables for a contribution of XX for DataManager to select automatically the variables with the higher contribution to reach the indicated Click on Continue button to go to next step Environmental layer generation Select Variables Analysis Variable analysis Frocessing Niche parameters EQOO options Environmental Keme l density parameters E00 calculation Lower Normal Higher Convex hull Allow a i F tolerance of 1 gt z Parameters Al
196. llow you to localize all the imported areas you can use the encircle presence areas feature see subsection 2 14 as shown in this figure where some areas are hardly visible in a full world map view but easily located thanks to the rectangles that encircle them and visualized zooming in a Bama Leet Y jara MLE bo LE Fl LL p Tah 7 4 Importing from Shapefiles You can import areas or samples from files in ESRI Shapefile SHP format which is a widely used format in GIS software Currently only shapefiles containing polygons or points can be imported that is Polygon PolygonZ PointZ or Point type shapefiles Other shapefiles containing types like Polyline are not supported by now Polygons will be converted to areas whereas points will be converted to samples A dialog box will be shown where you can see data contents from the shapefile to be imported 177 ModestR Software Quick start tutorial See hide fieldlist Import ShapeFile Options ontained in the file _ Import file C ModestRProject BD Anoplogaster cornuta shp Operators Values Sample 0 A gt Sample 2 Simplification tolerance in minutes 0 20 J Merge imported pe Sample 3 AND Sample 4 IOR Sample 5 NOT Sample 6 IN Sample 7 Sample 8 Sample 9 Sample 10 7 If you are familiar with shapefile format you can also add importation criteria to filter which data will be impor
197. llows to select which presence data from the maps will be used for hull calculation The possibilities are o Include only samples in this case presence areas if any are excluded This is the only enabled option for alpha shape o Include only areas in this case samples if any are excluded o Including all presence data both samples and presence areas Options that involve using presence areas to calculate hull require having all maps processed which is not necessary if you choose to only use samples Depending on the selected hull mode some options can be disabled For example you cannot include areas when applying alpha shape e Maps to include you can select to include all maps only sample maps maps that only contain samples but no presence areas or only area maps maps that only contain presence areas but no samples Some of those options will be automatically disabled 84 ModestR Software Quick start tutorial according to the selected hull calculation mode For example area maps cannot be included when using alpha shape transformation e Create a copy of the database as hull transformation involves irreversible map modification it can be prudent to make a copy of the database before performing this transformation Checking this option DataManager will ask you for a destination folder and file and will do this backup copy before modifying maps Hull area that will be added to the map will use as valid habitats the same
198. ltered results 4 8 3 Categories filter page The Categories filter page allows to load a categories oo Example of categories file Aonyx congicus Least Concern Arctictis binturong Vulnerable and the second column contains a category assigned Arctocephalus pusillus Other file and use it as filter A categories filter consists of a CSV file where the first column contains species to each species Arctogalidia trivirgata Least Concern Atelocynus microtis Near Threatened To load a categories file first select if the file has Atilax paludinosus Least Concern headers that have to be skipped and the field Bassaricyon alleni Least Concern separator used in the CSV file Then click on the Load Bassaricyon beddardi Least Concern file button and select the file Bassaricyon gabbii Least Concern Bassaricyon lasius Data Deficient The file will be loaded and the categories will be shown on the Filter by categories listbox To apply a filter by categories first check the Enable filter by category checkbox then select which categories you want to include checking them on the Filter by categories listbox The species that are included in the selected categories will appear in the right list Soecies in selected categories Take into account that the species listed in this list are the ones that are in the imported file independently of the species that are found in the current search When enabling this filter and selecting categori
199. ly branches without maps Show only species without maps S A Sharks o Search Carcharhiniformes Carcharhinidae B Cc E Hemigaleidae E Leptochariidae tis Level W Any Order Family Genus Species WW 4 Proscyliiidae aom a tt tel Results Taxonomy tree _ Search and reports tab panel Hexanchiformes Lamniformes en Orectolobiformes Pristiophoriformes E Squaliformes Results 0 elements found Moreover when some list is reported on the right panel for example a list of exported note exported maps you can almost allways copy the contents of those lists to the clipboard by 75 ModestR Software Quick start tutorial clicking on them with the right button and selecting the Copy to clipboard option that will appear on a contextual menu 3 2 Default settings in DataManager You can set some default settings of DataManager in the Options Preferences menu option Some filter defaults CSV format options and other ones can be configured You can also modify the data folder where DataManager will search for the reference world map but unless you have modified the default installation options it is unnecessary and can provoke DataManager not to run correctly g Preferences Fiter defaults CSV Exportation options E Show only branches with maps Decimal separator Field separator Show ony species with maps Data folders Reference map
200. main exportation options of DataManager are e Taxonomy data exportation you can export all or part of the taxonomy data to a CSV file as explained in section 6 12 e Maps exportation you can export species distribution maps to standalone map files or to presence data in different formats pseudosamples valid samples ASC rasters optionally including environmental variables You can also export maps as JPEG images optionally including a kernel density graph to a Darwin Core style file or generate a summary report e Metrics and other data exportation You can also export metrics data and environmental variables DataManager uses rasterized maps data to calculate presence richness and other metrics rarity patch index with a specific resolution Of course this option requires maps to be previously processed as seen in section 3 6 Complementary to those data you can export data coming from environmental variables data files Options and generated output are explained in section 6 17 You can export maps data to Maxent or to RWizard applications Those options are explained in sections 6 13 and next ones You can also export environmental data or any other raster data cut off to species EOO for any rank of species This option is explained in section 6 19 You can also exports latitudinal gradients for several metrics Options and generated output are explained in 6 20 20 RWizard applications are plug in applications
201. mental layer 6660 98 3 13 Calculating niche of occurrence with a per species environmental layer 100 3 14 Batch map areas or samples modification cccccceeseccceessececeesececeeeeceeeeeeceeseneeeeees 104 3 15 Searching aemagMeo data cccccssssssesssssrsercsssrcncsvsrcnversreareseusencusarencavsrenvensrsens 105 3 16 Forcing map updating to current map version ccccsseccceseceeeseeeeeececeueceeeeeceseeeees 106 3 17 Extracting taxonomy data from ITIS database cccccccccceseccceeeeceeececeeeceeeneeeeeneeees 107 4 First Steps in MRFinder ccccccsceccccccscsccccccsceccccccscsccccccscncescececscescccecncesess 111 4 1 Default settings IN MRFINdE eessen a E 111 4 2 Moving across the world Map esssesssseeessreessreresrreresrresssreresrrerssrereserrrsseeressrersseerese 112 4 3 Adding selections to search for species ccccccssseccceesececceesececeesececeeaeceeesenecessuneess 112 4 4 Impor nge selection seier e ES 113 4 5 Using predefined selections sssseusssseresrrersrrrrsrreresrresssreresrrerssrereserersseereserereseerese 113 ModestR Software Quick start tutorial 4 5 1 Querying for selections in a point of the MAP ccceseccccseeceeeeseceeeeseceteeeeess 115 4 6 SC OO CONS ee E EA 115 4 7 PPO AN Sl O e coy essence seueeeesean ares ees coueuasn ere esunnenseectuaceun 117 4 8 Be lf a ctor el ag a 0 ee E ee eee ne eee 118 4 8 1 Taxonom
202. mes of the selected species to the clipboard e Toa CSV flat file this option has the same operation that the corresponding option of DataManager You can find more details in section 6 12 e Toa CSV structured file this option has the same operation that the corresponding option of DataManager You can find more details in section 6 12 8 7 Exporting maps You can export maps data of the selected species using the Export Maps in the exportation tools of the search result window see section 4 8 You will see three options to export data e To standalone map files this option has the same operation that the corresponding option of DataManager You can find more details in section 6 13 e Toa CSV file s this option has the same operation that the corresponding option of DataManager You can find more details in section 6 14 e Tosummary data this option has the same operation that the corresponding option of DataManager You can find more details in section 6 23 8 8 Exporting statistical data You can export statistical data of the selected species using the Export stats in the exportation tools of the search result window see section 4 8 You will see two options to export data e ToaCSV structured file this option will generate a CSV file with the following columns o Subclass Order Family Genus and Species those columns will be shown in a structured way similar to the used when exporting taxonomy to a CSV structured file in Dat
203. minutes by cell SM ie Metrics _ pf Richness Select metrics and variables to output CSV matrix longitude X latitude CS list in columns Select richness count method Count if species is present in one cell O Count if species occupies at least 25 Excel worksheet 2007 or higher ESRI ASCII Raster matrix WV Rarity index _ 4 AO index _ pf EQO index _ W Patch index dw 4 Latitudinal range index wd 4 Habitat areas oe Environmental Variables 1x1 minute blocks in cell Set exportation zone boundaries aol gal Marine a gall Terrestrial 5 L Nuevo Cell coordinates Longitude Latitude H 53 Center gt Center Right 3 Top l4 E 6 G Left Bottom W Clip data to selected region CSV Exportation options Field separator Decimal separator 7 i F Select habitats to include W Sea W Land F Al freshwater W Lentic habitats W Small Channels V Small rivers W Large Channels W Large rivers W Wetlands Small Ditches W Lange Ditches Reservoirs V Small Drains W Large Drains An important aspect that has to be pointed out is that while in DataManager only rectangular areas can be set to calculate and export metrics in MRFinder irregular areas can be used regarding the selected area in the map The process is this e f you selected a rectangular area to analyze in the MRFinder map the boundaries of this area adju
204. mplates Intersect using visual template the result will be File Edit Samples View Layers Mapping ModestRtools Options Help ADMIN Y PRUEBAS BO8 Bed OC a 0o 26 8 9 Sid ui FLL en z F Samples 7 Valid V Invalid Freshwater habitats Coordinates Decimal Degrees Detail Level 1 Viewing from 24 58081 6 040792 to 58 18497 39 95609 Ready 2 14 2 Automatically adding river basins visual templates When working with sample data from terrestrial species it can be interesting to see in the map in which river basins the species is present As pointed out above ModestR provides a collection of predefined visual templates corresponding to administrative areas for all over the world and more recently it also includes visual templates corresponding to river basins They can be found under the node World basins in the tree of visual templates River basins are grouped by continent and hierarchically organized in 6 levels from main large basins to smaller basins 62 ModestR Software Quick start tutorial You can manually add visual templates of those basins just as any other template going to Layers Visual templates Add visual templates and selecting the wanted templates either in the left tree of in the right active map a Add a stored selection gt 5 a g ModestR preselections 5 World Basins Q Basins of Africa lt lt 4 fi Basins of Asia Basins of Australasia 4 fi Basins of Europ
205. mples located in points that comply with the validation rule colors are eligible by the user File Edit Samples View Layers Mapping ModestRtools Options Help BO8 8 4 93 a oo 26 9 9 gt Bis MAUMEE Map 2 Map Tools FreeHand O Tet A Placemark If you have selected to apply validation to areas the zones of the area where the validation rule is not true will be deleted Areas validation can require a certain amount of time depending on the complexity of the area Fim Edit Sampin view Too Opiom Hale BS Hkh Fla oe 286 aii Original area of presence in the map 25 ModestR Software Quick start tutorial File Edi Sarge Vie Teede cat ara Hap Jagd Deh dp a2 oo fe pease If we apply the validation the zones 7 of the presence area where the ial _ ee Bier Fall T zi Dii Love validation rule is false are erased from the initial presence area Aia Low Hed Hgh Tanie Dees map z onmi it Fma en Once a data cleaning task ended and only if this cleaning involved samples MapMaker will allow you to save a report of the cleaning operations done in CSV format containing a list of the cleaned samples and details about the variable ranges they didn t comply with As said before this report will only be generated when cleaning samples and will not include details regarding areas cleaning The reason for this is that even a relatively small region will easily contains thousands of 1
206. mported file A dialog bow will be shown to select the importation settings A brief explanation of each option of this dialog box will be shown in an emerging tooltip if you place the mouse on it Set importation options for samples CSV files CSV import options Merging method First row contains headers Select coord columns order in CSV file Overwrite existing maps Decimal separator ag Longitude Latitude Add data to existing maps Latitude gitude Seay eili Field separator 9 z Skip existing maps F Samples conversion Sample point size 100 W Skip samples in 0 0 coordinates J Make the sample habitat auto checked F Skip samples with same longitude and latitude coordinates Consider and remove duplicated samples if they are equal until th decimal Select valid habitats for the species Land All freshwaters _ X Cancel Lentic habitats Small Channels Small Ditches Wetlands C Small rivers C Large Channels Large Ditches C Reservoirs Large rivers Accept In the dialog box you can select the correct options for the format of the CSV file to import Most of them are the same than when importing GBIF data Therefore you can refer to section 6 7 for an explanation of those options The options that are specific to CSV importations are e The order of the coordinates in the CSV file Longitude Latitude or vice versa e lf the first row contains headers in that case first r
207. n 2 2 Making a range distribution map in MapMaker You can make two main kinds of distribution maps in MapMaker range maps and sample also called occurrence maps To make a range map you simply have to draw on the map a zone or area occupied by a species typically using the Freehand tool Once a zone selected on the map the Fill Selection and the Valid habitats groupboxes will be displayed at the left tool panel Then select which habitat of this zone is occupied by a species using the checkboxes of the Valid habitats groupbox Finally use the Fill button on the Fill Selection groupbox or alternatively use the wanted option of the contextual menu that you can display clicking with the right button on the map 12 ModestR Software Quick start tutorial File Edit Samples View Process Tools Options Help Bese Beh OR 4 5 20 8 we Valid habitats checkboxes and filling tools on the tool panel and on the context menu 000 sag 8 Pee BE Zoom Fill Sea Fill Land l Fill all freshwater habitats objects ample 5 Fill small rivers Selected samples Delete selected objects Fill lentic habitats Fill wetlands Fill reservoirs Fill small ditches Fill large ditches Fill small channels Fill large channels Fill small drains Fill large drains el 0 Viewing from 70 79903 50 44567 to 73 05214 59 33085 Ready You can see that only the corresponding
208. n all the world independently from the range selected for the analysis This metric is calculated globally for all the latitudinal band without taking into account longitudinal cells e SD AOO standard deviation of the AOO of all species present in the latitudinal band taking into account the AOO that each species occupies in all the world independently from the range selected for the analysis This metric is calculated globally for all the latitudinal band without taking into account longitudinal cells e Mean EOO mean of the EOO of all species present in the latitudinal band taking into account the EOO that each species occupies in all the world independently from the range selected for the analysis This metric is calculated globally for all the latitudinal band without taking into account longitudinal cells e SD EOO standard deviation of the EOO of all species present in the latitudinal band taking into account the EOO that each species occupies in all the world independently from the range selected for the analysis This metric is calculated globally for all the latitudinal band without taking into account longitudinal cells e Mean Latitudinal Range mean of the latitudinal range occupied by all species present in the latitudinal band taking into account the area that each species occupies in all the world independently from the range selected for the analysis This metric is calculated globally for all the latitudinal band
209. nce area for the species The maximum value of this column will be obviously 1 if a species takes up all the areas with valid habitats for it into the bounds of the selected area but take into account that this column is calculated with a precision of 1 x1 188 ModestR Software Quick start tutorial o Mean Real Area Reference Area this column summarizes the mean of the real area reference area ratio explained before for all species of each higher taxonomic level from genus to subclass o SD Real Area Reference Area this column summarizes the standard deviation of the real area reference area ratio explained before for all species of each higher taxonomic level from genus to subclass If there is only one species in a higher level for example in a genus this value will be obviously empty e ToaCSV flat file this option will generate a CSV file where there are no summarize rows for higher taxonomic levels than species so only some of the columns described above for the CSV structured file option will be exported They are Subclass Order Family Genus Species Rare Species AOO km2 Maximum Latitude Minimum Latitude Maximum Longitude Minimum Longitude Real Area Reference Area 8 9 Exporting region coordinates You can export the coordinates of the region you selected in the map to do a search in MRFinder using the Export region coords in the exportation tools of the search result window see section 4 8 You will see
210. nd Not found Not found Not found No species name neither synonyms for this species have been found on GBIF dat No species name neither synonyms for this species have been found on GBIF datz No species name neither synonyms for this species have been found on GBIF dat 0 Erigeron frigidus 0 Santolina melidensis 0 Odontites asturicus 0 Odontites foliosus 0 Odontites granatensis 0 Odontites kaliformis 0 Linaria aguillonensis 0 Linaria arenaria 0 Linaria gharbensis 0 Linaria nigricans 0 Carduus bourgeaui 0 Callitriche cribosa 0 Chaenorhinum rodriguezii As the first columns of this CSV file contain the taxonomic levels from class to species required by a ModestR database this kind of CSV file can be imported in DataManager to add taxonomic data to a database as explained in section 3 3 But is important to point out that is necessary to review it before and particularly to delete the species for which no taxonomic data have been found in GBIF 110 ModestR Software Quick start tutorial 4 First steps in MRFinder MRFinder is an easy to use software application to make the most of the data stored in ModestR databases created with DataManager MRFinder allows for finding which species are present in any area of the world and to generate and export several data reports and statistics about those species The MRFinder user interface is quite simple and very similar to MapMaker as the most usual tools are always visib
211. nd area data have been mentioned in 4 12 3 and 4 12 4 But MRFinder also has exportation features to export selections e Export map as image in File Export Current map view as image you can export the current map view you have in the screen to an image in JPEG or BMP format Options such as adding a grid scale or quality adjust will be shown e Export current selections to KML or Shapefile File Export Current selections To KML or To Shapefile you can export current selections to KML or Shapefile formats e File Export Current selections To ASC raster generates a raster in ASC format with the selected precision where the cells where there is a selection have a value not null usually 1 131 ModestR Software Quick start tutorial 5 First steps in MRMapping MRMapping is an easy to use software application to build maps with data coming from several species distributions Those data will typically come from databases created with DataManager MRMapping allows adding any number of species distribution data to a map optionally grouping them by any rank lass order family It also can calculate overlappings between distributions and occupied areas The MRMapping user interface is quite simple and very similar to MapMaker as the most usual tools are always visible at the left tool panel You also have contextual menus that will appear when you click with the right button of the mouse on the map Moreover quite all menus butto
212. new area will be inferred from the already existing presence data samples and areas However you can undo changes using Edit Undo or modify this new area as any other area using Unfill feature see section 2 2 If you want to display a density map just for presentation or analysis purposes you can also use the option to add a kernel density map to the data as explained in section 2 9 5 2 9 Working with rasters To make easier visually analyzing relationships between species distributions and environmental variables or just to have appealing images to use in some documents presentations etc you can add raster data to MapMaker maps This is only for visual purposes and it doesn t affect distribution maps Raster data will appear when exporting a MapMaker map to an image file see section 7 6 to export images from MapMaker There are two main ways to add raster data using environmental data that you already have integrated in ModestR o directly loading raster data from an ESRI ASC file We explain both of them in the next subsections It must be pointed out that currently ModestR only supports raster data with a maximal resolution of 1 Moreover as using a raster of a resolution 1 for all the world is a heavy duty we recommend to ordinarily use rasters of a resolution of 5 which may be enough precise for mere visualizing purposes 34 ModestR Software Quick start tutorial 2 9 1 Adding environmental data as raster En
213. ng Maxent to the currently opened ModestR map in MapMaker using the File Import ESRI ASC probability distribution data menu option This importation option allows producing range maps from probability distribution data You should have previously generated one ESRI ASC file that will contain a probability matrix where each element of the raster matrix represents the probability of presence for a species in a cell of a specified size usually 5 x5 Only probability matrixes with values between O and 1 are supported When using this importation option you first have to select the ESRI ASC file Then a dialog box will allow you to set several settings e Default probability cutoff the minimal probability under which presence data will not be imported If for example you select 0 75 only cells with a probability gt 0 75 will be imported to the map e Use minimal probability at presence this option is only available if you are importing data to a map where samples already exist In this case this option allows you to use as probability cutoff the lowest probability value where a sample exists in your map For example you can download samples to MapMaker for the species X then import a probability distribution data file to the map and MapMaker will automatically find the probability values in the points where there are samples in your current map and use the minimum of these values as probability cutoff to import probability data The
214. ng the mport Import presence data From another ModestR database menu option In this case the expected format of the origin database is the original format of the Modest R database No modifications have to be done Once selected the origin database to import maps from a dialog box as seen in the figure will allow setting the importation options First two options affect taxonomic data e Import only maps for species already existing in the current database if selected no new taxa will be added Therefore only maps _ corresponding to class order family genus species that already exist in the currently opened database could be imported If a map for the species X exists in the origin database but the species X doesn t exist in the currently opened database the map will not be imported e Import maps from all species of the origin database if selected all maps of the origin database could be imported Consequently new taxonomies will be added to currently opened database if needed So if a map for the species X exists in the origin database but the species X doesn t exist in the currently opened database species X will be added to taxonomic data in the target database including lower levels if necessary like genus families etc and the map will be imported Take into account that all the superior levels are compared to determine if an imported species corresponds to an existing species Even if they have the same name if they differ
215. nloaded using some dispersal capacity variables By default mean distance variable is selected to perform data cleaning Before using other variables it is recommended to see section 2 6 for more details about dispersal capacity cleaning If you select to look for synonyms MapMaker will first check if the species you entered is considered as a synonym of another one according to GBIF and ask you if you want to use it to search samples in GBIF 16 ModestR Software Quick start tutorial Information j Di According to GBIF information species name Iurus alatus is a aL synonym of species Tsurus paucus with a confidence of 100 Click on Yes to continue downloading data using the main species name provided by GBIF surus paucus Click on No to continue downloading data using the species name you provided Isurus alatus Click on Cancel to cancel downloading task No Cancelar When importing samples either from a CSV file or from GBIF database or when manually adding a sample you will have to select how MapMaker will treat those samples Several options will be displayed in a dialog box when importing from GBIF or CSV files when adding manually a sample only some options will be available and they will be displayed in the left tool panel Set importation options for samples data Samples conversion Sample point size 100 W Skip samples in 0 0 coordinates a Skip samples with same longitud
216. nly considered an indicator of collinearity among the variables Thus you have the change choice of removing those variables significantly related and therefore that are redundant But this is an optional step If you just want to include all variables you can simply continue Take into account that if two variables are very correlated the way that one of them if a linear function of the other one VIF cannot be calculated Involved variables will be marked to allow you to remove one of them if you want As you could see when calculating VIF you can also see the coverage percent of each environmental variable into the EOO That is for how much area of the estimated EOO there are values for each environmental variable This can also allow you to remove inadequate variables that have a very low coverage in the species EOO For example a Niche of Occurrence calculation Hull Select Variables Correlations Variable analysis Set ranges Processing Correlation and variable redundancy analysis Quick start tutorial Environmental Occurrence calculation Select Venables Conelatons Variable analysis Set ranges P Hul Select the variables to calculate the Environmental Occurrence sale 3 a Environmental Variables Marine Bathymetry Calcite fy cpom F Chia mA Cloud cover Temperature Terrestrial Altitude F Altitude 6 x6 AltitudeJ Aspect Blo1 F B010 F B011
217. ns Reservoirs Large rivers S Accept 147 ModestR Software Quick start tutorial 6 10 Importing data from distribution models You can import distribution data from distribution models as ESRI ASC raster matrices of probability like the obtained using Maxent2 to the currently opened ModestR database using the Import Import presence data From ESRI ASC probability distribution data menu option A similar option but limiting the species to be imported to a specific branch of the taxonomic tree can be found in the contextual menu clicking with left mouse button on the desired element of the tree selecting the option Import presence data for this branch From ESRI ASC probability files This importation option allows to produce range maps from probability distribution data You should have previously generated one or more ESRI ASC distribution files that will contain a probability matrix where each element of the matrix represents the probability of presence for a species in a cell of a specified size usually 5 x5 Those are the files that DataManager can import to generate new maps or to add data to existing maps Only filenames which name matches a species already existing in the database will be imported DataManager will be aware of the filename format used by some software like Maxent which uses a low dash between genus and species so you don t need to modify it That is Ateleopus_indicus asc will be recognized by D
218. ns 163 6 20 Exporting latitudinal gradients cccccccessecccceseccccesscccceesececeesecesseseceeteneceetenseeeeas 164 6 21 Exporting species data to Maxent ccccccecccssccceecccseccenestenceteuseeeeeseeetenseeeuseeeeseens 167 6 22 Exporting species data to RWizard applications ccccccccesecccesseceeececeeseeeneseeeneeees 168 6 23 Exporting sudaa CA ln cose csercctessrsercssarencarsrenvanersens 168 6 24 Exporting JNES BMP imiges SMM cccccccsssnssetresccsssseeccecsseesseseanseseeeeeauaaseoooas 169 6 25 Exporting JPEG BMP density map iMageS ccccccccccceesesseeessseeeeeeeeecessseeeeeeeeeeaeees 171 6 26 Managing environmental Variables cccccccssseccccesscceeessececeeseceseeeeceeeeeeceeseeseeetes 172 7 MapMaker import export files format cccccsccssccssccsscssccesscescssccessseseesces 175 7 1 Import sample data from a CSV file sssoesenesseenseseesesrrrssrreresrrrrssreresrrrssreresrreesseerese 175 7 2 Importing samples from GBIF online database sssessssesersrerrserresrrrsrrreerresrrreens 175 7 3 Importing areas from ESRI ASCII probability distribution models sseseeeseserensss 176 7 4 Importing from ShapefileS esssssssensesseresrresssrrresrreresrresssreressrenssreresererssreresereesseerene 177 7 5 ADOPTS TO HI EOS reaS 179 7 6 Export Map view tO an image FIl cccccessccccessececeesececceeecceceesececeeeceeseeeceeeeeeeeeten 180 7 7 Exp
219. ns and other elements have a tooltip that briefly explains their usage and that will be shown when you place the mouse over an element We recommend you to see the section 2 and particularly the 2 1 and the 2 16 for an introduction about moving on the world map and using some map tools 5 1 Creating a map in MRMapping MRMapping will usuallly work using the data of a ModestR database A database can be selected using the File Select database menu option MRMapping will automatically use the last used database when running it again Once a database selected you can add species distribution data from this database to the map going to File Add Maps from ModestR database MRMapping will display the taxonomy tree of the database You can directly expand nodes with the mouse Only select a species with a map that is will distribution data will be shown in the tree To help you finding a map you can also use the search box than can be displayed using the magnifying glass button on the bottom left corner In the search box you can write some part of the species you are looking for and coinciding names will be shown in the Results list This feature is the same than the explained in 2 19 for MapMaker To select the species you want to add to the world map just check the corresponding checkbox As you could see you can directly add all the species of a rank e g a whole family by checking it on the tree so you don t have to check species by spe
220. nsity matrix will be The greater it is the more the density will soread out far around presence areas Default factor is x1 e Allow a tolerance of X Apply a of tolerance on the potential areas of presence to consider them as valid with regard to the range between min and max values for each environmental variable involved in the currently selected environmental layer in the presence data of the species e Range determines the range or maximal area for which NOO will be calculated Options are o Full layer to calculate NOO for all the area covered by the currently selected environmental layer o Visual template if you have a visual template currently added on the map you can calculate NOO only within the bounds of this visual template For example you may want to limit the NOO to the river basins where the species is present see 2 14 2 Note that templates have to be previously added to the map to be able to use this feature o EOO you can calculate NOO only within the bounds of the EOO Extent of Occurrence of the current species If you select this option EOO options will be shown on the right panel where you can set how EOO will be calculated Once settings established you just have to click on Apply button to start NOO calculation Once completed results will be displayed on the map and on the right panel Density data map ModestR MapMaker New Map1 RASTER PolarKernelSmoothingTemplate alle Fi
221. ntage of species with the lowest AOO a species will be considered rare if its total presence area all over the world AOO is in the range of the X species with the lowest 120 ModestR Software Quick start tutorial AOO where X is the value you enter in the corresponding field In this case you can also select the taxonomic level for example a specific class or order that will be took into account to calculate this just by selecting it on the tree at the right side By default all species in the database are took into account e Maximum Extent of Occurrence EOO a species will be considered rare if its EOO calculated when processing the species in DataManager all over the world is less than the value you can enter in Km e Percentage of species with the lowest AOO a species will be considered rare if its EOO calculated when processing the species in DataManager all over the world is in the range of the X species with the lowest EOO where X is the value you enter in the corresponding field In this case you can also select the taxonomic level for example a specific class or order that will be took into account to calculate this just by selecting it on the tree at the right side By default all species in the database are took into account As said before you can go to Filtered results page to see the species that currently comply with all the current filter settings remember that all filters are applied to obtain those fi
222. nter species scientific name or LSID to be imported from GBIF Species Isurus alatus Options Select region boundaries 5 W Check if species is a synonym according to GBIF From longitude 180 0 to 180 04 Batch mode autoconfimation of each step From latitude 300 E to 90 0 E Data cleaning options Mean distance Latitudinal dispersion E Longitudinal dispersion Kind of records ta download 7 All V Observation E Living specimen E Unknown BS Defaults Human Observation Fossil F E Machine Observation V Preserved Specimen E Literature Occurrences temporal bracket Optenally enter start andlor end dates using the tomat YYYTIHALoD Start date __ fa End date fea Occurmences modified since a date ronal enters date using the tamat YYYYMALOD Modified since _ IE Then you can choose if you want MapMaker to look for synonyms in GBIF database You can also select the type of records you want to download from GBIF the rectangular area to be used as boundaries by default it is the whole world the start and end date of the occurrences to retrieve and the occurrences added or modified into GBIF database since a particular date Remember that to obtain a brief explanation of what each option and field is just place the mouse on it to see a tooltip However a more complete description can be found on GBIF documentation You can also select to apply a data cleaning once data dow
223. nvenient approach may be using a different environmental layer to calculate the NOO of each species This ad hoc environmental layer should be generated using the environmental variables that influence the most each species distribution In MapMaker it is already possible to create and environmental layer in this way see section 2 11 for a specific species In DataManager it is possible to do the same but for a collection of species Using this option DataManager will determine for each species which are the variables that influence the most each species distribution using the variable contribution approach already described in section 2 11 It will generate on the fly an environmental layer with those variables and use it to calculate 100 ModestR Software Quick start tutorial NOO In this way each species NOO will be calculated using the variables that influence the most the species distribution To apply NOO using an on the fly created environmental layer for each species in DataManager select the tree branch from which you want to apply it and select Mapping Apply Niche of Occurrence to this branch Using a per species layer menu option or the Mapping features Apply Niche of Occurrence to this branch Using a per species layer option in the contextual menu of the tree node The following dialog box will be shown where you have to select at least two environmental variables to be used to generate the environmental layer for each species
224. o the map as presence areas Perform options Kernel density map options Kernel density hull options Environmental Kemel density map Environmental Kemel density hull Information Information Total 2 coverage 100 00 Total coverage 100 00 Parameters Parameters Lower Lower Normal a 0 k ing factor X 1 00 ing factor X 1 00 Soothing Smoothing Allow a tolerance of 5 z Allow a tolerance of i Visual filtering Range Perform Range By habitat Full layer D Ainii Full layer IMU ni Add area Show over map E00 EQD F Show only significant densities DK cose R I cose Besides those settings in both displayed dialogs we can see and eventually modify the following settings e Total coverage This value indicates the of presence data that are included in currently selected environmental layer and that could be used to calculate kernel density A value too low indicates that few presence data can be used so results could be poorly significant A low value can eventually appear if you are using an environmental layer that does not cover all the world and or current presence data are 57 ModestR Software Quick start tutorial out of the area covered by the environmental layer Or for example if you are using an environmental layer generated with environmental variables for the sea areas and presence data are on land areas e Smoothing factor determines how smooth the de
225. oints of the vertexes of the areas to calculate convex hull However when you add a presence area to MapMaker you have to select a valid habitat and MapMaker will visually show the target area according to this habitat But this is actually just a visual presentation MapMaker doesn t have the real data of the resulting area this requires a posterior rasterization process that will be made by DataManager That is why calculating the convex hull of an area in MapMaker is not allowed When processing maps in DataManager the maps are rasterized and only real presence area is took into account Therefore in DataManager convex hull including areas can be accurately calculated see section 3 8 2 8 2 Using alpha shape hull with samples The alpha shape algorithm calculates one or more polygons that contain some or all the samples on a map depending on a parameter usually called the alpha value Intuitively the a shape algorithm can be seen as rolling a circular object of radius a making it to lean against the standing out nails on a board that represent the points of a set If we connect the nails that constitute the edges of the set for this object of radius a we obtain one or more closed areas that constitute the a shape see Edelsbrunner amp M cke 1994 work for more details As the a value is increased the a shape tends to the convex hull while it tends to the initial set of points when it is decreased This feature cannot be used
226. om GBIF Remember that to obtain a brief explanation of what each option and field is just place the mouse on it to see a tooltip However a more complete description can be found on GBIF documentation e Select region boundaries indicates the rectangular area to be used as boundaries by default it is the whole world for the occurrences to be downloaded from GBIF e Temporal bracket indicates the start and end date of the occurrences to retrieve e Occurrences modified since a date download only the occurrences added or modified into GBIF database since a particular date e Data cleaning options allows selecting variables to apply a dispersal capacity cleaning once data downloaded see section 2 6 for more details about dispersal capacity cleaning e Skip samples in 0 0 coordinates don t process samples whose coordinates are 02 longitude and 02 latitude as those samples are usually erroneous data e Skip samples with same longitude and latitude coordinates skip samples whose longitude and latitude coordinates have the same value as those samples are usually erroneous data e Consider and remove duplicated samples if they are equal until the Xth decimal this allows setting when two samples will be considered as duplicated thus avoiding adding them twice If for example we configure this option to take into account until the 2th decimal samples like 122 4567 9 4568 and 122 4598 9 4560 will be considered duplicated If you 144
227. ome error has corrupted data by checking this option you can ensure that maps will be correctly processed and updated Force rechecking all samples this option forces ModestR to fully recheck the the habitat validity of all samples in the maps to be processed This option is not usually required as ModestR automatically check samples when needed But if some external modification has been done on a map or some error has corrupted data you can ensure that samples will be rechecked by checking this option 81 ModestR Software Quick start tutorial Stop on errors to allow you to process maps in an unattended mode by default DataManager will not stop when it encounters a problem when processing a map but it will continue with the next one At the end of the process a report with the encountered errors will be displayed But if you prefer to stop immediately on any error you can check this option o Calculate patch index enabling this option patch area and patch index are calculated for each especies those metrics can be exported as seen in 6 17 Otherwise those data are not calculated and then cannot be used later This option makes map processing dramatically slower so if you don t expect to need those data you can disable this option to make processing quite faster Anyway if you disable this option now you can reprocess maps later and enable it to force patch area calculation use Reprocess all maps menu option It is import
228. on 2 6 in DataManager current variable ranges cannot be shown because data cleaning in DataManager will be applied to several maps and not to a single one as in MapMaker 89 ModestR Software Quick start tutorial continuing it is interesting to point out that many of the options and settings that are displayed on this dialog box are autoexplained just by placing the mouse cursor on one element usually a short emerging explanation will be shown Data Cleaning calculation Select Variables Set ranges Processing Validation mode combo box Set vaniable validation ranges and options Selected Variables Variable settings Marine Name Bathymetry Bathymetry EE TE Calcite Chlorophyll a Sea surface temperature Silicate Automatic mode Validation mode Autoselect best larger n of accepted values ne Apply to All Automatic validation mode will select for each vanable the outlier calculatio mode that provides the larger range Missin g va lue o pt ions of accepted values so potentially less outlier values Missing value options Select the variable on the list to gt invalidate an area if the value for this variable is missing Apply Dont takeina ao E E E E R to All see its outlier determination Dont take into account this variable when its value is missing settings Allowed invalid variables 0 e a ry at Allowed missing variables 5 W Make a copy of the da
229. on land habitat for example ModestR will assume that both habitats are valid for this species This assumption is done in several calculations and map transformations like EOO calculation niche estimations or hull transformations for example e Taxonomy restrictions ModestR supports taxonomy databases that have to include from class to species levels It assumes that there cannot have two taxons of the same level with the same name For example you can t have an order named X in a class A and another order also named X in another class B In this case ModestR will only keep the first order inserted with the name X e Default settings ModestR provides many features to work with distribution data Some of them can be somewhat complex and there are usually several parameters to adjust some data processing features Most of the times ModestR will provide default settings that can be valid for the common cases In this way ModestR tries to be simple to use particularly for new users But once familiar with those settings ModestR allows you to modify and parametrize many features e Task cancelation and backups to offer a better interactive user experience ModestR has been designed to allow users canceling running tasks whenever it is possible This feature is ModestR Software Quick start tutorial particularly useful in applications like DataManager that is aimed to process large dataset But take into account that even if ModestR allow
230. ones that are currently accepted in the map For example if you apply hull transformation to a map that contains samples that have sea as valid habitat the corresponding hull area will also have sea as valid habitat It should be stressed that unlike in MapMaker where convex hull can only be calculated using samples but not areas as explained in section 2 8 in DataManager it is possible to include areas when calculating convex hull because it will always use rasterized data to calculate hull therefore data where presence areas have been converted to a matrix and constrained to correct habitats for a species As an example below we show a map before and after applying convex hull transformation in DataManager samples have been hidden in resulting map Has it can be seen convex hull area is added to the map with the sea as valid habitat so other ones such as land are excluded because the previously existing samples have sea as valid habitat 85 ModestR Software Quick start tutorial ee Te i a Era en i aes a ES a Ry L L nimh r Tat m J k Pai _ After applying hull transformation a report will be shown in the right panel indicating the correctly transformed maps and also the incorrectly processed ones which were not updated A brief message will report the encountered problem that prevent processing each incorrectly processed map The most usual problems are that the map was not processed yet see s
231. ort presence areas and SAMPIES ccccsssccccsssececeesecceceecceeeesecessuecessegeceeseeseeetas 180 7 8 Export presence areas to ASC rasters ccccsccsecsecsececcecceccsccuecsecsessessessesseseeseeseucees 181 7 9 Export environmental data clipped rasters sssssesssesessrrersesrrrreesrrrrreesrrrreessrrrress 181 7 10 Export occupied areas summary repOft ss sssessseessressserssrersreesrrresrersrerssreesrersrersseee 182 7 11 Export environmental layer report sessssessessereesssrrrssrrrrssrrrssrrerssrreesrrereserresereeseerene 182 ModestR Software Quick start tutorial 8 MRFinder import export files formmat cccccssccssccsscssscssccescsscnsccesssesensees 184 8 1 Importing selections from Shapefiles ccccccccssscccsesccceeccceesceeeecseeecseeeeseeneeeeeass 184 8 2 Importing selections from KML c cccccceeeccceeecccenececeneceeeeeeseuececeuececeuecseeeeeeeeeeeeaes 185 8 3 fae siani n TOWN e AE E LEETE P EEE PEE AE ENES 186 8 4 ep 4 010 gE gM MEN A eee E E a 186 8 5 Exporting latitudinal gradients acsiscavewirncedivieausnnstenanchresve miancsaceviasbenaaahaveniatureteanenss 187 8 6 Exporting taxonomy to a CSV file or to clipboard essssssssssesssserrssrrrerreserererrreerrseeee 187 8 7 EXPONE MADS aE 187 8 8 POONER 187 8 9 Exporting region coordinates ccceeccseeccecccessceeeceeucecenceceuceeeuseeeeceeeeteneeteuseueeseuees 189 8 10 Export map view tO an image FiIlC ees cceeecceeecsc
232. ot E show Baos If we select the tab Region density map on the up right tabs we ll see the corresponding density map Areas Visual templates World Basins Basins of Africa 0 World Basins Basins of Africa 1 World Basins Basins of Africa 1 World Basins Basins of Africa 2 World Basins Basins of Africa 3 World Basins Basins of Africa 4 World Basins Basins of Africa 5 World Basins Basins of Africa 6 World Basins Basins of Africa 7 World Basins Basins of Africa 8 World Basins Basins of Africa 9 65 ModestR Software Quick start tutorial In this density map the most frequent conditions in the selected region are highlighted in warmer colors than the less common conditions If we select another visual template on the left list the corresponding data and density maps will appear Comparing the maps of different geographical areas can provide information about how different they are in terms of the variables used to create the environmental layer we are using a9 Polar environmental layer regions viewer oleas i Areas Visual templates Full Layer Data map Region data map Region density Map World Basins Basins of Africa 0 World Basins Basins of Africa 1 World Basins Basins of Africa 2 World Basins Basins of Africa 3 World Basins Basins of Africa 4 World Basins Basins of Africa 5 World Basins Basins of Africa 6 World Basins Basins of Africa 7
233. ow will be skipped e Decimal separator and field separator 146 ModestR Software Quick start tutorial e Sample point size select the size of the visual point that will indicate a sample in the map This size has no importance when processing map It is only a visual parameter After importation you will see the list of species imported and an Importation Log that includes information about the imported data and eventual errors like format problems or species not imported because they are not found in the database 6 9 Importing samples from Darwin Core Archives You can import samples to a DataManager database from a Darwin Core Archive DwC which is a format notably used to share occurrence data through GBIF www gbif org To do that you can use the mport Import presence data From Darwin Core Archive of occurrences option or the analog menu item of the tree contextual menu In this later case only samples for the selected branch will be imported The first step will be to select the Zip file that contains the Darwin Core Archive data DataManager only supports Darwin Core Archives that contain a meta xml file which describes the structure of the ocurrences file which can be in CSV or text delimited format Moreover the occurrence fields that DataManager will require to import data are class order family genus specificEpithet or alternatively scientificName taxonRank decimalLatitude and decimalLongitude If some of the
234. p So the data for all selected species distribution have been merged and added as a single dataset with a single name and settings File Edit Samples View Layers ModestRtools Options Help ADMIN Y PRUEBAS BEGO P a amp B oa g6 8 9 Bw tk Map 2x anplue Gia Ze Detail Level Auto Low Med High Highest Order Sample Land Sea 1 mmm YY VY Detail Level 0 Viewing from 180 100 0346 to 180 100 0346 Ready In the last one the same data where added using the option Group by genus So the data for all selected species distribution have been grouped by genera Then the data of each group have been merged and added as a single dataset with a single name and settings As the selected species belonged to two different genera two datasets have been added 134 ModestR Software Quick start tutorial File Edit Samples View Layers ModestRtools Options Help ADMIN Y PRUEBAS BEBO Dl a lt zBioa ge ea er Bis Map ev aeelue Order Sample Land Sea 1 E YW V7 2 im 2 a Detail Level 0 Viewing from 180 100 0346 to 180 100 0346 Ready Independently from the option you used to add a set of species maps to the world map you can add more species maps later using a different option Moreover you can even add species from different databases to the same world map just by changing the selected database in the File Select database menu and going to File Add Maps from ModestR database an
235. p tools panel Click on the initial point in the map the drag to the final point The distance will be shown in the bottom status bar Take into account that the shown distance is the shortest distance between two points m ModestR MapMaker New Map1 maA File Edit Samples View Process Tools Options Help Zese Ben 93 4 00 20 8 9 E gt Map a D ul Detail Level Auto Low Med High Highest Map Tools Zoom Select Drag map Show distance Free Hand Rectangle Add sample Edit sample An arrow is show in the map Shortest distance is Arrow ard Mys eee e a ee shown in status bar rf Show V Borders Samples E Valid V Invalid gs ail m 4 H Zoom Detail Level 1 Viewing from 173 2221 38 29465 to 88 05872 82 28019 Ready Shortest distance 1722 21313167202 Km 2 16 3 Querying a point in OpenstreetMaps or GoogleMaps On higher zoom view you can wish to have some help to situate like geopolitical information For that you can use several options e Inthe toolbar you will find a button Open current view in GoogleMaps or another Open current view in OpenStreetMaps Those options will open a web browser with a view quite approximate to that you have in MapMaker using GoogleMaps or OpenStreetMaps e f you want to look up a precise point you can click on this point in the map with the right mouse button and on the contextual map select Query current coordina
236. pecies only present in the land will be excluded from search The next tab is the Species tab where you can define a previous filter of the ranks you want to search for By default this filter is empty meaning that the search will include all the species of any rank from the selected database But it can happens that you only want to search for species of some particular families for example In this case you can click on the Change button A tree showing all the taxonomy of the current database will appear You can check in this tree any ranks you want In this way MRFinder will only search for the species of those ranks when performing the search You can always clear any filter using the Clear button in this tab 116 ModestR Software Quick start tutorial ModestR MRFinder DB Elasmobranchii DB lo amp File Edit View Options Tools Help Z4Qa 428 4 eg 0 AIA ARG 42BeEs f z JE Select species from Elasmobranchii DB Mp Classification Fui rate f Elasmobranchi Detail Level Batoids g a Sharks Auto Low Med High Highest V Carcharhiniformes Heterodontiformes Hexanchiformes Map Tools Draj Search options Lamniformes D Zog Species Orectolobiformes ee Fred bia P Groupping and simply Pristiophoriformes This filter allows to select the ranks or want to search a Squaliformes 5 SIREN Com HE F z If empty all th
237. pecies to be processed using Environmental Occurrence feature You should enter settings for EOO calculation if e you selected EOO as range calculation in the first step or if e you selected to apply variable contribution analysis in the previously described step In both cases EOO is required In any other case EOO settings will appear disabled because it is not required 96 ModestR Software Quick start tutorial Environmental occurrence calculation e i Processing Bcent Of Occurrence settings BOO for sample based maps FOO for area based or mixed maps Alpha shape Convex hull of _ Areas Kemel density Kemel density Areas Convex 5 Areas Alpha Convex hull eas hull of samples shape of samples areas samples estimation of samples Parameters Parameters Alpha value 6 0 degrees Alpha value 6 0 Maps to Alselectedmaps Only areas mixt maps gt Only sample maps W Make a copy of the database and apply niche on it Cancel There are different Extent of Occurrence options for sample maps and for maps with areas range maps EOO options for sample maps are Convex hull EOO is calculated as the convex hull area of the samples If there aren t not enough samples to calculate convex hull it is assumed that EOQO AOO More details about convex hull can be found in 2 8 Alpha shape EOO is calculated as the alpha sh
238. pha shape Alpha value 6 0 degrees Niche calculation range Kend Full layer density ieee estimation Edent of occurence Occupied river basins Maps to process Exclude maps with less than 2 distinct samples Export density maps as images W Make a copy of the database and apply on it x Cancel r Previous Start gt In the next step the options dialog box is shown The parameters you can set are e Smoothing factor determines how smooth the density matrix will be The greater it is the more the density will soread out far around presence areas Default factor is x1 e Allow a tolerance of X Apply a of tolerance on the potential areas of presence to consider them as valid with regard to the range between min and max values for each 24 This feature has already been explained in 2 9 for MapMaker where this analysis can be done interactively for a species It can be a good idea to do it first in MapMaker for a single species to better understand how it works 103 ModestR Software Quick start tutorial environmental variable involved in the currently selected environmental layer in the presence data of the species e Niche calculation range determines the range or maximal area for which NOO will be calculated Options are o Full layer to calculate NOO for all the area covered by the currently selected environmental layer o Visual template selecting this option a right panel will appear where yo
239. ple maps if cs CDOM you included sample maps in the analysis The EOO can be calculated using the alpha shape convex hull or kernel density modes already explained before see e g 2 8 Colinearity analysis Press this button to calculate VIF Variance Inflation Factor of each But you can also select Full extent to calculate variable variable You may consder renovng vale wth an VIF2S0 sets Calcuste commonly considered an indicador of high collinearity contribution report taking all the area where data from the selected variables are available If you included area maps in the analysis you should also have to select the EOO mode for those maps Click on Continue button to start analysis Contribution of variables to species distribution Extent Of Occurrence settings EOO for sample based maps Kemel density Full extent Are Alpha shape Convex hull Options Only areas mi maps eon lt ros coronae D 162 ModestR Software Quick start tutorial Once analysis completed results are exported to a CSV file The columns of this file are e Class order family genus and species for each analyzed species e For each one of the variables included in the analysis there are the following columns o Contrib Percent the relative of contribution of this variable to the presence absence of the species The sum of the Contrib Percent of all variables should be 100 o Min
240. plete the remaining fields You can also easily add edit or delete types using the buttons for types To edit or delete a type you must select it first on the tree Take into account that deleting a type all variables within this type will also be deleted To change a variable from one type to another you can edit the variable and just change its type or drag and drop the variable over the target type on the tree 174 ModestR Software Quick start tutorial 7 MapMaker import export files format 7 1 Import sample data from a CSV file You can import samples from a CSV file to add them to a MapMaker map On the main menu select File Import Sample data from CSV You will have to select the file where the CSV data is located A dialog box with the importation options will be shown Set importation options for samples CSV file CSV import options Select coord columns order in CSV file V First row contains headers Longitude Latitude Decimal separator E i First column contains species name i AT Pa Field separator 7 F Samples conversion Sample point size 100 W Skip samples in 0 0 coordinates T Skip samples with same longitude Make the sample habitat auto checked Ei T coordinates Consider and remove duplicated samples if they are equal until 4 gt th decimal Select valid habitats for the species Sea C Land All freshwaters Lentic habitats Small Channels Small Ditches Small Drains E
241. pplications RWizard http www ipez es RWizard is a GUI interface for R statistical software which can integrate a type of extensions called RWizard Applications Several of those RWizard Applications have already been developed to specifically use data exported form ModestR To export data from DataManager to those RWizard applications for ModestR select the wanted node in the tree then go to Export Export maps of the selected branch To RWizard applications in main menu or equivalent option in the tree contextual menu There are currently implemented options to export data to KnobR MapsR FactorsR and EnvNicheR Depending on the option you select a dialog box with the required options will be shown Depending on the case the options are quite similar to the ones already explained to export metrics or presence data see 6 14 and 6 17 6 23 Exporting summary data DataManager can calculate and export several metrics from maps like richness data rarity index etc When selecting Export Export maps of the selected branch To summary data in main menu or equivalent option in the tree contextual menu a dialog box to select output file is shown Then a CSV file is generated containing the following columns for each select species 168 ModestR Software Quick start tutorial e Taxonomy Class Order Family Genus Species e Total Area Of Occupancy of the species Total AOO e Total area for each habitat type occupied by the species Sea Ar
242. r each species distribution map in the selected branch Cells where the species is present will be exported with a 1 value Take into account that a huge amount of disk space can be required when using this option with many species and at a high resolution Remember that MapMaker can be used to visualize ASC rasters like the exported using this option For example this may be the result of a map exported to ASC raster displayed in MapMaker ModestR MapMaker DB asas22 ModestRDB RASTER D 00tmp Prionace glauca ASC Pea Fe Ex File Edit Samples View Layers Mapping ModestRtools Options Help ADMIN Y PRUEBAS BOSE HGU OR az 2G BIJ eS un FALLA Map Memar z Detail Level Auto Low Med High Highest Mao Tools Zoom Select gt Drag map Show distance FreeHand Rectangle Add sample Edit sample Arow Tet Placemark Show Samples V Valid V Invalid gt Coordinates Decimal Degrees 4 Detail Level 0 Viewing from 180 121 7277 to 180 121 7277 Ready 6 16 Exporting samples to Darwin Core Archive style You can export maps of any branch of a DataManager database to CSV data in a format that can be easily adapted to generate a Darwin Core Archive DwC which is a format used to share occurrence data through GBIF www gbif org To do that you can use the Export Export maps 156 ModestR Software Quick start tutorial of selected branch To Darwin Core Archive data op
243. r the root node of the tree This node will not really contain data but it s just a way to organize the selections So just enter the name an optional description and click on Save The node will appear on the left tree Let s assume now that you have a the countries for the world and you shapefile that contains all want to import them under the Countries node that you have created To do that Select the Countries node in the tree ss Descripbon Under this node will add countries eclechons Select childs of this node when selecting it Selection data No data in thes selection Expori 9 impart E Clear Adding new sclechon Discard Save Click on the Import selections button On the dialog box select the shapefile type in this case and then select the wanted file to be imported 2 gt A file like this can be found in the DIVA GIS web site http diva gis or 126 ModestR Software Quick start tutorial e ModestR will import the data from the file and show you the importation settings dialog box here expanded If you are familiar with shapefile format you can also add importation criteria to filter which data will be imported To do that use the See hide fieldlist button to see the list of fields contained in the shapefile Then you can select a field to see the values it takes and add criteria that will be used as filter when importing Import ShapeFile Ontiors See hide
244. rder Family Genus Species Species matching criteria 222 D seach Status bar Clear all ZS Close otal species in region 222 Species matching criteria 222 Region Bounds Long 86 19 to 77 48 Lat 0 31 to 73 43 Following each page of this window will be explained 4 8 1 Taxonomy filter page In this page you can apply filters on the search results using taxonomic criteria On the left side of this page you can see a taxonomic tree similar to the one shown in DataManager when exploring a ModestR database see section 3 1 The difference of course is that only species and their corresponding higher taxonomic levels found in the searching are shown in this tree You can explore it and also use the Search button to look for some taxon in a similar way than using the search panel of DataManager see section 3 1 You can also see three buttons at the right up of the tree that allow to add remove filters If you want to select only some taxa from the species found in the area you can add filters just by selecting in the tree the taxon you want to include it can be any level from class to species and clicking on Add button Filters will be added to the Filter selection list box If you add several filters they will work as an OR operation that is species that comply with any of the filters at least one of them will be included in later data processing When you add a filter the Species matching criteria will be updat
245. rdinates system 63 ModestR Software Quick start tutorial Besides visualizing the whole environmental layer in the map ModestR also allows showing only a portion of this layer corresponding to any geographical area To do that the first step is generating and storing an environmental layer using the wished variables as explained in section 2 11 The next step is adding to the map the visual templates that correspond to the geographical areas we want to visualize the corresponding portion of the environmental layer This can be done using predefined visual templated drawing your own ones or importing them as explained in 2 14 For this example we added to the map the visual templates corresponding to the main river basins of Africa File Edit Samples View Layers Mapping ModestRtools Options Help ATI NELI lt 5 209 o m SOL uFitaias Samples V Vad V iaid aD Coordinates Deca O Degrees peni Zoom Detail Levet 0 Viewing from 58 90924 42 48753 to 98 53102 45 19205 3 E Current Env gt Capa NOAA a0 metros hd Next the wanted environmental layer has to be loaded going to Mapping Niche of occurrence Load environmental layer and selecting it in the list of stored layers For this example a layer that contains data from land areas has been used Next we ll go to Mapping Niche of occurrence Polar data maps for visual templates A dialog box will appear Areas Visual templates
246. re o None in this case no EOO estimation is done and EOO is merely assumed as equal to AOO Area Of Occupancy As assumed area of samples in ModestR see section 1 1 is just a convenient estimation but not a precise value this option is not recommended in most of the cases 13 This EOO calculation during map processing doesn t modify the maps in any way It s just done to obtain EOO area estimation It s totally different from applying a hull or niche transformation to maps as explained later in this chapter 80 ModestR Software Quick start tutorial O Convex hull EOO is calculated as the convex hull area of the samples If there aren t not enough samples to calculate convex hull it is assumed that EOO AOO More details about convex hull can be found in section 2 8 Alpha shape EOO is calculated as the alpha shape hull area of the samples If there aren t not enough samples to calculate alpha shape hull it is assumed that EOO AOO More details about alpha shape hull can be found in section 2 8 Kernel density estimation EOO is calculated as a hull area based on the density estimation kernel smoothing of the samples If there aren t not enough samples to calculate density estimation hull it is assumed that EOO AOO More details about density estimation hull can be found in section 2 8 EOO options for area and mixt maps are O None in this case no EOO estimation is done and EOO is merely assumed as equal to AO
247. re than one to generate several clipped rasters Next selected the target folder where the file s will be saved in ESRI ASC format Be careful because any existing file with the same name will be overwritten MRFinder will clip the rasters for each selection That is if there are three selections currently on the map the selected raster will be clipped for each one of those selections So you ll have three files resulting for each one of those clipping operations A report in CSV format is also generated with data about clipped areas in km and simple Statistical measures max min mean std and quartiles for the rasters in the clipped areas This option is similar to the one described for MapMaker in section 2 9 4 4 12 4 Calculating areas for selections You can use MRfinder to calculate areas for any selection This method is intended to provide an approximate result as it is performed using a rasterization method with a resolution of 1 Go to File Export Selection area summary report option in main menu The generated report in CSV format contains the total area and the area of each type of habitat for each selection currently added to the map in km See more details in 8 14 130 ModestR Software Quick start tutorial 4 12 5 Export selections MRFinder importation and exportation formats are detailed in section 8 Exportation of species data resulting from searching has been mentioned in 4 9 and exportation of clipped rasters a
248. ree like the explained on section 2 19 To be able to save a map in a database you previously have to create this database and populate it with taxonomy You can also use an existing database like the provided in ModestR website for fish species Once a map saved either in a file or in a database you can save it anew just by selecting the Save option without having to reenter any data Save As options allows you to save it in a different file 72 ModestR Software Quick start tutorial Apart from those options that allow saving a map in a format directly readable by ModestR software you also have several options for exporting a map to other formats in the File menu such as JPEG BMP format shapefile CSV data etc The exportable formats are explained in the section 0 of this tutorial 2 19 Retrieving a map You can retrieve a map both from a standalone file with extension IPMMAC or from a ModestR database In the first case you just have to select the file that contains the map In the second case Mapmaker will display the taxonomy tree of the database either the default database configured in the Options Preferences menu or the database you selected if no database has been selected as default You can directly expand nodes with the mouse and select a species with a map which is identified with a little world icon at the right of the species To help you finding a map you can use the filter options that allow showing only speci
249. resolution ModestR calculations including areas presence detection metrics etc are done with a resolution of 1 If you use environmental variables into ModestR usually as raster grid data for example in ESRI ASC format maximal supported resolution is of 1 but coarser resolutions most of those data come in resolutions of 5 x5 are supported by ModestR and recommended particularly when working with worldwide rasters as they allow considerably faster calculations Samples habitat checking is currently done with a resolution of aprox 1 1 second e Minimal presence area as said above ModestR is intended to work with a resolution of 1 As a consequence ModestR is not designed to accurately work with presence areas smaller than a 1 width or a 1 height Even if they will be stored as part of the map areas smaller than those limits can eventually be omitted when processing maps so they will not be took into account to calculate richness presence data etc To enter areas smaller than 1 we recommend using samples As said above ModestR assumes that the area of a sample equals the area of the cell of 1 x1 where it is located e Species habitats ModestR supports assigning several different habitats to a species But when processing a map it assumes that a species cannot have different excluding habitats in different locations That is if aspecies has a validated presence area on a marine habitat and another
250. riable by selecting it in the tree and using Edit button or the equivalent option of the contextual menu The settings of the variable will be shown in the right panel and the read write mode will be activated to allow modifications You can select to save or to discard changes using the corresponding buttons on the bottom Environmental variables management Enwironmental vanable settings Environmental Variables Name Bathymetry Type Marine ae Marine Description Bathymetry Bathyetry m 6 x6 Calcite im CDoOoM Chia Short name Bat Cloud cower DA Units Depth File pa C modestrprojeciidata environmentvars marinas Nitrate bathymetry 6x asc FAR pH G d EE 3999 Fhosphate POC 180 50 Salinity ae P D a A a F P F is ie La Temperature Prueba Terrestrial Variables Types Cee ee Zi Import _G Dele L 32 Tyberghein L Verbruggen H Pauly K Troupin C Minur F de Clerck O 2012 Bio ORACLE a global environmental dataset for marine species distribution modelling Global Ecology and Biogeography 21 272 281 172 ModestR Software Quick start tutorial To add a variable you can use the Add button for variables or select an existing variable in the tree and select Add Var using this as template option in the contextual menu pressing the left mouse button The fields you can set for a variable are Name a brief descriptive name of the
251. rix Order Selected Variables 1 Cloud cover 2 Chla 3 Calcite 4 Bathymetry Polar space a 4 Previous Continue gt Click on Continue button to go to next step In this step environmental layer will be calculated according to entered settings This can take some time The resulting layer will be shown on the map and the distribution of the environmental data in the polar coordinates system will be shown in the dialog box ModestR MapMaker New Map1 lo se File Edit Samples View Layers Mapping ModestR tools Options Help 14 a2 OF a Oa 26 8 A 8 gt aa 3 Mao I i z Variable analysis Order Scale Options 5 a Data Color scale Cal 100 Large rivers Small rivers Lentic waters Small channels Large channels E Small ditches fama Detail Level 0 Viewing from 180 100 0346 to 180 100 0346 Ready Click on Continue button to go to next step The final step allows you to save and or to export a report of the generated layer In both cases you should enter a layer name before Then you can export a report to a folder and or save the layer to be able to use it later Exported report will contain several files such as an ASC raster for the X and for the Y components and a graph of the polar coordinates with the data distribution see 7 11 for details 53 Mo
252. romimus Capromimus abbreviatus Actinopterygii Zeiformes Parazenidae Cyttopsis Cyttopsis rosea Taxonomy data will be imported to the currently opened database All required taxonomic levels will be added to the database for each species contained in the CSV file If some taxa either a class order family genus or species already exists in the database it will be simply skipped 6 2 Importing taxonomy from another ModestR database You can import taxonomic data from a ModestR database to the currently opened ModestR database using the mport Import Taxonomy From another ModestR database menu option In this case the expected format of the origin database is the original format of a ModestR database No modifications have to be done Just take into account that this option only imports taxonomic data but not existing maps from the origin database 6 3 Importing taxonomy from phyloXML files You can import taxonomic data from a phyloXML file to the currently opened ModestR database using the Import Import Taxonomy From phyloXML file menu option DataManager will search for lt taxonomy gt elements to import using the lt rank gt element to determine the taxonomic level of the data You have to be aware that phyloXML files not always contain comprehensive taxonomic information so in some cases DataManager will not be able to import it For example a species name from a phyloXML file will only be imported if all superior levels until class le
253. ronmental Kemel density parameters Lower Smoothing factor X 1 00 Allow a tolerance of Niche calculation range Visual template E00 Occupied river basins Export density maps as images Z Make a copy of the database and apply on it o Visual template selecting this option a right panel will appear where you ll have to select a visual template e g a country a continent NOO will be calculated only within the bounds of this visual template 99 ModestR Software Quick start tutorial o EOO selecting this option a right panel will appear where you ll have to select the EOO calculation method NOO will be calculated NOO only within the bounds of the EOO Extent of Occurrence of the species o Occupied river basins selecting this option a right panel will appear where you ll have to select a river basin level O higher 5 lower NOO will be calculated only within the bounds of the river basins of this level where there are samples of the species See 2 14 2 for more details of how ModestR determines the river basins occupied by a species o Export density maps as images enabling this option a NOO density map of each species to be processed will be generated and exported to an image file This image corresponds to the Density map option explained in MapMaker see 2 13 Image files will be saved in a folder you will have to select in the next step o Make a copy of the database and apply on
254. s You can also directly load raster data form an ESRI ASC file using the the menu item Layers Raster templates Load raster from ESRI ASC Everything else works the same way as explained in previous section for rasters using environmental data integrated in ModestR 2 9 3 Raster color scale settings You can change lateral color scale settings corresponding to the currently displayed raster using the menu option Layers Raster templates Color scale settings or the button that appears at bottom of the color scale A dialog box will be shown where you can modify the number of labels to be shown on the scale and the maximum and minimum values to be shown on the map If you change this range areas of the raster with a value outside the range will not be shown This can be useful to show only areas where an environmental variable is within a specific range of values 36 ModestR Software Quick start tutorial Raster color scale settings B88 Color scale settings Num labels to show in scale E ae Display range Maximum value to show 0 50000 Minimum value to show 6000 00000 For example in the following figure altimetry data are shown using default options 4 pm 180 107 9664 to 180 107 9664 Ready n 180 107 9664 to 180 107 9664 Ready 37 ModestR Software Quick start tutorial 2 9 4 Raster data clipping MapMaker can cut off a raster to
255. s for example a selection for Spain and another for France but you are interested in having a global search and not a separated search for each selection you can significantly improve MRFinder searching performance by merging all those selections the way that two or mode overlapping or contiguous selections will be merged in one single selection This option is available in the Edit Merge current selections menu options or in the corresponding button of the toolbar It must be pointed out that this merging option has no the same effect that merging selections explained in 4 10 While this one implies a geometric operation to calculate the polygons resulting from the union of the involved selections the one explained in 4 10 does not perform any geometric operation but just a logical union of several selections to consider them a single one regarding searching feature and display 4 12 3 Raster data clipping You can use MRfinder to cut off raster data to any pattern To do that the raster file has to be previously integrated in ModestR Details about how to integrate environmental data in ModestR are explained in section 6 26 Then add to the map the wanted selections either predefined ones or owner drawn as explained in previous sections Go to File Export Environmental data for selection option in main menu A dialog box will show to you the available variables those previously integrated in ModestR Select the wanted one it could be mo
256. s a raster template by clicking on the Show in map button e Edit layer details such as name or description by clicking on the Edit details button Using this option you can also see the variables used to generate the layer the polar coordinates and the data distribution into this coordinates and eventually export the layer report Exported report will contain several files such as an ASC raster for the X and for the Y components and a graph of the polar coordinates with the data distribution distribution see 7 11 for details e Delete an environmental layer that you no longer need by clicking on the De ete button 54 ModestR Software Quick start tutorial Environmental layers manager Layer name Creation time Africa 04 10 2014 ejemplo manual 15 01 2015 Espana 05 10 2014 Mar vars Oo 0S2014 Sudamerica 2 vars os oq2014 Terrestrial layer O09 2014 Terrestrial layer P O0o2014 2 13 Calculating niche of occurrence MapMaker can estimate the Niche Of Occurrence of a species NOO that can be defined as the set of areas which are located near the areas where the species is already present e g where there are samples in the polar coordinates system generated for a specific environmental layer Here the environmental layer refers to a polar coordinates system generated from the combination of values from several environmental variables as explained in section 2 11 above And near should be unders
257. s switching between Basic and Advanced modes that allows entering several transformation rules in the form IF X value THEN X new value Those rules are applied in the order they are added to each value of the rasters e Create merged raster merge all selected rasters after applying the previously selected transformations to them in a new raster This option can be useful to generate a new raster from two or more rasters using a merging operation such as the mean the values of the merged raster will be the mean of the corresponding values of the selected rasters The settings for this operation are the merging mode mean maximum minimum sum difference and the rule to apply when one of the rasters to be merged has a null value for some cell Raster Rescale tool Input files File Cell size minutes Longitude range Latitude range Althymetry_5 ASC 5 180 00 to 180 00 90 00 to 90 00 Bathymetry_10 ASC 10 180 00 to 180 00 90 00 to 90 00 Bathymetry_10_5 ASC 5 180 00to 180 00 90 00 to 90 00 Output Raster settings J Rescale cell size Rescale options Clip options Filter options 7 Clip data to selected region 2 eeg gt 0 00 amp k gt 1000 Transform raster values v v Filter data Removing rule Create merged raster 70 ModestR Software Quick start tutorial After configuring all settings clicking on the Export button each one of the selected input files will be processed and a new transforme
258. s tab will only be shown if the map contains samples Create a copy of the database as data cleaning involves irreversible map modification it can be prudent to make a copy of the database before performing this transformation Checking this option DataManager will ask you for a destination folder and file and will do this backup copy before modifying maps Once all those settings configured press the Continue button to perform data cleaning ModestR will then apply data cleaning to each one of the selected maps Once finished a summary report will be shown with the list of processed maps and the maps not processed indicating the cause When samples cleaning has been done a Report button will also allow you to save a detailed report of the cleaning operations done in CSV format containing a list of the cleaned samples for each processed species and details about the variable ranges they didn t comply with This report will only be generated when cleaning samples and will not include details regarding areas cleaning The reason for this is that even a relatively small region will easily contains thousands of 1 x1 cells which results in a very long and rarely useful report i ModestR DataManager C ModestRProject BD asrr DB o File Edit Import Export Process Options Tools Help 3B 7 iBF BMPR e yLeaeoul Database Taxonomy Classification s i Ef asir Search Data cleaning 3 A Actinopterygii
259. s you canceling a task at any moment the modifications made on data until this moment will usually not be undone That is why ModestR offers Undo features in most interactive applications like MapMaker or MRMapping and data backup warnings in applications like DataManager Particularly in DataManager it is probably recommendable to use integrated backup feature or just make your own copy of the database before launching tasks that will modify data This can prevent from losing original data in case of failure or if you decide to cancel the task before its completion but when some data have been already modified 10 ModestR Software Quick start tutorial 2 First steps with MapMaker Mapmaker is an easy to use software application to build distribution maps The MapMaker user interface is quite simple as the most usual tools are always visible at the left tool panel You also have contextual menus that will appear when you click with the right button of the mouse on the map In addition quite all menus buttons and other elements have a tooltip that briefly explains their usage and that will be shown when you place the mouse over an element ModestR MapMaker New Map1 c l File Edit Samples View Layers Mapping ModestR tools Options Help DO D ROBI sem r FALLA _ Detail Level y Auto Low Med High Highest nd Map Tools Zoom Select Show distance FreeHand Rectangle Emerging ainsi ay ee Add sample
260. se fields are empty samples cannot be imported The next step is to configure the importation setting that will be shown in a dialog bog quite similar to the shown when importing from CSV sample files or GBIF see sections above The main difference is that you can select to only import samples from species already existing in the database or to also import samples for new species In this last case new taxons class order family genus or species will be added to the database if needed using the information included in the Darwin Core Archive you are importing Set importation options for Darwin Core Archive samples Taxonomy importation options Merging method Import only maps for species already existing in the curent database Import maps from all species included in the Dw Archive add new tasonsa Grouping level Group samples by species Group samples by subspecies if exists Skip existing maps Overwnte existing maps Add data to existing maps Samples conversion Sample point size 100 Skip samples in 0 0 coordinates 7 Make the sample habitat auto checked yl Skip samples with same longitude and latitude coordinates Consider duplicated samples if they are equal until 4 th decimal Select valid habitats for the species Sea C Land All freshwaters ae Cancel Lentic habitats Small Channels Small Ditches Small Drains Wetlands Small rivers E Large Channels f Large Ditches Large Drai
261. selected file will be transformed according to the operations that you ll select Next in the output settings you can check which operation you want to apply to selected files Operations will be applied in the order they are shown in the dialog box independently from the order you check them You can check only some operations at least one it is not mandatory to check them all When checking one operation operation options will be shown in a tabbed panel Available operations are e Rescale cell size allows changing cell size of a raster The available settings for this operation are the new cell size and the rescaling mode mean maximum or minimum e Clip data to selection region allows clipping a raster to a particular rectangular region that you can define on the settings for this operation Remember that you can also clip a raster to any arbitrary shape using other Modestr features see 2 9 4 and 4 12 3 e Filter data allows filtering rasters to remove data values that comply with a specified rule For example we can add a rule such as x gt 1000 to remove all values bigger than 1000 from the selected rasters the x in the rule represents any value of the raster e Transform raster values allows converting raster values using one of those rules o Transform no data to zero o Transform any data to a specified value o Transform zero values to no data An advanced mode is also available a vertical left tab allow
262. selected variables are shown in a list You can optionally calculate Variance Inflation Factor by clicking on the Calculate VIF button This is just optional You can skip this step and click on Continue button to go to next step In the case you click on the Calculate VIF button the VIF of each variable will be shown in the list VIF can be useful to detect high correlated variables and then decide to remove some variables To remove a variable just select in on the list and use the Delete selected button Environmental layer generation VIF can be calculated for the full extent or for Select Variables Analysis Processing Niche parameters i eee a visual template given that a visual template Selected Variables aeatinCow ene MIE has been selected in the previous step as Bathymetry 91 93 z O Calcite 97 96 bae pa extent used to calculate VIF can be different oe sion i from the extent selected for the DA 97 96 Depth mare environmental layer ModestR doesn t explained before Take into account that establish any limitation in this sense so the convenience of using one or another option is left to the user Click on Continue button to go to next step Visual template 102 ModestR Software Quick start tutorial The next step will allow you to set how the contribution analysis will be done This analysis is the key step when calculating NOO using a per species layer For each species this analysis wi
263. sible in the higher level so the checkboxes to make 1 World map data comes from from OpenStreetMap with OpenStreetMap contributors http www openstreetmap org copyright 2 From ModestR v3 0 freshwater data is provided separately from ModestR package which only contains a world map with land data If you need freshwater data you can download it from Modestr website Once installed you will be able to show those data in ModestR Moreover ModestR will be able to discrimate between freshwater habitats when creating maps cleaning data or calculating areas for example 11 ModestR Software Quick start tutorial them visible will only be enabled when the map is displayed using this detail level You can directly come back to the main world view using the Full button on the top of left tool panel ModestR MapMaker New Map1 o J File Edit Samples View Layers Mapping ModestR tools Options Help BOZEGBEAGW OF amp amp Map Tools Zoom Select Drag map Show distance FreeHand Rectangle Add sample D Edit sample F F F Il Sea ll Land Il freshwater habitats Add as visual template UnFill Selected samples V Valid V Invalid Delete selected objects To drag the map you can use the Drag map tool When dragging an arrow will appear indicating where the location situated at the beginning of the arrow will appear when you end the dragging operatio
264. sic tasks can be performed filtering which species among the found ones will be processed and process those selected species to generate and export several data This dialog box consists for several pages that can be selected using the top tabs Pages one to three offer different filtering options Page four Filtered results allows you to see in any moment which species are currently selected from the species found in the map searching according to the current filter settings Last page shows the different export options that will be applied only to the selected species after filtering At the bottom of this dialog box you can see a status bar In this bar there are two counters 118 ModestR Software Quick start tutorial e A counter labeled Total species in region that indicates to total of species found in the last search including all areas selected e A counter labeled Species matching criteria indicates how much species are currently selected according to the filters settings Initially this counter will indicates the total of species found in the selected areas Select the filters to apply to the species found Taxonomy filter Rare species filter Categories filter Filtered results Export data Found species ff3 Elasmobranchi GBIF Class Actinopterygii Batoids Sarcopteryaii Family Sharks Genus Species lv Add a Remove Clear All Taxonomy Filter Selection Class O
265. sing the checkboxes on the bottom Once results shown in the list you can click on any of them to directly find it in the left tree ITIS Taxonomy database export tool Select ranks to be exported Dunseiect aa Jy Plantae a 4 1 Biiphyta J Viridiplantae At least 3 eters are required to start searching Entertext to search Arc 4 1 Chlorophyta Streptophyta 4 Charophyta B Embryophyta HQ Anthocerotophyta Bryophyta 4 Andreaeobryopsida 4 Andreaeopsida 3 Bryopsida 4 1 Bryidae 4 Buxbaumiidae 3 E Dicranidae Archidiales 3 Archidiaceae 1 Archidium Archidium alternifoliurr E Archidium donnelli E Archidium halli Archidium minus Archidium ohioense Archidium tenerrimum 1 1 Bryoxiphiales El Dicranales EIO Grimmiales El Pottiales M Scouleriales Diphysciidae OF EE WW Taxon Plantae Archidiales Archidiaceae Archidium Archidium altemifolium Archidium donneliii f Archidium hallii Species Archidium minus Archidium ohioense Archidium tenerrimum Arctoa Arctoa anderssonii Arctoa fulvella Arctoa hyperborea Arctoscyphus Archeophylla Archilejeunea Level Order Family Genus Species Species Species Species Species Genus Species Species Species Genus Genus Genus Show only results in the selected kingdoms F Plantae IM SA Protozoa v Fungi V Sg Archaea
266. sing the corresponding options in the Edit menu or in the context menu displayed clicking on a node with the right mouse button Once populated you will see the taxonomic data organized in a tree where you can expand or collapse the different levels clicking on the corresponding nodes Species with a map of course in a newly created database no one will still have maps are identified with a little world icon at the right of the species like in MapMaker database view see 2 19 To help you finding a taxon of any level you can use the search page on the right You can write some part of the species you are looking for and coinciding names will be shown in the Results list Clicking on one of those results it will be selected in the tree When you will have maps in the database to help you browsing contents you can use the filter options that allow showing only species with without maps or only branches were there are don t are species with maps for examples T CP Hicri Dota Homga ii daR BC E bhh tok mgri Eger Prec Upem oleh Map Filter options Dabest iioi Chel cola i Fa Acher erai Ea phobi i arretir eTe fact atini ie shaw Gtk bert cide adh aps Sire Oh tener nih eps GHW ujor D ihe orc E marha E S sole ara eth iG Iwas OF far a alk La Bs EpRLEF D aajn oll G Te er re ieee en Lacctadhdes aie eth GB i larch schists Tarcorhine hertane flancortine hett ra
267. sted to the nearest integer degree will be used by default to calculate and export metrics e lf you selected an irregular area to analyze in the MRFinder map the boundaries of this area will be used by default to calculate and export metrics But the output will be a matrix adjusted to the rectangle that circumscribe the irregular area using the nearest integer degree but where the values corresponding to the cells outside of the selected irregular area will be set to zero 186 ModestR Software Quick start tutorial e Inany case you can modify area boundaries disabling the Clip data to selected region in the metrics dialog box and setting different rectangular boundaries 8 5 Exporting latitudinal gradients MRFinder can calculate and export latitudinal gradients for several metrics from maps from selected species When selecting Export gradients in the exportation tools of the search result window see section 4 8 a dialog box to select exportation settings is shown with the same options and operation as the corresponding option in DataManager You can find more details about latitudinal gradients exportation in section 6 20 8 6 Exporting taxonomy to a CSV file or to clipboard You can export taxonomic data of the selected species using the Export taxonomy in the exportation tools of the search result window see section 4 8 You will see three options to export data e To clipboard this option will copy the list of na
268. t many of the options and settings that are displayed on this dialog box are autoexplained just by placing the mouse cursor on one element usually a short emerging explanation will be shown 46 ModestR Software Quick start tutorial Environmental Occurrence calculation Hull _ Select Variables Correlations Variable analysis Set ranges Processing _ Set variable validation ra Selected Variables Contrib Cover Variable settings PAR 28 52 100 00 OK Name Calcite Calcite 16 75 100 00 OK Chla 16 65 100 00 OK Validation mode Nitrate 13 14 100 00 OK Tolerance DO 7 43 100 00 OK 7 Validation mode combo box Units Allow a tolerance of 1 2 Appi to al Missing value options Missing value options Invalidate an area sample if the value for this variable iayfissi Dont take into account this variable when its value is missing Minimum accepted value 6 274E 05 Maximum accepted value 8 926E 05 Main Select the variable on the list to Main variable settings see its validation settings and ae ee basic information Allowed missing variables 4 x cance 4 Previous Continue D gt Then you can select how validation will be done for each variable To do that you must select a variable on the left listbox The corresponding settings for this variables will be shown on the right up panel Th
269. t in columns format this option necessarily produce a multiple sheet or multiple file output as the area occupied by each type of habitat in each cell will be outputted in a separate sheet or file e Youcan also set richness count method count a species if it is just present in the output cell or in turn set a threshold of 1 x1 minutes cells occupation that has to be exceeded to count a species in this cell For example if you set a cell output of 5 x5 you could want that only if a species occupies at least 20 of this cell that is 20 of 5x5 5 so 5 cells of 1 x1 minutes the species has to be counted so the value for this cell incremented e You can also select which habitats have to be included in metrics calculus By default all habitats are took into account If you exclude one habitat all samples or zones with this associated habitat will be excluded from the metrics calculus e You can define the zone boundaries to be examined in degrees with a minimum of a 12x12 zone Take into account that rarity index patch index and area index are always calculated in a world basis independent from the zone boundaries selected for the output e You can select how cell coordinates will be shown in output using the coordinates of the center or one corner of the cell e You can also select any environmental variables you want to output for the precision and boundaries and with the same format that you selected It must be point
270. t to show the updated map as many times as you want You can also clear all filters using the Clear all filters button on this window 4 9 Generating and exporting data Once filtered the species you want to include you can go to the Export data page to generate and export several different data about selected species and in different formats To select a 122 ModestR Software Quick start tutorial data exportation process you just have to click on the desired button Some buttons are associated to different options regarding the exportation format like for example the Export stats option that will allow you to select a flat or a structured CSV format Select the filters to apply to the species found Taxonomy filter Rare species filter Categories filter Filtered results Export data Metrics exportation Statistics exportation Taxonomy exportation Map data exportation Selected regions coords export To grouped summary To flat CSV file ool To fiat CSV file To full summary To structured CSV file To structured CSV file l To structured CSV file To presence data Copy to Clipboard Copy to Clipboard lt i z To standalone map files Export regions amp Export Maps coords B Export taxonomy m Export gradients 9 Export Stats Clear all x filters S Close Total species in region 222 Species matching criteria 222 Region Bounds Long 86
271. tR Software Quick start tutorial X 1 5 if you select to consider both mild and extreme outliers as invalid X 3 if you select to consider only extreme outliers as invalid You can also set a custom value of X in the options shown for this validation mode o JackKnife outliers this validation mode to detect outliers is described in Chapman s Principles and Methods of Data Cleaning 2005 and it is considered quite reliable ModestR supports two variants of this method the one proposed by CRIA and the one proposed in DIVA GIS both area described in Chapman s book o Custom in this case it is the user that will manually set the minimum and maximum values of the range of valid values for a variable Any value that fall outside this range will be considered an outlier e Missing value options under the tabbed box that show the information for the variable two radiobuttons allow you to select what to do when there is no value for the variable in a particular area sample You can select between two possibilities o invalidate an area sample if the value for the variable is missing that is if the variable have a null value in this location in this case an area sample will be cleaned considered invalid as soon as there is no value for the variable for this area sample no matter the values for the other variables o Don t take into account this variable when its value is missing in this case if there is no value for the variabl
272. ta cleaning can lead to biased results because longitude values of occurrences near the extremes i e 1802 or 1802 are very different so potential outliers while occurrences can actually be quite close 21 ModestR Software Quick start tutorial data whether areas or samples It will also determine the coverage percent of each variable that is the percentage of presence areas samples where there is a not null value for a variable This can helps you to determine if a variable is really useful to perform data cleaning Those data will be shown in the next step as shown in the figure below You can see on the left the list of selected variables with a new column where the coverage percent is presented As you can see in this example the A thymetry variable has a very low coverage smaller than 1 ModestR will even show you a warning message in those cases and show the values in another color In this example this low coverage is because presence data correspond to a marine species so there are no althymetry data in those areas You most likely remove this variable from the list by going to the previous step using the Previous button and deleting it from the list of selected variables Then you will return to this step using the Continue button Before continuing it is interesting to point out that many of the options and settings displayed on this dialog box are autoexplained just by placing the mouse cursor on one element usually
273. tabase and apply niche on it q Previous continue Then you can select how outliers will be detected for each variable To do that you must select a variable on the left listbox The corresponding settings for this variables will be shown on the right up panel The available settings are e Validation mode this is the way the values for this variable on the presence zones whether samples or areas will be evaluated to determine if some sample area has to be cleaning or not Any validation mode will determine the range minimum and maximum of valid values for the variable so any value that fall outside this range will be considered an outlier The difference between different validation modes will be in the way they use to determine this range By default the validation mode will be set to Autoselect best But you can manually select between the following modes o Autoselect best this mode will evaluate for each map which one of the other available validation modes returns the less outliers and uses this mode to clean data That is with this mode you will always obtain the minimal number of outliers o Quartile outliers this option use a validation based on the values of the Q1 and Q3 quartiles of the values took by a variable in the current presence areas samples This option will consider any value of this variable as invalid if it is outside the range Q1 X Q3 Q1 Q3 X Q3 Q1 where X will be 90 Modes
274. tal layer The following dialog box will WIF Calcite V CDOM be shown where you have to select at least two WF chia Pig Cloud cover cover a environmental variables to be used to generate the FA DA E Depth environmental layer details about how to FA vo Nitrate integrate environmental data in ModestR are FA PAR J pH explained in section 6 26 EI Phosphate i POC F Salinity A relevant consideration is that is highly EG Sticate 1 Temperature recommended to use variables with the same cell He pe size 5 minutes for example when creating an Tn Aspect environmental layer Environmental variables with BA 50 different cell sizes are supported but this can lead iaia Layer extent to less accurate results Anyway the Full extent environmental layer will always be calculated using x Cancel Continue gt the lowest cell size among the used variables and all variables will be previously downscaled to this cell size In this dialog box you can also select the Layer extent which can be e Full extent the layer will be calculated for the area for which selected environmental data is available For example if you selected environmental variables that cover the entire world the environmental layer to be created will also cover the entire world e Visual template this option will only be available if you previously added a visual template to the map before starting the
275. tart tutorial 4 2 Moving across the world map MRFinder offers the same features available in MapMaker to move across the map and zoom in and out Please see subsection 2 1 for more details Moreover the same informative elements that can be added to the map in MapMaker area available in MRFinder and work in the same way See subsection 2 16 1 for more details The same as in MapMaker you have Undo and Redo options in MRFinder Operations that can be undone in MRFinder are those that affect the selections you add to the map 4 3 Adding selections to search for species To find which species are present in an area you simply have to select on the map the desired zone typically using the Freehand or the Rectangle tool It must be pointed out that Freehand tool allows to search for species in an irregular area which can be a very flexible feature but being more complex it will take more time to process so we recommend you to use Rectangle for searching in rectangular areas and use Freehand only when searching in irregular areas is needed Another option available in the left tool panel to select an area is the option Enter a region to manually enter a region In this case a dialog box will be shown where the coordinates of a rectangular region can be entered When accepting it this rectangle will be shown in the map The default coordinates that will be shown in this dialog box will be took from the current selection if any This way you c
276. ted To do that use the See hide fieldlist button to see the list of fields contained in the shapefile Then you can select a field to see the values it takes and add criteria that will be used as filter when importing You can also directly write a condition in the textbox The syntax of the conditions is similar to the syntax of a WHERE clause in SQL You also have the Merge imported polygons option which is checked by default This option will merge imported polygons so overlapping polygons will be merged and therefore data simplified But in case of errors when importing shapefiles try to import them with this option unchecked The same way MapMaker will apply by default a simplification factor of 0 2 minutes to imported polygons This options can positively affect performance but if you really need to import data with a precision higher than this you can set simplification tolerance to zero If the imported Shapefile contains points that will be converted to samples a dialog box will be shown Set importation options for samples data Samples conversion Sample point size 100 Skip samples in 0 0 coordinates Make the sample habitat auto checked F Skip samples with same longitude and latitude coordinates Consider duplicated samples if they are equal until 4 th decimal X Select valid habitats for the species E XX Cancel Sea Land E All freshwaters T Lentic habitats Small Channels Small Ditches
277. ted invalidated But it will be stored and used in case you later modify a sample to make it as habitat auto checked e Use first and foremost data from existing maps when available to determine valid habitats for a species if the map for a species already exists in the database DataManager will look for data from this map samples and zone selections to determine which habitats are valid for this species If no map exists habitats selected above by the user will be used DataManager will download data and automatically transform it in ModestR maps storing them in the database You can configure the importation for adding downloaded samples to already existing maps if any or for overwriting existing maps After downloading you will see an Importation Log that includes a link to the information about the datasets that provided the downloaded data Importation log Save loo Heterodontus francisci Samples imported 141 coords 0 0 skipped 5 Valid habitats Sea Used datasets http www gbif org dataset 802df304 7762 11e1 a439 00145eb45e9a http www gbif org dataset fT0d00d00 aa57 4209 abaf be2aedGa7idd http wew gbif org dataset b6015b60 6706 4339 88e5 2741854e8r07 http www gbif org dataset 197908d0 5565 1108 b290 b8a03c50a862 http www gbiforg dataset 56caf05f 1364 4724 85f6 0c82520c2792 http www gbiforg dataset 8f79c802 a58c 447f 90aa 1dba0790825a http www gbif org dataset 7a25f7 aa 03fb 4322 aaeb 66719e1a9527 http
278. tep Next step is selecting the environmental variables that will be used to calculate Environmental Occurrence Of course in the ideal case you should select the variables that affect the most the species distribution Anyway you can always select most variables and ModestR will help you to choose the best ones in the next steps Next step allows you to optionally calculate Variance Inflation Factor VIF A VIF value higher than 30 is commonly considered an indicator of collinearity among the variables Thus you have the change choice of removing those variables significantly related and therefore that are redundant But this is an optional step If you just want to include all variables you can simply continue Take into account that if two variables are very highly correlated the way that one of them if a linear function of the other one VIF cannot be calculated Involved variables will be marked to allow you to remove one of them if you want 93 ModestR Software Environmental occurrence calculation 4 Selected Variables Depth Bathymetry Chla DA PAR DO Nitrate Cloud cover Calcite CDOM Colinearty analysis Press this button to calculate VIF Variance Inflation Factor of each variable You may consider removing vanables with an VIF gt 30 as it is commonly considered an indicador of high collinearity 2 Calculate Previous Continue gt Quick start tutorial In
279. tes in OpenStreetMaps or in GoogleMaps Those options will open a web browser and use GoogleMaps or OpenStreetMaps to show a marker in the exact coordinates where you clicked on 2 16 4 Encircling presence areas Another useful feature is encircling presence areas When you see a map in full extent or with low zoom level it is not always easy to visually localize small presence areas or samples in the map To help you doing this you can ask MapMaker to encircle presence areas using the button in the toolbar or the option View Circle presence zones in the main menu MapMaker will encircle all areas and samples of the map as shown in the figure making easy to visually locate all presence areas 67 ModestR Software Quick start tutorial rao pies Teku ol Hip Masao iG a oo ee Eg a ania c oe a m Bee Haji ar fa weed ft ol SR Peo a DESE T 2 16 5 Showing environmental data at mouse cursor If you have environmental variables integrated in ModestR see section 6 26 you can add some of them to be shown with coordinates on the mouse cursor when moving on the map To do that you can use the environmental variables selection button on the toolbar or the menu View show environmental variables at mouse and just select which variables to add in the tree that will be shown We recommend not to add more that 2 3 variables to avoid reducing performance Save this selection as de
280. th a precision of 10 160 ModestR Software Quick start tutorial ncols 30 nrows 12 xllcorner 120 ylicorner 0 cellsize 0 166666666666667 nodata_value 1 CECE ey eee ee ey Bees Wee ee es Dees es ye ee We Wes ee Be es es Bey es es E As the ESRI ASCII format does not support several pages if you select this output format and several metrics to be outputted you will be warned that one single ESRI ASCII file for each selected metric will be generated When exporting metrics such as richness in this format using the Export zero as NODATA checkbox you can select if a zero value for a cell will be exported as NODATA usually will not appear when showing the raster in a viewer or as zero will be shown as a zero value 6 18 Exporting variables contribution report The variables contribution report feature performs a statistical analysis for selecting those variables that are more affecting the most the distribution of one species or more species This analysis will be performed for each species the environmental variables selected are checked within the EOO or the full extent all the area where there are data for the selected variables of the species then an index of instability is calculated using the fluctuation index of Dubois 1973 modified by Guisande et al 2006 Once the instability index is calculated the percentage of contribution of each variable to the index is calculated Those environmental variables with a
281. that contains all the samples present on a map Areas cannot be took into account At least three samples are required to calculate convex hull As an example we ll assume we have a map with the samples shown below ModestR MapMaker New Map1 le File Edit Samples View Process Tools Options Help BESGEGh OR HO 2ODF ue Sr ui fLAeo Map a a Full Deta Level Aso Low Med High Highest 4 Map Tools Zoom Select Drag map Show dstance FreeHand Rectangle Add sample Edt sample Detail Level 1 Viewing from 178 5878 35 4137 to 98 94543 79 67474 Ready To calculate convex hull area for those samples just go to Mapping Hull transformation Convex hull menu item A dialog box will be shown where you can select the wanted feature Convex hull options Convex hull calculation options Perform Visual simulation Add as presence area Kaw Extent of occurrence EOO is defined by IUCN as the area contained within the shortest continuous imaginary boundary which can be drawn to encompass all the known inferred or projected sites of present occurrence of a taxon IUCN 2013 28 ModestR Software Quick start tutorial Visual simulation this option will just add a visual template to the map that shows the convex hull No modification is made on the map Visual templates can be deleted using the Edit Delete all visual templates option or the corresponding button of the toolbar How
282. the main file formats used by MRFinder to export data from species from a ModestR database Remember that some exportation defaults concerning CSV format can be set in the MRFinder default settings Several MRFinder exportation options are similar to some DataManager exportation features The difference is that MRFinder exportation options will be applied to species present in one specific area that can be additionally filtered as explained in section 4 8 while in DataManager you just select one taxonomy branch to be exported 8 1 Importing selections from Shapefiles In MRFinder you can import selections to search for species from shapefiles This is introduced in 4 4 You can import areas from files in ESRI Shapefile SHP format which is a widely used format in GIS software Currently only shapefiles containing polygons can be imported that is Polygon and PolygonZ type shapefiles Polygons will be converted to selections To import a shapefile go to File Import selection From shapefile menu After selecting the file to be imported a dialog box will be shown where you can see data contents from the shapefile to be imported See hide fieldlist Import ShapeFile Options ontained in the file Import file C ModestRProject BD Anoplogaster cornuta shp Operators Values gt Sample 0 A b utton lt Sample 1 lt gt Sample 2 Simplification tolerance in minutes 020 J Merge imported pe Sample 3
283. the next step you can select how validation will be done for each variable To do that you must select a variable on the left listbox The corresponding settings for this variables will be shown on the right up panel Before continuing it is interesting to point out that many of the options and settings that are displayed on this dialog box are autoexplained just by placing the mouse cursor on one element usually a short emerging explanation will be shown The available settings are Environmental occurrence calculation Variable Analysis Set ranges Hull Processing H Selected Variables VIF Depth Bathymetry 44 04 Ch a 9 08 DA 3 99 PAR DO Nitrate Cloud kover Calcite B CDOM Select the variable on the list to see its validation settings and basic information Vanable contribution analysis O Use always all selected vanables Select best variables for a contribution of 80 Variable contribution calculation mode E Full Extent Extent of Occurence Custom Validation HAM UM Allowed invalid m variables V Validation mode combo box O 00000000000000000000 O 00000000000000000000 Allowed missing 9 Vanables e Variable contribution analysis here you can select to always use selected variables to determine Environmental Occurrence or to perform a statistical analysis for selecting those variables that are more affecting the most the distribution of ea
284. there may be several ones and show to you this dialog box Import ShapeFile Options Import file C ModestRProjectiBDVWUCN data terrestial mammalsiTERRESTRIAL_MAMMALS NOV2013 shp Simplification tolerance in minutes 0 20 Merge imported polygons Optional filtering criteria eft blank to import all Use those same options for the next files Here you have the Merge imported polygons option This option will merge imported polygons for each species so overlapping polygons will be merged and therefore data simplified This option can cause errors when importing shapefiles that is why it is disabled by default The same way DataManager will not apply by default a simplification factor to imported polygons even if this options can positively affect performance If you are familiar with shapefile format you can also add importation criteria to filter which data will be imported To do that use the See hide fieldlist button to see the list of fields contained in the shapefile Import ShapeFile Options Import file C ModestRProjectiBD IUCN data terrestial Operators Values mammals TERRESTRIAL_MAMMALS_NOV2013 shp gt Abrocoma boliviensis lt Acerodon humilis on Acerodon jubatus Simplification tolerance in minutes 0 20 V Merge imported polygons S Acerodon leucotis g AND Acerodon mackloti i S i j Optional filtering criteria eft blank to import all legend al ee eee or
285. tion or the analog menu item of the tree contextual menu DataManager will add unique ID s for each occurrence as required by DwC format Exported format will contains headers for each column and a row for each sample from each map exported The format is based on the template provided by GBIF in http tools gbif org spreadsheet processor with 45 data fields for ocurrences but only some fields will be filed by DataManager which are e occurrencelD already explained above e class order family genus taxon names for those levels of the species e specificEpithet specific species name For example for Isurus paucus it will be paucus e infraspecificEpithet if you used subspecies at species level in the database this field will be the subspecies name For example for Acipenser oxyrinchus desotoi it will be desotoi If you used species names it will be empty For example for Isurus paucus it will be empty e scientificName full species name For example for Isurus paucus it will be Isurus paucus for Acipenser oxyrinchus desotoi it will be Acipenser oxyrinchus desotoi e taxonRank rank of the taxon associated to the samples It will be species by default but if DataManager detect a species name with three words it will use subspecies rank For example for Isurus paucus it will be species for Acipenser oxyrinchus desotoi it will be Acipens
286. tleast 25 1x1 minute blocks in cell 2 ee Habitat areas b Environmental Variables Set exportation zone boundaries gall Marine Cell coordinates ae Bathymetry Longitude ce l Calcite From longitude 180 o 18 aan B Fj ComM Right O Top J Cha From latitude 90 ti i Lett Bottom G Cloud cover hPa DA CSV Exportation options Depth Decimal separator 7 Field separator T Do if Nitrate Select habitats to include P FJa PAR W Sea W Land Prem pB Phosphate All freshwaters FG Poc F Lentic habitats W Small Channels Small Ditches W Small Drains Fl Salinity e E Si Small rivers W Large Channels W Large Ditches W Large Drains F Silicate F Large rivers Wetlands W Reservoirs ne e You can set the precision of the output adjusting the width in minutes of the cells that will be used If for example you select 5 cell width one metric value for each 5 x5 minutes cell on the world map will be generated e You can select which metrics will be in the output in the left selection tree o Richness the number of different species present in each cell of the selected dimensions This will be equivalent to a 0 1 presence matrix if you select only one species for the output ML sarea o Rarity index for each cell as CRI a aan where n is the richness of the cell and Area is the occupied area taking into account all the world of
287. tline Samples to include or just export presence areas as they Include only valid samples where added to the map ree D Include all samples KML files are widely recognized by GIS software and applications like GoogleMaps or GoogleEarth Anyway we have detected that some applications x Cancel la Ok have problems to correctly read and interpret KML files that contain very complex polygons In this case shapefiles seem to work better e To Shapefile this option is similar to the KML exportation excepted that you have to select exporting presence areas or samples Currently you cannot export both data to the same shapefile 7 8 Export presence areas to ASCrasters This option generates a raster in ASC format with the selected precision where the cells where the species is present have a value not null usually 1 but can be selected by the used This option is located in the menu File Export To ASC raster Export ASC raster options Select precision Precision 5 minutes ESRI ASCII options 7 9 Export environmental data clipped rasters This option allows exporting environmental data clipped to presence areas or visual templates It s explained in section 2 9 4 The exportation format is an ASC raster It is located in the menu File Export Environmental data A report in CSV format is also generated with data about clipped areas in km and simple Statistical measures max min mean std and
288. to be provided by the user as data files in ESRI ASCII or CSV format There exist free datasets available in Internet such as Bi Oracle for example that are fully compatible with ModestR 4 Futher information about Maxent software can be found in Steven J Phillips Miroslav Dud k 2008 Modeling of species distributions with Maxent new extensions and a comprehensive evaluation Ecography 31 2 161 175 DOI 10 1111 j 0906 7590 2008 5203 x 2 Tyberghein L Verbruggen H Pauly K Troupin C Minur F de Clerck O 2012 Bio ORACLE a global environmental dataset for marine species distribution modelling Global Ecology and Biogeog 21 272 281 20 ModestR Software Quick start tutorial Therefore the first step will be to integrate those data in ModestR to allow it to use them when needed To do that you can use the menu Layers Manage environmental variables either in MapMaker or in DataManager Details about how to integrate environmental data in ModestR are explained in section 6 26 Once environmental data has been made available to ModestR automatic data cleaning can be started using the menu Mapping Data Cleaning Automatic environmental based cleaning of MapMaker A dialog box like the shown below will appear Data Cleaning calculation Select Variables Set ranges Processing Select the vanables to calculate the Data Cleaning 3 Environmental Variables _ gall Dispersal capacity Marine
289. to select which samples apply to all only already valid ones only already invalid ones or none You can also select to add placemarks to validated invalidated samples to make easier localizing them on the map You can also select to validate areas of presence using the validation rule Use the Apply button to clean presence data according to the validation rule In this case if you selected to apply validation to samples samples located in a point where the rule is true will be set as valid Otherwise they will be set as invalid Nevertheless if a sample is dynamic as explained in previous section and it is invalid because of its habitat it will always remain invalid 27 ModestR Software Quick start tutorial An example of how results can look like is shown in section 2 6 above 2 8 Using hull transformations tools Hull transformations tools allows you to see add a hull as an area of presence to a map This feature can be used to estimate the Extent Of Occurrence EOO of a species ModestR provides three different hull transformations convex hull concave hull and density based hull Concave hull uses the alpha shape algorithm Density based hull uses a normal kernel smoothing algorithm Those features are mainly aimed to see add a hull calculated from sample data occurrences Therefore they commonly do not take into account presence areas other than Samples Convex hull transformation calculates a single minimal convex polygon
290. tood assuming a probability density based criterion a kernel density estimation is calculated for the polar coordinates system using the presence of the species The lowest density where the species is already present e g where there is a samples is used as cutoff Therefore all the areas with a density above this cutoff value will be considered as being part of the Niche Of Occurrence of the species In other words the Niche Of Occurrence of the species is composed of all the areas whose environmental conditions are near to those where the species is already present in a polar coordinates system environmental layer defined using a set of environmental variables This option is intended to be applied on sample based maps as range maps already include presence areas It also requires that you have an environmental layer already created as explained in section 2 11 You can use a previously stored environmental layer for example It is very important to point out that as seen before an environmental layer is built upon several environmental variables And to perform niche of occurrence those original environmental variables are needed besides the environmental layer itself Consequently to obtain accurate results those original environmental variables must still exist with the same names and data 17 Environmental Occurrence was formerly called Niche of Occurrence in previous versions of ModestR But from version 2 1 Niche o
291. tribution maps from shapefiles As explained in section 7 4 you can import a single shapefile to a distribution map in MapMaker But if you want to import a set of shapefiles or a single shapefile that contains distributions maps for several species this option can be laborious For this situation it can be more interesting to import shapefiles directly to a ModestR database using DataManager as it allows importing several distribution maps in a single operation Next we explain the steps to follow e First of all you have to have a ModestR database already created and containing the corresponding taxonomy with the species you want to import DataManager will only be able to import shapefiles that contain a data field that identifies the species names of the maps to be imported or alternatively to use filename as species name Those species names have to exactly match with existing species in the target ModestR DataManager cannot import distribution maps for species that don t yet exist in the ModestR database e Next go to Import Import Presence data From shapefiles menu option either in the main menu or in the contextual menu for any branch of the taxonomy In this latter case only species included in the selected branch will be imported whereas in the first case any species of the database will be imported e DataManager will warn about the fact that this task can modify the database and suggest doing a backup As imported data will OVERW
292. ts concerning many species such as richness metrics latitudinal gradients etc In this way DataManager is a very powerful tool to perform studies involving hundreds or thousands species in a very simple way In this section we ll briefly explain the main steps to work with DataManager 3 1 DataManager user interface DataManager user interface is easy to use When you open DataManager it will try to reopen the last used database if one Otherwise it simply show an empty panel Anyway you will see a window with a main menu and two main parts e Onthe left half a taxonomy tree where the taxonomic data in a tree view is displayed Of course if you don t open a database previously no information will be displayed here e On the right half a tab panel where initially a search and filtering page is displayed Other pages can be displayed in this tab panel depending on the features you use Quite all menus buttons and other elements have a tooltip that briefly explains their usage and that will be shown when you place the mouse over an element ModestR DataManager C ModestRProject BD Elasmobranchii DB ol fete File Edit Import Export Mapping Process Layers Tools Options Help 3 8 SE ibPEoe YLau Dataranave Database Taxonomy Classification Saif Elasmobranchii a Search Batoids i i Pristiformes Fites Rajiformes Show only branches with maps Show only species with maps Torpediniformes Show on
293. tutorial P Minded RataManager Coded RP njer EM Fleunckranchii GRF OB eae pol fama File Edi mpat Export Preece Opti Took Hep Detanase Tandy Caesticatan H Fasemcohrandhi CEF geamh Empty maps H Actinoptarvct Hig Fatos B Fastehranchi Results of the last cearch for empty maps U ij arapha Cherwdosebchus afian H rini Chioscylum dolgznow ge Sarcoptarg Chinscylom hesselts yg Sharks Here yin gels OeT ORL Jeter Hike hemninink F quatina tarqorabatodes Daphus fatina Kopheiethus confines Kopketethus mechergneus buno Fic boob roK Margate forse Hurnrets ghji Cargorantrnn ansiar vanh cublcspe 3 16 Forcing map updating to current map version As explained in section 3 6 above map processing is necessary to rasterize maps which in turn is necessary to calculate metrics and other summary data as well as to perform searchings with MRFinder Map processing is necessary when you add a new map to a ModestR database when you make modifications on a map or also when the reference world map that ModestR software uses is updated This last condition occurs usually because you installed an update distributed through the ModestR website When DataManager detects that a new version of the reference world map has been installed it will indicates that distribution maps have to be reprocessed to take into account changes in the new reference world map But sometimes you can be sure that some of the maps of your ModestR database
294. u ll have to select a visual template NOO will be calculated only within the bounds of this visual template o Extent of Occurrence selecting this option a right panel will appear where you ll have to select the EOO calculation method NOO will be calculated NOO only within the bounds of the EOO Extent of Occurrence of the species o Occupied river basins selecting this option a right panel will appear where you ll have to select a river basin level O higher 5 lower NOO will be calculated only within the bounds of the river basins of this level where there are samples of the species See 2 14 2 for more details of how ModestR determines the river basins occupied by a species e Exclude maps with less than X distinct samples maps will less than X samples will be skipped This option can be useful to skip maps that we consider that have too few data to calculate a meaningful NOO e Export density maps as images enabling this option a NOO density map of each species to be processed will be generated and exported to an image file This image corresponds to the Density map option explained in MapMaker see 2 13 Image files will be saved in a folder you will have to select in the next step e Make a copy of the database and apply on it as NOO involves irreversible map modification it can be prudent to make a copy of the database before performing this transformation Checking this option DataManager will ask you for a destination folder an
295. uplicates if enabled only distinct samples usually considered until the 5 decimal will be used to calculate kernel density This avoids biasing density because there are many duplicates of some samples e Smoothing smoothing factor determines how smooth the density matrix will be The greater it is the more the density will soread out far around presence areas Default factor x1 has been adjusted to return a density area with a standard deviation of the distances between cells of the presence areas near the original standard deviation of the distances between samples e Maps to include you can select to include all maps or only sample maps maps that only contain samples but no presence areas You should take into account that density hull can only be calculated on samples but not on areas So if you select to include all maps only the samples of those maps will be used to calculate hull Therefore maps without samples will be excluded e Create a copy of the database as hull transformation involves irreversible map modification it can be prudent to make a copy of the database before performing this transformation Checking this option DataManager will ask you for a destination folder and file and will do this backup copy before modifying maps 87 ModestR Software Quick start tutorial Hull area that will be added to the map will use as valid habitats the same ones that are currently accepted in the map For example if you apply
296. using the File Export menu options When exporting presence areas using this option you should take into account that presence areas are actually stored in a different way than they are displayed in the map For example when the user selects a zone and then selects the Sea habitat to fill in this selection land part will not be filled But the data exported by default will be the coordinates of the zone selected by the user not the exact zone filled To export presence areas clipped to the coastline either for land or sea areas you should select the corresponding option which is available when exporting to KML or shapefile Two precision levels are proposed medium and high Medium precision is faster and quite precise when working with large areas For an exact clipping to coastline you can use the high precision option but this can require a very long time Samples in turn will be exported using their exact coordinates Only valid samples will be exported The exportation formats you can select are 180 ModestR Software Quick start tutorial e To CSV you can export to this format either presence areas or samples See section 6 14 for details of the output formats e To KML in this case a KML file will be generated with polygons corresponding KML export options to the presence areas and placemarks a AE EA for samples As explained before you can F Cip to coastine Medium precision select to clip presence areas to coas
297. ut this setting provides a way to be more flexible For example you can select 10 22 Chapman A D 2005 Principles and Methods of Data Cleaning Primary Species and Species Occurrence Data version 1 0 Report for the Global Biodiversity Information Facility Copenhagen Available online at http Awww gpbif org orc doc_ id 1262 91 ModestR Software Quick start tutorial variables and allow that up to two variables of these take outlier values before considering a sample area as invalid Allowed missing variables Indicates how many variables can be missing have a null value before considering an area or sample as invalid for the species By default it will be set to N where N is the number of selected variables That is if all variables have null values for a sample area the area will be considered as valid Take into account that this parameter will be applied only if the variables with missing values are not individually configured as directly invalidating an area when their value is missing as explained above That is this rule will be applied only if after applying the rules for each individual variable the sample area has not already been considered as invalid Cleaning options in this tab page you have to select which samples and areas apply to all only already valid ones only already invalid ones or none You can also select to add placemarks to validated invalidated samples to make easier localizing them on the map Thi
298. variable This name will be shown in the tree Type a descriptive type for the variable This type will appear in the tree as the upper level The variable will appear hanging from it Use types to classify and group variables by some criteria that can make easier to find them Description Short description of the variable This description will appear when selecting the variables in the tree Enter a description that makes easy to understand what the variable is Short Name a short 3 4 characters to name the variable This name will be used in MapMaker when adding an environmental variable to be shown at the mouse cursor on the map Units this optional field allows entering the measuring units for the variable i e Km C mol l etc This will be used in MapMaker when adding an environmental variable to be shown at the mouse cursor on the map File the file associated to the variable This file has to contain data for the variable usually for all the world Use the Se ect button to select a file Format select the format of the variable data CSV or ESRI ASC If you select CSV settings the variable is intended to be stored in a CSV in matrix form where rows correspond to longitudes and columns to latitudes Data have to be arranged in the way that top left corner corresponds to the maximum latitude typically 902 and the minimum longitude typically 1802 For this format you have to indicate the following fields o Cell siz
299. vel are also mentioned in the phyloXMLL file or if the genus level already exists in the target ModestR database 6 4 Importing taxonomy from ITIS database As explained in section 3 17 DataManager provides a tool to browse and extract data from ITIS taxonomic database to a CSV file This CSV file can be directly imported to a ModestR database as explained in section 6 1 141 ModestR Software Quick start tutorial 6 5 Importing Map Files from MapMaker map files You can import map files to the currently opened ModestR database using the mport Import presence data From standalone map files menu option Asimilar option but limiting the species to be imported to a specific branch of the taxonomic tree can be found in the contextual menu clicking with left mouse button on the desired element of the tree selecting the option mport presence data for this branch From standalone map files ModestR DataManager can import map files generated with MapMaker and saved as standalone map files files with PMMAC extension This option will ask the user for selecting a folder and it will import all map files from this folder to the currently opened database Maps to be imported must contain taxonomic information at least the species name and the species assigned to the map has to already exist in the target ModestR database 6 6 Importing Map Files from another ModestR database You can import map files to the currently opened ModestR database usi
300. vironmental Occurrence to this branch on the main menu or Mapping features Apply Environmental Occurrence to this branch on the contextual menu of the tree node The first step is selecting the range calculation Environmental occurrence calculation for the environmental occurrence and the EOO Range calculati mode There are two options for the range ii Full tent Extent of Occurence e Full extent the environmental Select the variables to be used to calculate the Environmental occurrence occurrence will be calculated for all Environmental Variables SOE Marine b Bathymetry available environmental data For example if you use environmental variables that contain data for all the world the environmental occurrence will be calculated for all the world If you use environmental variables that contain data for a single country the environmental occurrence will be calculated for this country EOO Extent of environmental occurrence be calculated only for the area contained in the EOO of the species This EOO occurrence will Calcite CDOM Chla Cloud cover DA Depth DO Nitrate PAR pH Phosphate POC Salinity Silicate Temperature GE Terrestrial Fg Altitude Altitude 6 6 Altitude Aspect will be calculated according to the settings you have to enter in a later s
301. vironmental data needed to use this features are not included in ModestR so they have to be provided by the user as data files in ESRI ASCII or CSV format There exist free datasets available in Internet such as Bi Oracle for example that are fully compatible with ModestR Therefore the first step will be to integrate those data in ModestR to allow it to use them when needed To do that you can use the menu Layers Manage environmental variables either in MapMaker or in DataManager Details about how to integrate environmental data in ModestR are explained in section 6 26 Then you can easily add one environmental variable to the map using the MapMaker menu item Layers Raster templates Add environmental raster template or the corresponding button of the toolbar A dialog box will show to you the available variables You can select only one variable it should be visually confusing to show more than one You can also select if the raster has to be shown only on sea or o land habitat or on both Select variable to be shown as raster Options a g Environmental Variables paN g Marine E Apply logarthm function to data a Bathymetry Calcite id Chlorophyll a Sea surface temperature Apply on habitat Silicate All lal Salinity Only sea i Phosphate _ P pH Only land PE PAR Mia Nitrate Cloud cover G Dissolved oxygen 0 gt Transparency M Diffuse attenuation Fj Poc F cpom BathymetryBis
302. with areas so it is mainly useful in sample maps At least four samples are required to calculate alpha shape but depending on their relative distances it can be impossible to calculate a not null alpha shape As an example we ll assume we have a map with the samples shown below Lat 24 67367 Lon 38 80027 ym 61 52311 29 6976 to 58 3263 36 90842 Ready 10 Edelsbrunner H amp M cke E P 1994 Three dimensional alpha shapes ACM Trans Graph 13 1 43 72 30 ModestR Software Quick start tutorial To calculate concave hull area using the alpha shape for those samples just go to Mapping Hull transformation Alpha shape menu option A dialog box will be shown where you can select the wanted feature Alpha shape options Parameters Alpha value degrees Perform Visual simulation Add as presence area XK cose e Alpha value this value is the main parameter we have to provide to the alpha shape algorithm e Visual simulation this option will just add a visual template to the map that shows the alpha shape hull No modification is made on the map Visual templates can be deleted using the Edit Delete all visual templates option or the corresponding button of the toolbar However visual templates are not saved with the map For the example map above and an alpha of 6 degrees this will be the result 31 ModestR Software Quick start tutorial As you can see alpha shape
303. wm B Ateleopodiformes Map data cleaning Beryciformes Cetomimiformes Correctly transformed species TELLIT Lampriformes Lophiiformes Myctophiformes Notacanthiformes Polymixiiformes Saccopharyngiformes Stephanoberyciformes Stomiiformes H Zeiformes Batoids Elasmobranchii Holocephali Myxini Sarcopterygii Sharks Melamphaes acanthomus Melamphaes ebelingi Melamphaes eulepis Melamphaes hubbsi Melamphaes indicus Melamphaes longivelis Melamphaes lugubris Not transformed species Species Gibberichthys latifrons Gibberichthys pumilus Hispidoberyx ambagiosus Melmnhaes danas Problem All variables are within ranges Nothing to All variables are within ranges Nothing to All variables are within ranges Nothing to All variahlac are within rannas Nothinn ta 92 ModestR Software Quick start tutorial 3 11 Applying Environmental Occurrence Environmental Occurrence rudiments have been explained in section 2 9 where MapMaker Environmental Occurrence feature was detailed We suggest you to do some tests in MapMaker where results are instantly visible to understand how Environmental Occurrence works In DataManager you can apply Environmental Occurrence to any taxonomic group of species in a single step To do that select first the tree node you want to apply Environmental Occurrence to all the database a single class order etc Then select Mapping Apply En
304. works its limitations and to properly interpret results obtained with ModestR e ModestR types of maps ModestR supports three types of presence maps o Sample maps or maps based on occurrence records Each sample is basically a pair of longitude and latitude coordinates that identify a location where a species is present Being a point area of a sample cannot be accurately evaluated Therefore in terms of presence area calculation ModestR makes a simple assumption considering that the area of sample equals the area of the cell of 1 x1 where it is located But that this is just a convenient assumption and not an accurate value Other areas calculated from sample maps such as Extent of Occurrence area using convex hull or alpha shape will be accurately calculated as they are polygons but not just points o Range or area maps range or area maps are maps where species presence is demarcated by polygons or areas In this case areas can be accurately calculated ModestR Software Quick start tutorial after dividing them in small cells with a precision of 1 x1 Being more complex range maps require more computing time to be processed by ModestR o Mixt maps ModestR supports maps that mix samples and areas even if we don t encourage this option as this makes more complex to process maps and more difficult to correctly interpreting results Anyway ModestR will generally handle mixt maps the same way than area maps e ModestR
305. x will be shown where the list of currently stored environmental layers is displayed You should select the layer you want to use for NOO and click on Continue Environmental niche calculation Select the environmental layer be used to calculate niche Africa 04 10 2014 ejemplo manual 15 01 2015 Espa a 05 10 2014 Name Mar 2 vars o H Sudamerica 2 vars 09 09 2014 Enter a layer description Terrestrial layer 03 09 2014 Terrestrial layer P 03 09 2014 Layer settings Included variables Layer name Creation time Name and Descript Polar space Data Color scale Bathymetry Depth In the next step the options dialog box is shown The parameters you can set are e Smoothing factor determines how smooth the density matrix will be The greater it is the more the density will spread out far around presence areas Default factor is x1 e Allow a tolerance of X Apply a of tolerance on the potential areas of presence to consider them as valid with regard to the range between min and max values for each environmental variable involved in the currently selected environmental layer in the presence data of the species e Range determines the range or maximal area for which NOO will be calculated Options are o Fulllayer to calculate NOO for all the area covered by the currently selected environmental layer Environmental niche calculation Range and parameters cessing Envi
306. xpo right mouse button Export taxonomy of this branch Import samples from GBIF for this branch 18 For test purposes you can also download a sample ModestR database from the Modestr website TThere are some examples available in the section Download Data files of the website 76 ModestR Software Quick start tutorial In this way you can add child nodes at the different levels of the taxonomic tree but of course is a quite tedious option b Import taxonomic data from a CSV file the most recommended a phyloXML file or another ModestR database This option allows you to import existing data maybe previously exported from other databases or catalogs The accepted import formats are explained in sections 6 1 6 2 6 3 This is the preferred way to easily populate a ModestR database with your already existing data For test purposes you can find a CSV file with a comprehensive taxonomy of fishes ready to be imported to DataManager in the ModestR website in the website go to section He p amp Doc and search for the Sample file Ipez csv c Import taxonomic data from ITIS database http www itis gov This option is explained in section 3 17 If you only have a list of species that you want to import to a database but not the corresponding higher levels class order etc you can be interested in the taxonomy search tool integrated in DataManager explained in 3 18 Nodes can also be cut and pasted deleted or renamed u
307. xporting taxonomy to a CSV file You can export taxonomic data of any branch of a DataManager database using the Export Export taxonomy of selected branch menu option You will see two options to export data to a CSV file in two different formats e ToaCSV flat file data will be exported to a CSV file using the field delimited selected in the preferences Options Preferences menu First row will contain headers Each 151 ModestR Software Quick start tutorial data row will contain the class order family genus and species in this order The Map exists column indicates with a 1 or a zero value if there is a map in the database for this species or not respectively Here is an example Class Order Family Genus Species Map exists Mammalia Carnivora Ailuridae Ailurus Ailurus fulgens Mammalia Carnivora Canidae Alopex Alopex lagopus Mammalia Carnivora Canidae Atelocynus Atelocynus microtis Mammalia Carnivora Canidae Canis Canis aureus Mammalia Carnivora Canidae Canis Canis latrans 1 1 1 Mammalia Carnivora Canidae Canis Canis adustus 1 1 1 1 Mammalia Carnivora Canidae Canis Canis mesomelas e Toa structured CSV file data will be exported to a CSV file using the field delimited selected in the preferences Options Preferences menu First row will contain headers Next row will contain a class Next row will contain an order of this class and so on until species level Once listed all species of a genus next genus will be
308. y Ner pig Eere S E 119 4 8 2 Rare species filter DAG Ci 2s2ctscsecadacacsassoedscaunoedacaimoiuancieaiacaneuaisiecexatseeaenneemreass 120 4 8 3 B S a EEE a Oc 21 ee en E E A EAN A A AA E 121 4 8 4 Color map and filter clearing ccccccceseccccesscceceesececseececeeeceeeeusecessusecetsuneess 122 4 9 Generating and exporting data cccccescccssecccssececsscecescecenecesenecesenceseeeceseuecensueeenens 122 4 10 Selections ECITOM cccccccssssssssesccceccccnssscecccces Gl eie EEE EEE 123 4 11 Managing user predefined selections ccccccesccccssseccccsececcescceeeesececeueceeseneceeeeees 124 4 12 Other tools eosssssssennssssesserenssssereeensn M nnna MQMMMCssssesccccecsceasseseccceesseaassees 129 4 12 1 Simplifying selections MET AQMD orveneusarcncassrenvensrsens 129 4 12 2 Merging selections c ccccc0c E n aeeoea ee O noanean 130 4 12 3 Raster data clipping w CET O 130 4 12 4 Calculating areas for SCIOCTIONS ccccccesseccccesecccceesecccsusececeueceeeeeeceeseneeeeeas 130 4 12 5 Export Selections A C MMMM cs vaesrccrenersercusarensarsrenvanersens 131 5 First steps in DARPA PIB 0 0 05s AMEN occ eM occccccccscsessssesescscecececccsess 132 5 1 Creating a Map IN MRMapping ccccceccssccsseccscceseceseccseccseccaeeseecseeeeesseeseeesseeeeeees 132 el Ore INS TOP a O 135 5 2 PNANGING NTA TINGS 0 RMD
309. y set And b manually validated samples will be took into account when 19 ModestR Software Quick start tutorial calculating data presence or richness for example while invalidated one will be stored with the map but not took into account for any calculation e Setsamples as habitat auto checked if you added or modified samples setting them as manually validated unvalidated you may want to reset them as habitat auto checked this way MapMaker will automatically check their validity regarding the valid habitats they have associated To do that you can select an area that contains the samples you want to modify using the Freehand or the Rectangle tools from the left tool panel and then use the context menu item Selected samples Set as dynamic samples pressing the right mouse button to show it To make all samples of the map to be dynamic use the option in the Samples menu of the main menu e Modify samples valid habitats you may have downloaded or imported sample data and added them to the map indicating some habitats as valid but now you want to modify this selection for example to add more freshwater habitats as valid for a species To do that just go to the Samples Modify samples valid habitats in the main menu 2 5 Importing data to a MapMaker map Besides importing samples from GBIF or CSV files as explained below MapMaker can also import existing maps or data from other sources such as distribution models generated with Max
310. y visible samples will be deleted 4 Show Detail Level 1 Viewing from 118 7569 7 395771 to 48 28186 46 5621 Ready Zoom Modify samples marker size to modify the size of the visual point that will indicate a sample in the map you can select an area that contains the samples you want to modify using the Freehand or the Rectangle tools from the left tool panel and then use the context menu item Selected samples Set size pressing the right mouse button to show it To modify the size of all samples of the map use the Samples Modify samples marker size in the main menu Remember that this size has no importance when processing map It is only a visual parameter Validate unvalidate samples if you want to manually validate or invalidate samples either dynamic samples or not you can select an area that contains the samples you want to modify using the Freehand or the Rectangle tools from the left tool panel and then use the context menu item Selected samples pressing the right mouse button to show it You will find options to validate unvalidate all selected samples or only those that are valid invalid To validate unvalidate all samples of the map use the options in the Samples menu of the main menu Remember that if you manually validate or invalidate samples this has two side effects a samples become not habitat auto checked So they will not be checked anymore but keep the valid invalid status you manuall

User`s Manual

Contents

Download Pdf Manuals

Related Search

Related Contents