AEGRO Workpackage 10: Documentation for genetic reserve
Contents
1. 8 Retain state for Element Number List The Element Number List now supports Retain state in the same way as Element Lists do 3 New property Retain state which allows the state of a screen to be retained between sightings 4 New property Save result which allows a screen to be used for navigation only purposes without affecting the data in a sighting CT http www cybertracker co za http www steventonconsulting com CyberTracker aspx Y Projekte AEGRO Berichte Final F Annex 2010 02 03_14 06 26_Cybertracker2009 doc 162. individuals of different species or make more detailed monitoring on a single species basis within the plot Fig 10b Geo referencing can be done by geo referencing one or few fixed reference points e g the four edges of a plot or recording the margins of the plot A small number of reference points we would prefer in ordinary field experiments with regularly shaped plots Only the preferred method is currently available for plots Fig 10 c Geo referencing outlines may be necessary for irregularly shaped plots e g due to the agglomeration of plants These should be better referred to as patches see below Y Projekte AEGRO Berichte Final F Annex 2010 02 03_14 06 26_Cybertracker2009 doc 5 Working document C Germeier C H hne amp L Frese January 2010 MonitoringPlot Action Target ReferencePoints MonitoringT arget fais Georeference Plot Designation Dpparian 001 Plot Count species in plot Single Species Monitoring Desciphion points to bridge Control Start new site Click white arrow to save and MonitoringPlot fale ReferencePoints atts Status Start new location Plot length m enter a further reference point Use back to go for a new plot Click black arrow to save and Plot width m reusing your previous inputs d ee other actions Click next to return without saving 4 gt 1 gt amp A AVAR E a Define monitoring plot b Actions within a plot c Record reference points Fig 10 Define and geo refer
3. A O SiteDescription Northern margin of an l Distance 10 Direction Siw i a Controls for GPS and save b Check GPS c Check inputs Fig 8 Record GPS position for a site and save it Actionlype l o l You can check your GPS Fig 8b by clicking the triangle The already entered data Fig 8c you can check by clicking the black circle A click to the black arrow saves the entered information and leads you back to enter another site Fig 6 a The white arrow saves your information and leaves you at the screen and you can continue with next to choose between three actions at a site or return for a new site or location Fig 9 Define and geo reference a monitoring plot for repeated observations during a survey Fig 10 Count species in a transect Fig 11 More detailed monitoring on a single species basis Fig 13 b which are observation of patches demographic monitoring census and individual monitoring and sampling 4 gt Fig 9 Choice between actions at a site Use case 1 Define and geo reference monitoring plots A plot is normally identified by its position in an experimental field design matrix lane plot The counters Fig 10 a can be changed by a click Plot size parameters are documented to facilitate area related quantitative calculations and indicate the status of the plot in the survey e g control treated etc After having input this information you can choose to geo reference the plot count the
4. a Y Projekte AEGRO Berichte Final F Annex 2010 02 03_14 06 26_Cybertracker2009 doc 8 Working document Census Navigation CensusNavigation gle Count individuals PlotStatus PlotLength Plot width Lane Plot C Germeier C H hne amp L Frese Control 25 10 1 2 January 2010 CohortCount CohortCount fagis Single Species Moni Genus Avena Species murphyi Patch Monitoring Length 12 Width 4 Patchld 1 000000 Shape Ellipsoid g Density scattered b Check background a Select method c Check background patch Fig 16 Demographic monitoring Please assure with the black circle background data that a respective plot or patch has been defined or entered and the correct species selected before Fig 16 b Numbers indicating respective counts or percentages can be selected from the radio lists Fig 16 c With the white arrow you save and return to the previous screen Fig 16 a From there you can use the back button to return to the previously entered patch Fig 14b or plot Fig 13c e g for additional individual sampling Use case 5 Individual monitoring sampling individual Individual Help a U ER Disease Individuals are identified individual number characterised by sex stage and general condition e g abiotic stress pests or diseases and geo referenced You can give additional information in the comment field In case of stresses pests and diseases it woul
5. and save with ok With a click to start you get to the GPS timer Fig 2 15 minutes The time choice determines how long the GPS is allowed to search for a signal until a measurement is taken and recorded in the database Fig 2 The time between start and end of the GPS measurement is displayed by CyberTracker as O 100 completed Fig 2 Set GPS Timer Before starting the monitoring in the survey some general ee raphe information should be entered These are the ee CE Ee Ee ea administrative unit country state region province district nformatior nearest village or town the name of the protected area if you are monitoring in a protected area and some details of the site On the screen shown in Fig 3 you can choose between these options In surveys covering a broad geographic range like the AEGRO crop case studies or other prospective missions visiting various areas and sites acquisition of this general information needs to be done in the field tool In case of monitoring by the protected area management only for one area these settings are constant for all surveys and can be recalled with each login of a registered user before uploading survey data Datalype Fig 3 Choose which type of data you want to enter B Documentation of administrative unit and protected area where the survey is made This is necessary to easily identify the political administrative unit and if applicable the protected area
6. observations In case of high density the species completely covers the ground what would be normally expected for a patch The length is the longest extension of the patch the width the shortest usually orthogonal one Next gets you to a screen shown in Fig 14 b where to choose actions to be done within a patch geo referencing demographic monitoring and individual sampling The preferred method to geo reference irregularly shaped patches will be to geo reference the whole outline of a patch Therefore you activate the GPS Timer Fig 15 with the white arrow It 1s stopped with the black arrow The option geo reference fixed points is similar to the same procedure w A V lt 4 gt for monitoring plots Fig 10 c Fig 15 Start timer to record outline of a patch Use case 4 Demographic monitoring census A demographic census observing the number or percentage of different development stages of plants can be made on a plot or patch basis even patches may be observed within plots Fig 16 b In a plot it starts from single species monitoring and demographic monitoring cf Figs 9 b 13 b in a patch from demographic monitoring Fig 14 b The census is based on four cohorts seedling juvenile plants before flowering flowering plants and senescent plants after flowering Absolute numbers of individuals can be counted or percentages estimated First decide which method counting or estimation you want to use Fig 16
7. says you are How does the Element Formula control work The formula property is a regular expression meaning it can hold expressions like 1 2 If you set the formula to this the output will be 3 However there is also support for more complex expressions 1 A 2 where A is the number value of the Elements in the Element A property 2 1 2 3 works because parentheses are supported 3 max 1 2 produces 2 and min 1 2 produces 1 4 abs 5 produces 5 5 Today works with the Output as date property Today 1 is yesterday 6 date 2007 5 20 produces a date see 5 7 1f 1 lt 2 3 5 produces 3 8 if 1 gt 2 3 5 1 produces 6 You can place the result of the calculation in the Result element which will then become part of the sighting data If you put the result into a global value using the Result global value property then you can later reuse that value in the formula itself This provides the ability to do counters Try this Y Projekte AEGRO Berichte Final F Annex 2010 02 03_14 06 26_Cybertracker2009 doc 15 Working document C Germeier C H hne amp L Frese January 2010 On screen 1 drop an Element Formula control Set the Formula property to Test 1 Set the Result global value property to Test Now everytime you save and return to this screen the number will automatically increment http www cybertracker org CyberTracker 20Change 20History pdf
8. Working document C Germeier C H hne amp L Frese January 2010 AEGRO Workpackage 10 D10 7 A CyberTracker application to gather data for in situ baseline monitoring User Manual Introduction In the previous reporting period it was decided to use CyberTracker for the implementation of field tools operating on mobile data acquisition devices A pilot application has been developed and first tests have been made in the Beta case crop study A description of the survey tool used is available from http aegro bafz de uploads tx_neofileshare 2008 05 27_10 33 31_cybertracker260508 doc Five use cases have been identified to generate demographic and genetic baselines for crop wild relatives in situ 1 Define monitoring plots A plot is geographically localised described and documented for continued monitoring to control the success of management plans 2 Count individuals species wise in plots or transects 3 Define patches A patch is an agglomeration of individuals of a certain plant species It is geographically localised described and documented for continuing monitoring 4 Demographic monitoring census An occurrence is geographically described within a plot or patch see previous case cases and the demographic status number or percentage of individuals in certain age cohorts is observed This can be done on a patch or a plot level 5 Individual monitoring sampling An occurrence is geographically described Individuals are
9. ack feature sets up a timer that takes a GPS reading at fixed intervals You can customize how long those intervals are from 1 second up The track system internally has 2 separate modes of operation short interval and long interval For short intervals 60 seconds or less the device is prevented from going to sleep on it s own and the GPS is left permanently connected For long intervals more than 60 seconds the device can be shut down and the alarm system will be used to wake it up take a reading and shut it down again How can I edit my timer tracks There is no support in the CyberTracker UI for track editing However since the CyberTracker database is a Microsoft Access MDB file you can open it and modify the Waypoint2 table directly How do I make the screen state persist between sightings e g so a list keeps it s selection Several controls allow you to persist their state by using their Retain state property You will need the Studio version to change this property Click the Lock toolbar button in Sequences mode select the control and check that property What does the GPS Accuracy number mean Accuracy is a number that the GPS provides to give some idea of the uncertainty of the reading This number ranges from 0 to 50 and should typically be multiplied by 10 meters 32 feet to get an idea of the area you are dealing with For example a value of 3 5 means that the GPS knows you are within 35 meters of where it
10. d be useful to refer to the agent When the save button white arrow is pressed then the GPS signal for this particular plant is measured and recorded in the database The counter for the individual number automatically proceeds to the following one Information in the radio lists is obligatory You cannot proceed without having selected one female monoecious 45 Puccinia coronata Fig 17 Document and geo reference individuals Y Projekte AEGRO Berichte Final F Annex 2010 02 03_14 06 26_Cybertracker2009 doc 9 Working document C Germeier C H hne amp L Frese January 2010 Summary of the screen flows in flow diagrams Welcome Datalype Acquire general geographic inforn General geographic information NUTS LAU Protected Area i OU Action Type Define monitoring plot Monitoring arget fa Ga l r NAI Fig 18 a Flow diagram of complete application general information single species monitoring Y Projekte AEGRO Berichte Final F Annex 2010 02 03_14 06 26_Cybertracker2009 doc 10 Working document C Germeier C H hne amp L Frese January 2010 PatchMonitoring MonitoringT arget Help Fig 18 b Flow diagram of complete application single species monitoring Datalype A Acquire general geographic inform Actionlype Fig 19 Flow diagram of recording sites and general geographic information Y Projekte AEGRO Berichte Final F Annex 2010 02 03_14 06 26_Cybert
11. ence a monitoring plot You can enter the designation of a reference point e g geometric position in the plot a description of the point facilitating revisit and record GPS position with the white arrow which leaves you in this screen for recording a further reference point With the black arrow you get back for choosing other actions in the plot Fig 10 b You can check your GPS with the triangle and your background data with the circle Next brings you back without saving a GPS record Use case 2 Count individuals species wise in plots or transects To monitor biodiversity on a taxon level for one or more genera crop groups individuals can be counted in plots or transects Fig 11 shows screens used to count species in a plot The first screen Fig 11 a for choosing the crop group genus is opened from the second selection in Fig 10 b You choose a genus and open a list of species with next p elp All Sightings damascena 000 Distance 10 fatua 005 Direction Sw hinila 000 Elevation 345 Slope 5 insularis 001 LandElement Lower slope longiglumis 010 Soil Clay Silt Action Define monitoring plot ludoviciana 022 Plots 7 Choose a genus and next to otstatus ontro count respective species macrostachya 000 PlotLength Oe Use back to do other g tane 1 observations in this plot or to go murphyi 005 Plot 5 for a new plot transect E ee Count species in plol 4 3 EA 4 Genus Avena a Choose a genus b Enter counts fo
12. located geo referenced and samples are taken from them for genetic analysis These are illustrated by screenshots from the revised CYBERTRACKER AEGRO2010 MDB application Acquisition of general information All use cases have in common a need for general geographic and project information A User and survey identification The start screen Fig 1 requires entering your name and an identifier of the survey you are to perform Both observer name and survey identifier are required You cannot proceed without having Text Editor ok Welcome ESP2010AvenaAEGRO 3 tart TENS Crop Wild Relatives Crop Wild Relatives Welcome 2010 2010 Observer Name Observer Name Text is required Andreas Katsiotis survey Identifier gt gt Fig la Enter name and survey identifier Fig 1b these are required Tap to Edit Y Projekte AEGRO Berichte Final F Annex 2010 02 03_14 06 26_Cybertracker2009 doc 1 Working document C Germeier C H hne amp L Frese January 2010 input these data Fig 1 b A survey is a set of observations taken Set GPS Timer for a certain purpose and as a unit for evaluations and P calculations We recommend a survey identifier containing country year target crop project acronym e g 5seconds AA ESP2010AvenaAEGRO in the indicated sequence to optimize 30 seconds sorting On tap to a text field a text editor opens There you enter 2minutes A information
13. on revisiting if a recorded patch area overlaps with a previously recorded one they are considered the same patch After fusion one of them is considered successor of both Like a plot a patch can be described in shape and size and or geo referenced Due to mostly irregular shape the most exact way to geo reference a patch would be to take coordinates around its entire margins Patches are documented from single species monitoring Fig 9 then choosing genus species Fig 13 a and patch monitoring Fig 13 b Monitoring Type murphyi a Choose genus and species b Choose patch monitoring Fig 13 Start patch monitoring Y Projekte AEGRO Berichte Final F Annex 2010 02 03_14 06 26_Cybertracker2009 doc 7 Working document C Germeier C H hne amp L Frese January 2010 PatchMonitoring GeoReferencingProcedure GeoReferencingProcedure Help sid Patch Help MonitoringT arget onitoringT arget falas Geo reference outline ape Circular scattered Ellipsoid Rectangular medium Radiating fhion regut q gt 4 gt a Input patch information b Actions in patches c Geo referencing methods Fig 14 Describe patches The patch number is an automatic counter while shape and StatGPSTimer density have to be selected and size parameters entered Plants can be scattered or of low density within a patch in these cases it is questionable to speak of a patch and may be preferable to make individual
14. r the species c Check background info Fig 11 Count species within a monitoring plot Y Projekte AEGRO Berichte Final F Annex 2010 02 03_14 06 26_Cybertracker2009 doc 6 Working document C Germeier C H hne amp L Frese January 2010 Here you can enter species counts by click to the digits Fig 11b Again you can check all background information you Transect Halis have already collected Fig 11 c with the black circle You can save with the black arrow which leads you back to the list of genera for choosing another one Fig 11 a With back you come from there to the screen for choosing another action Fig 10 b A further back will bring you again to the plot description and you can define another plot reusing your inputs An alternative would be to count species along a transect With the screen shown in Fig 12 you can define a transect enter identifying number and length and GPS record start and end points You record a start point with the white arrow With next you get to the screens to select a genus and count species cf Fig 11 a b After leaving there you use the back button from Fig lla to come back to the transect i A it 4 b screen Do not forget to geo reference the end point with the ee ey NF white arrow before starting a new transect or another action Fig 12 Define and geo reference a transect Transect Use case 3 Describe patches We call a patch an agglomeration of plants of the same species
15. racker2009 doc 11 Working document C Germeier C H hne amp L Frese January 2010 La Actionlype Action Target Monitoring arget fafa b sy Reference points _ Fig 20 Flow diagram for the definition monitoring plots o Action ype Monitoring arget ias T Fig 21 Flow diagram of counting species occurrences in plots and transects Y Projekte AEGRO Berichte Final F Annex 2010 02 03_14 06 26_Cybertracker2009 doc Working document C Germeier C H hne amp L Frese January 2010 o N Action I arget Monitoring arget fatale La Actionlype lt Select taxon Monitoringlype Fig 22 Flow diagram for preparation of single species monitoring PatchMonitoring MonitoringT arget Help gt _ Fig 23 Flow diagram of patch recording Y Projekte AEGRO Berichte Final F Annex 2010 02 03_14 06 26_Cybertracker2009 doc 13 Working document C Germeier C H hne amp L Frese January 2010 Fig 24 Flow diagram of individual monitoring Monitoring Type PatchMonitoring MonitoringT arget Help lt gt Fig 25 Flow diagram of demographic monitoring in plots or patches Y Projekte AEGRO Berichte Final F Annex 2010 02 03_14 06 26_Cybertracker2009 doc 14 Working document C Germeier C H hne amp L Frese January 2010 http www steventonconsulting com CyberTrackerFAQ aspx What are timer tracks The timer tr
16. tion66 c Quantitative qualifiers Fig 6 Enter site information You can enter additional information you consider important in a description field Note that information about distance and direction from the next settlement LAU2 is requested in the next screen Fig 6 c and must not be duplicated in the site description Distance means the distance from the next named settlement village or town LAU2 which has been selected before see Fig 5a The same applies for the direction The elevation measured by an altimeter and the slope of the surface can be entered as well Land elements and soil types for a minimal ecological site description can be selected in the next two screens Fig 7 This will lead you into a screen for recording the GPS signal Fig 8 LandElement Soillexture Lower slope a Land elements b Soil texture Fig 7 Ecological relevant landscape and soil features Y Projekte AEGRO Berichte Final F Annex 2010 02 03_14 06 26_Cybertracker2009 doc 4 Working document C Germeier C H hne amp L Frese January 2010 GPS ME 16 37 ESE options a Xfox SiteGPS Position All Sightings Off SurveylD ESP201 alas ObserverN ame Andreas Katsiotis Acquire general geo j 00 00 0 000 N Country ESP T 000 00 0 000 E Fovea emanas District Almeria JA am Location Nijar amp BOO AreaN ame Cabo de Gata Nijar AN SiteCode ESPNIj1 00 00 00 FarmN ame Finca Nijar 0 00 km h SiteN ame Campo Primero
17. village or b Protected Area town LAU 2 Fig 5 Search lowest administrative unit and protected area C Documentation of site details We understand the site as a point where a collection or observation event occurs Thus it is the lowest level of geographic description Heterogeneous description formats are found in traditional site or locality descriptions often covering administrative unit and protected area as well As there is no standardisation of a site identifier foreseen it has to be set by the observer collector We recommend a scheme of abbreviated country Location nearest town or village LAU2 sequential number e g ESPNij1 for a site near the village Nijar in Spain Andalucia Almeria see Fig 6b Additionally you should enter the name of the land owning enterprise farm forest research station etc and the name of the field or plot which also in many cases will be available Y Projekte AEGRO Berichte Final F Annex 2010 02 03_14 06 26_Cybertracker2009 doc 3 Working document C Germeier C H hne amp L Frese January 2010 SiteName SiteName Sitelnfo ESPNIij1 suggestion for a site code Country Location Number e g ESPNij1 To describe the site you can enter some additional agroecological fratures you consider important Ne es Press small button Sitelnfo to return to data capture screen Northern margin of an oat field to the forest a Names and description b Help for explana
18. which are owning and responsible for the observed occurrences of genetic resources The administrative unit within which the observation will be taken is selected Fig 4 from the hierarchy country state region NUTSI1 province NUTS2 district NUTS3 location LAU2 Layers may be skipped in case of small countries or subunits The application provides for subordination of each name to the correct level If observations are taken within a protected area the protected area is selected from a list or no protected area is indicated Fig 5 Currently the protected area has to be selected from all protected areas per country Y Projekte AEGRO Berichte Final F Annex 2010 02 03_14 06 26_Cybertracker2009 doc 2 Working document C Germeier C H hne amp L Frese January 2010 Andalucia3 opain2 Castilla La Manc Castilla y Leon Comunidad Yale e Navarra Principado de Ad lt gt Ja n M laga Country Province NUTS2 District NUTS3 Fig 4 Search administrative units Almeria4 ESPProtectedAreas Mojacar A Mojonera N jar Area Marina del Nord de Menorc Bahia de Cadiz Cabo de Gata Nijar gt gt gt gt gt gt gt ee oa ae x a miojo g nis OM Pl lw Go zi mi mia w 2 jjo a a zillo ale sis 13 2 219 2 1s 5 3 o o sis a Eo S z 2 2 B g y Zle D VO p z 2 TERR JHE Oo thd CA ae Camino de Santiago Ww a Location next
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