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1. CLX File Dir C Program Files CIAT MarkSim output Filename Search View Graph Path to file file file Use the browse facility to identify the file to be displayed The view file icon will display the file in the MarkSim editor I When viewing a file you are offered the option of editing it or viewing the data as graphics You may edit a CLX file but we highly recommend that you do not do so The parameters are interlinked and editing one without adjusting the set may result in serious errors The graph file icon will display the available climate data from the file Those available from a CLX file are monthly rainfall mean monthly temperature mean diurnal temperature range and solar radiation A DAT file contains the same variates less solar radiation A WTG file contains the simulated daily values of solar radiation maximum and minimum temperatures and rainfall for a whole year The graphs are presented month by month The CLI file contains monthly values for solar radiation maximum and minimum temperature number of raindays and sunshine hours In MarkSim sunlight hours are not estimates so this variate always shows missing values 99 These graphic displays are produced by TeeChart This software gives the user considerable control over the type of display produced To invoke the TeeChart graphics control press ctrl T This graph button at the lower left of the window Graph gives access to a different f
2. Be MarkSim A Computer Tool Thaf Generates Simulated Weather Data for Crop Modeling and Risk Assessment Version 1 2002 PG Jones P K Thornton jaW D ICEF a e P W Wilkens Wy Bees ee ont A 4 me f eA BOs Uh by Anrie L Joles RA l Nanni 3 5 p i w K kad A AP A 4 AE F ee A l A A F 5 Je er l fe A Z A 4 R i a 3 S 4 gt ey _ The International Center for Tropical Agriculture CIAT its Spanish acronym is one of 16 food and environmental research organizations known as the Future Harvest centers The centers located around the world conduct research in partnership with farmers scientists and policymakers to help alleviate poverty and increase food security while protecting the natural resource base The Future Harvest centers are principally funded through the 58 countries private foundations and regional and international organizations that make up the Consultative Group on International Agricultural Research CGIAR In 2001 CIAT received support from the following donor countries Australia Belgium Brazil Canada Colombia Denmark France Germany iran Italy Japan Mexico the Netherlands New Zealand Norway Peru South Africa Spain Sweden Switzerland Thailand the United Kingdom and the United States of America Our work was also financed by the following organizations and foundations the Asian Development Bank ADB the European Union EU the Uni
3. 68 editor 14 example 14 28 panel 14 select 28 30 GLIM analysis 49 graph button 24 file icon 24 graphics access 23 control TeeChart 24 tool 23 24 Index 83 grid climate 12 37 Africa 27 Latin America 27 dependent data 10 15 independent data 5 interpolated climate 5 20 22 icon configuration 34 editor 6 erase a map layer 34 erase all map layers 33 graph file 24 load layer 11 34 main menu 22 43 move map layer down 33 move map layer up 33 service 20 spatial 27 view file 24 window control 21 independent variate set 59 index of stability 57 information run 6 input facility 30 file MarkSim 34 forms 5 20 multiple CLX file 40 43 single CLX file 39 tool spatial coordinates 26 input format DSSAT model 20 interpolated climate grid 5 20 22 interpolated climate surface 58 interpolated data sets 51 interpolating daily probabilities 48 interpolation algorithm 51 inverse probit transform 48 84 MarkSim L lag effects 48 laplacian spline techniques 51 lapse rate model 51 52 Latin America climate grid 27 layer add 10 choose 21 control tool 10 21 33 34 control window 10 delete 37 polygon 33 projected 37 properties tool 11 12 set properties 11 stack 33 link function probit 45 load map layer 34 shapefile 34 35 36 load layer icon 11 34 log file 6 13 27 31 main menu icon 22 43 map background color 34 color 21 de
4. To produce the surfaces the first step consisted of clustering the available historical station data We used the rotated data in a two pass leader cluster algorithm analysis The first pass allocated stations as cluster leaders whenever they exceeded a minimum cluster distance The second pass reallocated the stations to their respective cluster leaders The distance measure was the Euclidean distance in the 36 dimensioned climate space We tested various exponential transformations on the rainfall data and chose the exponent 0 5 square root based subjectively on the evenness of cluster sizes Cluster sizes varied from 1 to 307 stations with a mean of 13 9 stations per cluster To calculate the expected parameter values of the model for any pixel in the interpolated climate surface first we need to know to which cluster the pixel belongs and second how the climate normals of the pixel adjust the parameter values within each cluster relative to the cluster mean values We use the cluster seed as the type climate for each cluster and calculate the Euclidean distance in climate space for each pixel The pixel is then associated with the closest cluster seed This need not be geographically close For each of the parameter types we fitted a regression submodel within each cluster to trim the parameters estimated for the pixel to the best estimate we could make from the limited data recorded for each pixel of the climate surface We dealt separate
5. functions gamma_av and gamma_p real function pu rain real rain if rain i1t 1 125 rain 1 125 r log log rain pu 1 2969 1009 009 r 1 1 2264 0 4363 r r return end real function avu rain real rain r log rain avu 7 99 1 045 r 4 78 1 0 2389 0 01541 r r return end The functions gamma_av and gamma_p correct the mean and shape parameter for a fitted gamma distribution when the samples are censored below the value of 1 They are for use with rainfall event values in the range 2 to 40 mm and gamma distribution shape parameters 0 3 to 2 5 Because the input parameters are distorted from these uncensored limits the function inside checks for valid inputs This functional fit breaks down very fast outside its fitted area These functions are fitted by stepwise regression in GENSTAT from all powers and cross products of the independent variates to the sixth power for a and p to the fourth power for ai and pi They are based on a Monte Carlo simulation of 100 000 samples for each of 14 by 13 points in the range For gamma_av the fit gives Abs Max residual 0 184 Standard Deviation 0 03576 76 MarkSim real function gamma_av average shape error logical error Gamma_limit real average shape a p ai pi error false if not gamma_limit average shape then error true return end if a average 40 p shape 2 75 ai 148 ante gamma_av 0 01196984 1 000303 a 0 2358
6. potential instability occur on the US Pacific Coast in Chile northeastern Brazil Sri Lanka and through some areas of Central Africa However in no area does the index reach 80 degrees Although this appears high the phase angles are rotated correctly and in fact there is little chance of a spurious rotation To save computing time the whole climate surface is rotated according to these rules and all operations in MarkSim are done in the rotated phase space 2p The only exception to this is when the user requests a climate diagram for a climate surface point Surface interpolation As noted above the rainfall model requires an extensive set of parameters 12 monthly baseline probits termed and monthly mean av and shape ps parameters for the rainfall event gamma distribution Twelve monthly standard deviations and the 66 off diagonal elements of the 12 x 12 correlation matrix for B are also 58 MarkSim required Three lag parameters d allow us to calculate a 12 x 8 probit transition matrix Interpolated climate surfaces commonly hold only climatic normals for monthly rainfall and maximum and minimum temperatures We therefore need some help to get 117 parameters from 36 monthly values This help comes from the structure that is inherent in the Markov process and similarities in climate processes within climate types that although not included explicitly in the model affect the model parameters in consistent ways
7. 136 167 158 18 120 74 121 0 99 130 1 58 34 Fa 124 36 19 47 0 24 G 181 izes 12 80 198 357 107 166 20 264 0 290 201 6 O 135 453 1388 255 102 39 21 44 108 95 550 275 150 174 402 47 287 208 358 22 259 81 515 26 156 47 0 124 44 356 128 18 23 36 201 231 86 95 37 0 0 474 172 0 233 24 10 2 34 7 128 364 103 272 22 0 31 365 29 VO 136 63 346 53 61 0 21 54 657 13 58 26 49 217 85 i76 105 3216 0 71 528 130 336 134 27 169 0 98 86 173 103 29 1265 295 23 124 1665 28 45 0 29 67 0 219 0 67 if iti 0 252 29 28 S52 66 33 109 362 139 307 123 187 0 30 3 116 227 20 260 21 ISS 352 327 13 0 31 0 147 0 67 34 He 0 END buenaven Interpolated 3 895 77 073 60 72 MarkSim Each data record contains the day number and the rainfall values for that day in each month in integer format in tenths of millimeters Missing days are blank DSSAT daily weather output WTG WEATHER BUEN From Interpolated Surfaces INSI LAT LONG ELEV TAV AMP REFHT WNDHT BUEN 3 895 77 073 60 26 59 11 5 99 0 99 0 DATE SRAD TMAX TMIN RAIN 01001 R es S150 BAAda 01002 14 7 259 AADA O1003 21 0 LG 21 9 346 01004 10 2 S262 PET Ara 01005 20 4 sics Zaa Lie 01006 15 9 13 6 22 1143 01007 27 4 33 4 21 2 0 0 01008 ee 29 3 20 437 6 One year s data constitutes one file The DSSAT naming convention is Site name NNO1 where NN is the year number It is hence not possible to simulate more than 99 years for any site The Site name is the same as the CLI filename The header consists
8. 38 solar radiation 50 temperature 50 years 42 simulation Monte Carlo 75 multiple 40 run 15 19 single CLX file input 39 single site run 15 16 site field DSSAT 17 site name 17 DSSAT 41 42 solar radiation simulate 50 spatial coordinates input tools 26 spatial entry 27 spatial icon 27 spatial input tool 6 14 26 window 6 13 spatially interpolated climate surface 51 stability index 57 stack layer 33 standard display 25 standard error 48 standard time rotate 52 stepwise regression 59 75 stochastic rainfall generator 44 surface interpolation 57 T TeeChart 24 39 graphics control 24 temperature data 51 range diurnal 30 simulate 50 theory MarkSim 44 64 title bar 21 tool climate diagram 25 configuration 10 34 37 generate data 15 38 39 graphics 23 24 input spatial coordinates 26 layer control 21 layer properties 11 12 select a latitude longitude point 13 spatial input 6 14 26 zoom 32 zoom in 10 11 zoom to area 21 transfer model parameters 23 transform Fourier 48 probit 45 49 transition matrix 60 transition probabilities correct 78 transmissivity 50 triad 60 vV validation functions 43 variability parameter 48 50 variance annual 48 50 view file icon 24 weather files panel 39 wW weather files panel view 39 weather generator DSSAT 50 parameter 44 weightings 56 wet day probability 44 rainfall 45 48 W
9. 774 30 Clxfile0 CLx Climate batch file CBF specifies the full path to a set of DAT files for which CLX files are required It is a sequential ASCII file that can be written by the user using a standard ASCII editor or can be produced using the drag and drop facility on the spatial input window Program Files CIAT MarkSim dat 09333000 dat Program Files CIAT MarkSim dat 15353013 dat Program Files CIAT MarkSim dat 806082 dat Program Files CIAT MarkSim dat H1308001 dat 2 2 R 8 CBFs must always reside in the data directory CLX batch file XBF is a free format comma delimited sequential file that specifies a set of run orders for rungen Each record gives the full path name of a CLX file a DSSAT site name random number seed number of years to simulate and output type DSSAT site names must be unique The random number seed is optional but the field must exist as zero or null Output types are c or q Appendix A 69 C PROGRAM FILES CIAT MARKSIM DAT MAYPEN CLX MAYP 1649 2 c C PROGRAM FILES CIAT MARKSIM DAT CLXFILE3 CLX CLXF 7039 2 c C PROGRAM FILES CIAT MARKSIM DAT CLXFILE2 CLX CLXG 11 2 c C PROGRAMFILES CIAT MARKSIM DAT CLXFILEO CLX CLXH 9814 2 c The XBFs must always reside in the data file directory DSSAT climate definition file CLI is used by the DSSAT crop model driver It is not used by MarkSim but if it does not exist it is created by rungen CLIMATE PTOP INSI LAT LONG ELEV TAV AM
10. Markdat Image directory C Program Files CIAT MarkSim output Output directory C Program Files CIAT MarkSim dat data file directory GLFFile6 GLF GLF name Markov98 ctr CTR file 3 mode of action Switch tor verbosity Likewise the user should have little contact with this communication file It varies a little depending on the action It can be viewed from the spatial input window and may be of use in debugging applications RUNGEN CTR is a MarkSim control file CC Program f iles Ciat MarkSim Markdat Image directory C Program Files CILAT MarkSim output Output directory C Program Files CIAT MarkSim dat Data file directory XBFFile2 XBF name CLIM CLI tilename 1 37 0 68 MarkSim This file mediates between the Pascal Delphi shell and rungen dil It varies a little depending on the action It can be viewed from the generate window and may be of use in debugging applications Georeference list file GLF contains a list of points with latitude longitude elevation and a CLX filename It is a sequential ASCII comma delimited file that is written by the user with a standard ASCII editor the MarkSim editor or may be constructed with the drag and drop facility on the spatial input window It is used to specify a number of points for which a CLX file is to be produced 2 588 65 585 30 Brasil CLXx 5 423 64 774 30 brasil1l CLx 3 895 F7 073 606 buenaven CLX 3 460 76 525 1523 Gali cnx 4 890 64
11. bY Take S iR Tet HO Ra le h4 Lae J iy BO temp Sanri 24 0 ahak 2ae8 davo BSS 247 hat ae Boek BRS Dee Yang Elat Fiag Tiss Tass Ph Eb Di IR Hat 16 4 SoH 1057 radn 14 5 Iss Ge Os Les te ae SO OURS TALS LAT ERO The first line consists of an identifier an indicator that it is an original data file or a model intermediate file in this case it is the latter and is labeled interpolated then the latitude longitude and elevation of the point The matrix that follows is the correlation matrix for the baseline probits or Beta variates AV is the mean rainfall event amount and P is the gamma distribution shape parameter Beta is the baseline probit RAINDAYS is the average rain days per month expressed as a proportion of the days in the month and S E is the standard error of the Beta value D1 D2 and D3 are the lag parameters and in an original data CLX N is the number of years in the raw data In an interpolated file it is always 2 Cluster is the cluster number associated with the interpolated point and Phase is the angle of rotation for season date standardization Rain temp rang and radn are the mean rainfall daily temperature diurnal temperature range and solar radiation for the interpolated point In an original data CLX file there is no record for solar radiation Climate definition file DAT is another file format used in the original calculation of the MarkSim model but also used as a data entry format for the end user
12. credit Though CIAT prepares its publications with considerable care the Center does not guarantee their accuracy and completeness Contents Introduction Getting Started 1 Tutorial Grid Independent Climate Data Grid Dependent Data Running the Simulation 2 User Reference Section Overview of MarkSim Operation The Map Window The Main Menu Service Icons 3 Theory The Rainfall Model Interpolating Back to Daily Data Annual Variance and the Variability of Parameters Simulating Temperatures and Solar Radiation The Climate Surfaces References Appendix A MarkSim File Structures Appendix B Functions for Correcting the Censored Gamma Distribution Index Page 10 15 20 20 20 22 44 44 48 48 50 51 62 65 65 74 74 80 Introduction MarkSim has a long history The rotation algorithm was written on the 6th of March 1978 not long after I had joined CIAT and started construction of the CIAT Climate Database Markov models of rainfall have been used in many areas A survey of the literature that I made in the mid 1980s came up with more than a hundred references However they have never been particularly successful in the tropics I wondered why and eventually came to the conclusion that the weather systems prevalent in the tropics do not include the frontal weather with travelling highs and lows that you find at temperate latitudes This means that the weather generating forces are completely diff
13. of 365 or 366 days by eight states for each year for which rainfall records are required In the course of testing the model with random resampling we found that it did not work well when the rainfall probabilities were very low Subsequent analysis showed that the use of the probit transform produces a systematic bias When resampling is used low probabilities are overestimated and high probabilities are underestimated after retransformation Simulations of completely random numbers were used to evaluate the empirical relationship of the standard error to the overall probability level Probits produced from runs of up to 200 years were summed to monthly means and retransformed to probabilities The variances of the retransformed monthly mean probabilities were then compared with the actual variances introduced in the simulations The bias in the monthly probabilities was found to be related completely explaining 100 of the variance and simply although empirically to the probability level and the standard deviation In the algorithm for the rainfall model with sampling this relationship is used to correct the monthly baseline probabilities by adding to them the correction factor Di defined as D b 0 55228 s 0 26154 s 3 50 MarkSim where for month i b is the baseline probability of a wet day following 3 dry days and s is the standard deviation of the baseline probability Simulating Temperatures and Solar Radiation
14. of the surface becomes zero as it passes through the station point In other words each station is on a small plateau or step in the interpolated surface This is usually much smaller than the pixel size and hence is not noticeable Second a usually small step occurs in the fitted surface as stations come into or drop out of the fitting window Where the station density is high with respect to the pixel size this is almost impossible to see Where the stations are not so dense it can produce unsightly straight lines or smooth arcs in the fitted rainfall data that are not tied to elevation Inspection of the surface s profile usually shows that these are negligible artefacts but they are unsightly and can undermine confidence in the surface maps Climate date standardization rotation The climatic events that occur through the year such as summer winter and start finish of the rainy season are of prime importance when comparing one climate with another Unfortunately they occur at different dates in many climate types The most obvious case is where climates are compared between points in the Northern and Southern Hemispheres but more subtle differences can be seen in climate event timing throughout the tropics What we need is a method of eliminating these differences to allow us to make comparisons free of these annual timing effects Let us look at two hypothetical climate stations They are in a typical Mediterranean climate war
15. recognize the path The display coverages directory B contains the background coverages that you can load to help you navigate the maps to find your sample points These are ESRI shapefiles and consist of various subitems These are explained in Appendix B The size of this directory will depend on how many coverages were loaded with your version of MarkSim These will be changing as we develop better backgrounds For more up to date information check on the MarkSim Web site and or wait for notice on the listserver For details of these see the front of this manual Again you can move these to another directory but remember to update the configuration Other standard ESRI shapefiles can be loaded into MarkSim from this directory or others The only restriction is that the projection and coordinates be geographic i e latitude and longitude that is to say MarkSim will not accept shapefiles in other projections UTM Lambert etc User input files are read from the DAT file directory which is loaded with the program files for your convenience and contains example files to get you started We strongly recommend that you move the directory out of the C program files path because it is not good practice to mix registered programs with users data even if Microsoft does so 36 MarkSim The definitions made in the configuration window are stored in the file MarkSim INI that can be found in the c Program Files MarkSim direc
16. size 22 polar coordinates 25 polygon layer 33 probability classes 60 coefficients 60 wet day 44 probit function 44 inverse transform 48 link function 45 transform 45 49 processing options batch 8 projected layer 37 pull down menu 21 Index 85 R rainfall event averages 59 61 gradient 13 model 44 48 monthly normals 61 simulate 38 wet day 45 48 random number generator 18 seed 16 18 38 41 42 random resampling 49 random sampling 48 recreate CLX file 14 regression analysis 59 coefficient 59 stepwise 59 75 submodel 58 report error 31 resampling scheme 48 right click menu 20 21 rotate to standard time 52 rotated display 25 rotation 52 57 rotation phase angle 55 run CLX file 40 clxgen 15 information 6 multiple DAT files 8 9 multiple sites 17 19 simulation 15 19 single CLX file 39 single DAT file 6 8 single site 15 16 rungen phase 15 23 rungen ctr See MarkSim control file S sampling check 47 SBN 72 SBX 72 scaling 59 search 86 MarkSim file 17 select CBF 31 climate normal file 30 31 CLX file 41 DAT file 9 GLF 28 30 single DAT file 8 select a latitude longitude point tool 13 26 selection menu color 34 service icon 20 set layer properties 11 set map background color 34 set up map 10 14 shapefile 10 21 22 33 35 72 load 34 35 36 SHP 72 SHX 72 SIMMETEO 50 simulate daily data 20 daily rainfall
17. to give you enough background to localize the area in which you are working If you are in doubt as to where the cursor is pointing the latitude and longitude appear in the lower right corner of the window In this case the cursor is on the right click menu header bar and hence is actually a few kilometers east of Buenaventura To measure distances on the map Select the zoom to area tool Left click on the map from where you want to measure A small blue dot will appear on the map at that point The distance from this point to the cursor is continuously displayed at the lower left corner of the map window Do not hold the left button 22 MarkSim down while moving the cursor or you will draw out the rectangular extent for the zoom tool MarkSim selects the data from which to calculate the model parameters from an interpolated climate grid These vary in pixel size and hence in precision For Latin America and Africa these are currently 10 arc minutes about18 km and for Asia 2 5 arc minutes about 4 km In mountainous areas this pixel size may not allow a full description of the terrain and in coastal areas there may be slivers of land that are not covered by the grid To check exactly where you are on the grid a set of shapefiles is provided that displays the grid outlines These are called america_grid shp africa_grid shp and asia_grid shp You will find them on the CD ROM with the other coverages Load them wit
18. to another The probabilities that we need to calculate the rain days per month are the state or stationary probabilities which except for the calibration stations we do not have As a fortunate consequence of some structural redundancies in the model these can be calculated from the monthly average rainfall and the estimates of B As noted above the model works in two parts One decides whether today will be a rain day the other decides how much rain should fall The two parts have a hidden link A triad is a binary form of three digits denoting rain on each of 3 days Thus triad t 101 means it rained yesterday it did not rain the day before yesterday but it did rain 3 days ago Within the model there are two classes of probability One the transition probability p t shows the probability of rain today given that the system is in triad state t The other the state probability s t shows the probability of the system being in a certain triad state The model calculates the transition probabilities as probits Thus the transition probability for a given triad t in month m is 3 P B 2tad 9 t m i where transforms from the probit form to a probability We can write a transition matrix that governs the relationship between these two types of probabilities Because we can calculate the p from the equation above we can use the transition matrix to calculate s d 000 1 P w Poo 0 0 0 0 0 0 000 001 0 0 1 Po P
19. where best to install MarkSim Y Hit Yes to proceed Read the notes on the following screens V Then choose the relevant installation type The largest set of data files is the map coverages These are Environmental Systems Research Institute ESRI shapefiles that are used to create the backgrounds for the maps you will use with MarkSim The directory is called coverages and is 582 Mb You can elect to leave it on the CD ROM if you are short of disk space In this case choose the option Typical when the Install shield requests it Leaving it on the CD ROM will not slow MarkSim operations to any great extent but it does mean that you have to have the CD ROM in the drive whenever you work If you choose to install it on the hard disk the install shield will attempt to put it in a directory MarkSimFiles on a disk with sufficient space You may override this and choose another site for it if you wish 4 MarkSim The climate grid files and all the model parameters are stored in the directory markdat this is currently 336 Mb It has to be installed on a disk and will be flagged read only We suggest that you install it if possible away from the program files on your C disk The install shield will attempt to put it in the directory MarkSimFiles as above The last choice you have is where to put the working directories dat and output These will contain your input and output files It is also best to keep these away from th
20. you have entered via the spatial icon these fields will be blank If you entered from choosing a point on the map they will show the values for that point If you decide to enter the latitude and longitude from the keyboard you can enter them as decimal degrees or as degrees minutes and seconds The elevation in meters is necessary for the operation of MarkSim However if you do not know it then you can use the key provided to fetch it from the DEM that is an integral part of the climate surfaces t In this version of the software the climate grids for Latin America and for Africa are at a resolution of 10 minutes of arc This is about 18 km at the equator In mountainous regions this resolution can give a poor estimate of the actual elevation of your chosen point so it is better to enter the known elevation if you have it 28 MarkSim If you enter a location by pointing at the map or typing in the coordinates you must enter a name for the CLX file This should be a valid DOS filename one to eight characters without a file extension 2 Georeference list file selection rn eee ee oe er me ee we errs eee eee me eee ee ee ae b GLF File Selection Georeference List File kf f Browse j BE in Se te ah A pl ott ghia iy ten sly ba g Amma ay dm ajpanie wa AOO A aan aariate Filename Select View Drag and ia GLF file drop file file creation creation The next option for georeferenced points entry is controlled by th
21. 0 Printed in Colombia September 2002 Jones Peter G MarkSim a computer tool that generates simulated weather data for crop modeling and risk assessment version 1 P G Jones P K Thornton wW Diaz and P W Wilkens edited by Annie L Jones Cali CO Centro Internacional de Agricultura Tropical 2002 1 CD ROM Manual MarkSim a computer tool that generates simulated weather data for crop modeling and risk assessment version 1 87 p CD ROM series ISBN 958 694 047 0 CD ROM ISBN 958 694 046 2 manual AGROVOC descriptors in Spanish 1 Tiempo meteorol gico 2 Modelos de simulaci n 3 Bases de datos 4 Condiciones atmosf ricas 5 Clima AGROVOC descriptors in English 1 Weather 2 Simulation models 3 Databases 4 Meteorological elements 5 Climate Title I Thornton Philip K IH Diaz William IV Wilkens Paul W V Jones Annie L Vi Centro Internacional de Agricultura Tropical VII Ser AGRIS subject categories P40 Meteorology and climatology U10 Mathematical and statistical methods LC classification S 600 4 J66 Copyright CIAT 2002 All rights reserved CIAT encourages wide dissemination of its printed and electronic publications for maximum public benefit Thus in most cases colleagues working in research and development should feel free to use CIAT materials for noncommercial purposes However the Center prohibits modification of these materials and we expect to receive due
22. 158 2 973477 amp 11 64334 pi pi 0 3975927 ai ai 22 32169 amp 23 56441 ai ai pi 1 026232 ai ai ai pi ai pi pi gamma_av gamma_av 40 end For gamma_p the function was not fitting at all well Taking the whole range I have split the fit parting the data file at average 9 Abs Max residual 0 0226 fit to lower part Standard Deviation 0 00225 Abs Max residual 0 0110 fit to upper part Standard Deviation 0 00125 real function gamma_p average shape error logical error qgamma_limit real average Shape a p ai pi p2 p3 p4 a5 error false if not gamma_limit average shape then error Crue return end if a average 40 p shape 2 75 ai s iJa Di i p Appendix B 77 p2 pi pi D3 p2 pi p4 p3 pi as ia t s if average 1le 9 0 then gamma_p 0 6707273 26 57797 p4 1 319750 6 289515 pi amp 0 5363049 30 09750 p3 0 0588292 amp 201 5118 p4 ai ai ai ai 6 980662 20 77201 p2 p2 amp 0 3990897 0 5076262 2 686214 a 0 9675789 a amp 250 15956 4a5 p p pi pi H T else gamma_p 0 0179229 0 6905722 1 141806 pi p3 7 837731 p2 158 0031 p4 35 21537 p3 1 737783 pi 0 4967813 ai al ai ai 1 179822 0 2637289 a 0 2545756 a a a 0 1941607 a5 0 0637321 a a5 0 0246295 p p p p p p end if 2 UR Rm gamma_op gamma_p 2 75 return end MarkSim operational function determines if a censored av shape parameter pair f
23. GEN weather estimator 50 window climate input 26 control icon 21 drag and drop 31 layer control 10 Index 87 map 20 22 spatial input 6 13 world climate 56 WTG file 23 available data 24 WTG 72 file example 16 output file 39 X XBF 7 40 41 68 batch file 17 construct 17 edit 18 editor 18 42 example 18 40 years simulate 42 Z zoom in tool 10 11 zoom to area tool 21 zoom tool 28 LICENSE AGREEMENT READ THE TERMS AND CONDITIONS OF THIS LICENSE AGREEMENT CAREFULLY BEFORE OPENING THE PACKAGE CONTAINING THE PROGRAM DISKETTES BY OPENING THE PACKAGE CONTAINING THE PROGRAM YOU ARE ACCEPTING AND AGREEING TO THE TERMS OF THIS LICENSE AGREEMENT IF YOU ARE NOT WILLING TO BE BOUND BY THE TERMS OF THIS LICENSE AGREEMENT YOU SHOULD PROMPTLY RETURN THE PACKAGE IN UNOPENED FORM AND YOU WILL RECEIVE A REFUND OF YOUR MONEY LICENSE GRANT The enclosed software is a proprietary product of CIAT and protected under US copyright law The software may be used only on computers owned leased or otherwise controlled by you Neither concurrent use on two or more computers nor use in a local area network or other network is permitted without separate authorization and the payment of other license fees You agree that you will not assign sublicense transfer pledge lease rent or share your rights under this License Agreement You agree that you may not reverse assemble reverse compile or otherwise t
24. INSI LAT LONG ELEV TAV AMP REFHT WNDHT Garl 4 340 72 316 213 2768 Tis 99x0 99 50 DATE SRAD TMAX TMIN RAIN 01001 2 9 33 2 ZR A 0 0 01002 21 2 38 6 23 wd 0 0 01003 EN EE 38 6 23 lt 0 0 0 01004 24 7 37 8 Z3 s0 0 0 01005 EN E 38 24 0 0 0 Z Go back and change the random number seed and rerun the job The file CARIO10O1 WTG will now contain different simulated data You can however exactly duplicate the original run by setting the random number seed back to 1243 If you leave the default seed the actual seed used will be shown in the log file so even if you did not specify it you can always repeat a run if you so require Tutorial 17 Running multiple sites The last exercise is to run the simulation for multiple sites You have already prepared a number of CLX files You can now run these from a batch facility This uses XBF or CLX batch file a CARONA og IEY UTSE es 9 Ware NY AEN ENCINO GR LER ag O maa Cee yr Wass peste t Fil Edit ee View Drag file file and drop C CIAT MARKSIM OUTPUT AFRICA CLX AFRI 4003 12 c C CIAT MARKSIM OUTPUT ASIA CLX ASIA 2919 12 c C CIAT MARKSIM OUTPUT BRASIL CLX BRAS 5336 12 c Full path to CLX file DSSAT Random Years Output site name number type seed The XBF is a comma delimited sequential file with the fields as shown above You can type the file into any ASCII editor but because the full path is needed on the filenames it is much more efficient to use the drag a
25. MarkSim uses the DSSAT weather generator Pickering et al 1994 based on routines of Richardson 1985 and Geng et al 1988 to generate daily values of maximum and minimum temperatures based on whether the day is wet or dry The parameters for generating these variables are the long term monthly means stored in the CLX site file The original code was part of the WGEN weather estimator Richardson and Wright 1984 and this was modified for DSSAT version 3 Tsuji et al 1994 The DSSAT modifications use standard deviations rather than coefficients of variation which make the estimator more stable than the original version If monthly climate parameters are used as input the routines use a combination of the regression equations in SIMMETEO Geng et al 1988 Pickering et al 1988 to compute the standard deviations Solar radiation data are generated from monthly mean values for daily solar radiation or from sunshine hour means if these exist in the CLI site file MarkSim uses the routines in the DSSAT generator which are again based on the equations in Geng et al 1988 and Pickering et al 1988 The monthly values of solar radiation are generated from the temperature normals using the model of Donatelli and Campbell 1997 which is a modification and improvement of the earlier model of Bristow and Campbell 1984 Briefly this model calculates daily solar radiation at the earth s surface as the product of potential radiation and
26. P SRAY TMXY TMNY RAIY PTOP 18 538 72 32 60 25 9 11 2 222 65 31 2 20 7 990 START DURN ANGA ANGB REFHT WNDHT 0 0 0 25 0 50 0 00 0 00 GSST GSDU 1 365 MONTHLY AVERAGES MONTH SAMN XAMN NAMN RTOT RNUM SHMN 1 15 7 2953 L837 18 0 2 2 939 0 2 ETS 29 9 28 6 33 0 3 0 339 0 3 19 4 30 4 19 2 53 0 8 99 0 4 2200 30 8 20 6 LTiinO 8 8 99 0 The variate codes are as follows in order of appearance INSI The DSSAT site name In this case PTOP representing Port au Prince Haiti LAT Latitude decimal degrees negative south LONG Longitude decimal degrees negative west ELEV Elevation meters above sea level TAV Mean temperature C AMP Mean diurnal temperature range C SRAY Solar radiation yearly average MJ m day TMXY Temperature maximum yearly average C 70 MarkSim TMNY RAIY START DURN ANGA ANGB REFHT WNDHT GSST GSDU MONTH SAMN XAMN NAMN RNUM SHMN Temperature minimum yearly average C Rainfall yearly total mm Start of summary period for climate CLI files Year Duration of summarization period for climate files Years Angstrom a coefficient yearly unitless Angstrom b coefficient yearly unitless Reference height for weather measurements m Reference height for windspeed measurements m Growing season start day Day Growing season duration Days Month number Solar radiation all days monthly average MJ m gt d Temperature maximum all days mon
27. SSAT output is required a DSSAT site name will be needed If you leave the option blank the name will be taken from the first four characters of the CLX filename Site names cannot be duplicated or there would be a confusion of CLI files Therefore if the first four characters of the CLX filename would cause duplication the name is incremented alphanumerically Thus ABCD becomes ABCE XXXO becomes XXX1 and ABZZ becomes ACOO If you enter a DSSAT site name in the space provided this is used to name the first site in the XBF and each subsequent one is derived by alphanumeric incrementation The number of years to simulate is mandatory there is no default and the creation of the XBF will not proceed until you do The same number of years is used for every record in the file The random number seed is optional If you leave this field blank or zero a seed is taken from the system clock independently for each record in the file The output type is set to c or d for every record in the file If you wish to change the number of years or output type for specific records in the XBF you can proceed to editing it afler you have exited from this window Click on save to create and save the file You will see it fill out in the right hand window There is an option above for sorting the records by CLX filename There is an editor for creating or customizing your XBF after you have created it with drag and drop EJ E diting C Program Files CIA
28. T MarkSum dat XBF FileS_XBF cid ZOMsle of aia gy C PROGRAM FILES CLATSMARFSIM DAT MAY PEN CL fer fe PF etme GQ PROGRAM FILES CIAT MARKS IM DAT MAYPEN CLX MAYP 1649 2 c C PROGRAM FILES C LAT MARKS IM DAT CLXFPILE3 CLX CLXF 7039 2 c C PROGRAM FILES C IAT MARKS IM DAT CLXFILE2 CLX CLXG_ 11 2 C PROGRAM FILES C LAT MARKS IM DAT CLXFILEO CLX CLXH 9814 2 Use the green arrows to scroll through the file User Reference Section 43 As you scroll the current record appears with the fields selected in the editing windows Or you can select a record for editing by merely clicking on it with the mouse The drag and drop facility will have placed a random number seed which is either constant through the file if you specified it or one calculated from the system clock if you did not The number of years will be the same number you specified throughout the file and likewise the output type will be constant You now have the opportunity to change all those at will to tailor your XBF to exactly what you want All of these options can vary from line to line as MarkSim interprets each line individually at run time You can also add or delete lines or change their order with the blue arrow keys These work by dragging the selected line up or down the file You can search for extra CLX files to include with the browse button Beware When you open the selected file the filename and path will be included in the editing wo
29. The file extension originally stood for data Unfortunately Mr Gates has usurped it for use as a system file extension in Windows 2000 It allows a user to have complete control over the climate simulated rather than rely on the interpolated climate surface If for example you wish to adjust the climate for a change in elevation within an interpolated pixel copy the data from the CLX file adjusting the elevation and temperature data by the standard lapse rate subtract 6 degrees per 1000 m of elevation Then resubmit the data as a DAT file Alternatively if you wish to enter the exact data from a known climate station use the MarkSim editor or any ASCII editor to enter the data The DAT file is a fixed format file conforming to the Fortran format a8 2f8 3 i6 1216 0 12f5 1 12f5 1 15353013 15 700 35 183 11743 fos Ale 159 73 iS A 9 5 4 ais 103 4235 iA 21 4 214 0 2 I IBT 19 2557 FET 20a 22 6 22 ie 883 820 B26 358 9 6 650 10 9 Td TB FO gr a oO MARKOV98 CTR is a MarkSim control file 2 588 65 585 30 Brasil 5 423 64 774 30 brasil 1 3 895 a ee 60 buenaven 3 460 76 525 1523 caida The user should have little reason to encounter this file It is used to communicate between the Pascal Delphi shell and the clxgen dll It consists of one or more lines in a fixed format with latitude longitude elevation and an identifier MARKSIM CTR is a MarkSim contro file C Program files Ciat MarkSim
30. They all resulted in a hard line across the map at some point where the rotation basis changed This led to climates that should have been grading imperceptibly from one type to another suddenly jumping at a discontinuity This would have given the users serious problems when fitting models in these areas The best solution found is to use BOTH the rainfall and the temperature in calculating the rotation phase angle Thus The vector diagram of the first phases of rainfall a and temperature a with the resultant vector am TITttTiTiittiitiititiit iii Vin dr aa dy ri The resultant phase angle and amplitude are then Y a COS p a COS p X a Sin p a sin p amaj kae 7 X m Y Pm angle rM A 56 MarkSim Unfortunately this does not completely solve the problem of fitting a model to climates with different weather determinants However the vast majority of climates in the world are either 1 Rainfall determined where temperature is not an important seasonal effect large areas of the tropics and subtropics 2 Temperature determined where rainfall is even throughout the year most of the rest of the tropics and some temperate climates or 3 Rainfall and temperature determined when the two variates are highly correlated summer rains most of the rest of the world The Odd Man Out is 4 Winter rains and hot dry summers almost only Mediterranean climates Luckil
31. This will happen from time to time as the basic database improves and interpolations are redone mE Selected Files of type CLX to construct a GLF file buenaven CLX cak CLX lA file list tulua CLX Pass all Erase selected Down l Up i l Erase all i Path gt i select Save 30 MarkSim The list of CLX files that appears automatically will be from the default output directory You can search for other sets by changing the path or drive 3 Climate normal file selection The third panel allows you to enter data from another climate data source The data are entered in a special fixed format file known as a DAT file These are used internally in the creation of the MarkSim models hence the fixed format The file is a fixed format file with the following FORTRAN format a8 2f8 3 i6 12f5 0 12 5 1 12f5 1 Here is an example nendersn 17 583 30 967 L292 3 a O LSG e EZS An Lt 2 2 amp 2 Bw 4 30 98 187 20 2 I 20 8 19 848 3 15 212 912 914 918 321 8021 0 20 8 Lo 5 1D 4 12 Laa LS LES LES OLS 529 6178 10 8 The values are filename latitude longitude elevation meters 12 monthly rainfalls 12 monthly mean temperatures and 12 monthly mean diurnal temperature range In MarkSim the diurnal temperature range is defined as the difference between mean monthly maximum and mean monthly minimum Latitude is decimal degrees with Southern latitudes negative Longit
32. a 9 0 0 0 001 010 0 0 0 O Pa Poo 0 0 010 5 OL 0 0 0 0 0 0 1 Po Pow _ gr O11 100 11 Pio Pio 0 0 0 0 0 0 100 101 0 O T P Pim 0 0 0 0 101 110 0 0 0 0 I Pye 0 0 110 111 0 0 0 0 0 6 ism ge aw Theory 61 Unfortunately this matrix is singular However the frequency of s S and that of Seo s The proof of this is simple Any rainfall sequence longer than 1 day must start with the triad 011 and finish with the triad 110 Thus in any sequence the frequencies must be equal if we discount a possible difference of one depending on the starting condition That is to say if the sequence starts with a rain period and finishes with a dry period there will be exactly one more 110 than O11 irrespective of the length of the sequence The same argument holds for triads 001 and 100 where dry days rather than rain days are counted The state probabilities sum to unity as do the transition probabilities and the state outcomes Adding alternative rows of the matrix eliminates four rows We can therefore apply these restrictions by adding in four rows to the matrix This then becomes positive definite and has a viable inverse l l 1 l p 1 l 1 p 2 1 p i l 0 i p 1 1 l2 l lt Duc 0 l 1 Dio l 2 1 0 l b l l 1 12 s gar 2 3 aa l erie 2 2 3 2 l l 3 alh 2 3 l l 2 3 2 ajl 2 l 2 2 3 2 2 oily We thus have a reliable algorithm to pass from transfer probabilities to state probabilities Calculating the average rainfall even
33. alls within the competence area of the correction functions gamma_av and gamma_p The boundaries coincide with the uncensored limits 2 lt av gt 40 mm 0 3 lt shape gt 2 5 These are the bounds of the fit for gamm_av and gamma_p the fit of which is highly unreliable outside these limits These boundary functions are calculated from the boundary points of the Monte Carlo function fitting set They therefore hold for slightly more or less than their mean fitted curve Hence the small adjustments after each limit is calculated logical function gamma_limit av shape real a p X av shape gamma_limit true c First screen equations may be out of range if sha ape it 0 604 0or shape gt 3 48 then gamma_limit false return end if av it 1 9 0r av gt 54 then 78 MarkSim gamma_limit false return end if x av 40 B s 40 YS3SS 473 0 BO Oxy 1 1922 0 SB ZAFFI left p p 0 005 if shape lt p then gamma_limit false return end if Kx fav 40 2 D F C 068 0 675 250 0 2 BS694 128 0Fx X fright Bp prats t shape gt p then gamma_limit false return end if x shape 3 a 40 1 00390 0 393 0 5999 x 1 4 4 61 3 x x t Lop a a 0 05 if av gt a then gamma_limit false return end if ifishape 1t 1 35 return Lower limit of bottom If not failed here then fit is good a 40 0 026763 10448 0 08326 x 1 5 9241 4 091 x x botra a a Q 05 i f av lt a then g
34. amma_limit false return end if return end Correcting the transition probabilities for censoring requires that we know the relationship between the transition probabilities and the rainfall distribution The transition probabilities are assumed to be distributed in probit transform with a binomial error The rain event size distribution is quite different it is a gamma a Appendix B 79 distribution Nonetheless they are inextricably linked in fact the probabilities of individual rain event sizes sum to the probability of rain However we have censored below a value of 1 mm so we can calculate the number of rain events that we have lost directly from the gamma distribution Then we can add that back in to the rainfall event probability to correct for the loss For any given day i let the probability that it will rain be p Then the probability that it will rain given the system state 001 can be written P o If the gamma mean and shape parameters for the day are a and y and the gamma probability function of observing a rainfall event greater than x is gamma a y x then the probability of observing a rainfall event less than 1 mm in system state 001 is P o times 1 gamma a y 1 and the corrected value is P oo 2 gamma a y 1 80 MarkSim Index A about box 21 access graphics 23 add layer 10 address directory 35 adjust data 66 Africa climate grid 27 analysis cluster algorithm 58 GLIM 49 regression 59 ann
35. an estimate of the atmospheric solar radiation transmissivity coefficient the ratio of the value of solar radiation outside the earth s atmosphere and its value at the earth s surface Potential radiation outside the earth s atmosphere is estimated as a function of the declination the half day length a factor accounting for the distance to the sun the day of year and the latitude Potential solar radiation is then modified by the transmissivity to produce an estimate of radiation at the earth s surface The transmissivity is estimated as a function of clear sky transmissivity daily maximum and minimum air temperatures and two empirical parameters Theory 51 The Climate Surfaces Spatially interpolated climate surfaces are now available for many areas These usually handle long term climate normals interpolated over a DEM by various methods Jones 1991 Hutchinson 1997 Pixel size depends on the underlying elevation model It may be as little as 90 m Jones 1996 which results in a massive data set or 10 minutes of arc about 18 km which is as large as is practicable in many instances In the latter case the normal elevation model is the NOAA TGPOO06 NOAA 1984 We have produced interpolated data sets at CIAT using data from about 10 000 stations for Latin America 7000 for Africa and 4500 for Asia Each set of surfaces consists of the monthly rainfall totals monthly average temperatures and monthly average diu
36. are reported differently in different data sets Sterne and Coe 1982 used a censoring at 0 1 mm all values including trace records were discarded They used a series of data where measurements greater than 0 1 mm were all reported more or less the same Unfortunately the widely differing sets of data from all parts of the globe that we have used in MarkSim almost 11 000 station records means that there is different reporting with the data not uncommonly being truncated below 1 mm It is a great shame to lose the well reported data that go below this level but in the interests of consistency we had to eliminate them 46 MarkSim This is rather high for a censoring level and we were worried that it might have a large effect on the fitted gamma distribution models We therefore took data from just over 9000 stations and fitted the gamma distribution to both censored and uncensored data The results showed clearly see Figure 3 1 that although there was not too much of a shift in mean rainfall size there was indeed a large effect on the gamma shape parameter Shape parameters fitted to 9184 stations e Censored w Uncensored e g Ry 5 a wa Shape parameter Data were a little Sparse for these Raintall mov month Mean rainfall event size 9184 stations censored uncensored 600 Rainfall immimonth Figure 3 1 The effects of censoring on the gamma distribution parameters actual data from stations
37. check the detail of what is available in the climate grid files When you load them the continent will turn black however if you select transparent fill in the layer properties window of the layers control tool and zoom in you will see the pixel outlines appear 38 MarkSim The generate data tool Panel select button single CLX file Clunate Input REI aes Output 0 Fie pions View the TLX Inpa File CLI file CLK File Di EON A an Simo nce AR A Climate Filename Wr pin Graph the _ Cimate Directory C AProgror Flee CIA TAM ark Sani ontout ceca CLI file Yeats to Generate 2 Random 4 Seed 3 eee Fie Rungen is views weather Hes i EAA OE WTG Hes sg i r K ti A l faa i fY ee NE View the So control file BF Fie Selection CLK Batch Fle View the lt log file Panel select button Control error reporting Batch process The generate data tool appears as the second page of the climate input window although the icon from the service menu will take you straight to it if you already have a CLX file constructed This tool takes the model parameters from the CLX file and uses them to simulate daily rainfall If you choose the DSSAT 3 5 output option then maximum and minimum temperatures and global radiation are also simulated You need to specify how many years of data you would like simulated a random number seed and the output file type If you do not specify a random number seed the
38. construct and save file then exit You will get a warning that the DSSAT name is blank but you can ignore it this time Your XBF will look like this C PROGKAM FITLES CIAT MARKSIM QUTPUT JUPARAL CLX CUPA 6859 8 4 TI PROGRSM FILES CIAT MARFSIM CUTPUT CLXFILE CLX CLXF 7333 2 PROGRAM FI ILES CIAT MARKSIMYOUTPL CLXFILE2Z CLX CLXG 7473 8 PROGKAM FILES CIAT MARKSIM gt CUTPUT CLXFLLEJ CLX CLXH 1263 2 PROGRAM er LAF MARES CAMO TPL ARIMAG 3500 Now you can run the file but also you can still edit F a that you can alter the details of the run for each record in the file The output type or number of years does not have to be constant throughout the XBF If you wish to change one or more lines go to the XBF editor and make whatever changes you need before running the file Just for fun it before running if you wish This has the advantage i a ee te oF e da Change the output for Juparal to c and the years to 10 Tutorial 19 Change the years for Carimagu actually Carimagua a CIAT station in the Colombian Llanos to 4 Hit run rungen check the files that appear in the output directory There should be one called JUPARAL GEN with 10 years of calendar output in it CLXFO101 to CLXFO801 CLXGO101 to CLXG0801 CLXHO101 to CLX0801 and finally CARIO101 to CARIO401 all containing 1 year each of DSSAT 3 5 output 20 MarkSim 2 User Reference Section Overview of MarkSim Operati
39. d Atmospheric Administration 1984 TGP OO6 D Computer compatible tape Boulder CO USA Pickering N B Stedinger J R Haith D A 1988 Weather input for nonpoint source pollution models J Drain Eng 114 4 674 690 Pickering N B Hansen J W Wells C M Chan V K Godwin D C 1994 WeatherMan A utility for managing and generating daily weather data Agron J 86 332 337 Richardson C W 1985 Weather simulation for crop management models Trans ASAE 28 5 1602 1606 Richardson C W Wright D A 1984 WGEN A model for generating daily weather variables United States Department of Agriculture USDA Agricultural Research Service ARS 8 USA 83 p Sterne R D Coe R 1982 The use of rainfall models in agricultural planning Agric Meteorol 26 35 50 Tsuji G Y Uehara G Balas S eds 1994 DSSAT Version 3 University of Hawaii Honolulu USA week Fe eee Ct E i i UMENIACHA Appendix A MarkSim File Structures The MarkSim parameter file CLX is the heart of the MarkSim application It holds the model parameters calculated in the first phase clxgen for transfer to the simulation phase rungen It is also critical file used in the construction of the model and hence holds some information that is not actually used in the operation of MarkSim The file is fixed format and should never be edited by the user because there are complex relationships between the parameters Do not succumb to the temptation
40. e in the lower windows To select a single DAT file Y Highlight it by clicking on the filename Use the pass selected button to transfer it to the file building list in the right hand window under selected files Tutorial 9 To select all DAT files in the directory use the pass all button You can change directory to add more DAT files from elsewhere in your system TE C PROGRAM FILES CIAT MARKSIM DAT MEX07160 DAT Pale ES SEA ener E aai PROGRAM FILES CIAT MARIKSIMWDAT HENDERSN UAT PROGRAM FILES CIAT MARKSIM DAT K 23003 DAT BS H FO PROGRAM FILES CIAT MARIKSIM DAT MEX07160 DAT Pass all Pass selected Save the CBF and exit Browse and select the created CBF with the browse function Y Open it and check it with the view file button When you now run it MarkSim will create three CLX files in the output directory 10 MarkSim Grid Dependent Data This is the main purpose of MarkSim From the interpolated grids you can produce a simulated daily output for most points in the tropical world Setting up the map The coverages directory contains ESRI shapefiles of map background information that you can use to display a map to navigate the climate grids We will start by making a map to use with the Latin America climate grid The background layer samcountries will be loaded automatically in the newly installed version of MarkSim You can change this default with the configuration tool but f
41. e program files directory MarkSim output can be voluminous so make sure that wherever you decide to put them there is sufficient disk space Hit Finish to start the installation 1 Tutorial This tutorial gives a quick introduction to some of the common operations you may be doing with MarkSim The software is designed to produce simulated daily weather data for any point in the tropics It runs off interpolated climate surfaces and operates in two parts The first creates a file CLX file of model parameters The second runs the MarkSim simulation to produce the daily weather data files For details of the operations see User Reference Section p 20 For how the model works see Theory p 44 MarkSim uses three main subdirectories two for working files and one for map coverages MarkSim offers you two types of input If you know the monthly average climate data for the point you wish to simulate you can enter them This type of input restricts you to points with actual climate data but it operates fully independently of the interpolated climate grids so it will work for anywhere in the world The second type of input is where you do not have climate data but know the whereabouts of the point you wish to model This works from the climate grids and will simulate any point in the tropics provided that it is on a climate grid This method is somewhat restricted at present it works for Latin America Africa and South East Asia i
42. e second entry panel and is the GLF selection With an ASCII editor such as Notepad prepare a file containing a list of latitude longitude points with or without elevation data and put a CLX filename on each line The data should be comma separated and could look like this 12 45 67 1 999 PtoVelho 3 5 76 5 967 Palmira 25 335 37 5 L600 Naiross Name the file filename GLF and put it in the data directory Now check the GLF selection option and browse the data directory to pick up the filename Y Alternatively use the convenient GLF data entry form by clicking on the page symbol at the right of the panel This will construct the comma delimited file as you type in the fields and also check the coordinates and filenames for validity You can also use this to edit a GLF and to validate one that has been prepared by an ASCII editor It checks that the CLX filenames are acceptable and that all coordinates and elevation are within realistic bounds User Reference Section 29 2 33 37 5 1800 nairobi Another way to enter georeference data into a GLF is to drag and drop the location information from a list of CLX files This would appear to be a circular argument because what clxgen is going to do is to create the CLX files However this is a quick way of updating a long list of CLX files which you might want to do if they have been damaged in some way or if the underlying climate grids have been updated
43. e with the layers you are displaying For example you cannot see two closed polygon layers at the same time If you wish to display a closed polygon layer i e topography below the country limits you should use samboundaries and not samcountries Set map layer color will take you to a color selection menu Set map background color allows you to change the background color This is usually the ocean and hence blue but it is in fact any area not covered by a loaded layer so this is not always the case The configuration tool Under the configuration icon are three screens The first is the most important This defines where the input files for MarkSim reside User Reference Section 35 The file directories you see displayed here are as they will be loaded in the standard installation of MarkSim If you have decided on another place to load MarkSim then they will display the new directory site The MarkSim data source directory A contains all the files that define the MarkSim model together with the interpolated climate surfaces that allow the model to interpolate to a given point This directory is 362Mb The contents are described in more detail in Appendix A You may move the physical directory and files to another directory or disk unit if you wish but if you do so please note to update the configuration to denote its new address 2 NOTE The final on the directory address is mandatory Without this MarkSim will not
44. egression 59 co Kriging 51 color map 21 map background 34 selection menu 34 set map background 34 comma delimited file ASCII 40 68 configuration 35 icon 34 tool 10 34 37 construct CBF 8 CLX file 12 XBF 17 control error reporting 27 coordinates Cartesian 25 polar 25 copyright 21 correct functions 74 78 Index 81 transition probabilities 78 correct file 7 correlation matrix 49 61 surrogate 49 coverage directory 10 coverage file 72 coverages directory 21 create CLX file 26 D DAT editor 7 file 23 66 available data 24 directory 35 example 5 30 select all 9 select single 8 single 6 8 multiple run 8 9 data adjust 66 check 7 16 climate 23 clustering 58 directory 28 enter 6 66 grid dependent 10 15 grid independent 5 multiple georeferenced point 14 15 sets interpolated 51 simulate 20 temperature 51 DBF 72 debug 32 default 10 map 37 output directory 30 delete layer 37 directory address 35 coverages 10 11 21 DAT file 35 data 28 82 MarkSim default output 30 display coverages 35 file 35 MarkSim 31 Marksim data source 35 output 36 display coverages directory 35 map 72 rotated 25 standard 25 distortion censoring 47 diurnal temperature range 30 Donatelli and Campbell model 50 drag and drop 14 17 40 41 window 31 DSSAT climate definition file See CLI file daily weather output See WTG file 23 model input for
45. egression coefficients as a result of differential effects of the variates Although the effects of fitting both terms were often statistically significant their inclusion would have led to an undesirable instability of the regression as predictor when we present new data with slightly different values Because we know the bounds of the clusters we did not want a model predicting values outside these bounds Inspection of each cluster for each of the parameters would have been far too time consuming We therefore compiled a list of the independent variates ordered by the number of times that they occurred in each parameter set of parameter regressions We then fitted the maximal model for each parameter and progressively eliminated variates until none showed a regression coefficient that would force a prediction out of the cluster bounds Details of the regression analyses can be found in Jones and Thornton 1999 Rainfall event averages If we were to have fitted climate surfaces to rain days per month the av parameters could be easily calculated as the monthly rainfall 60 MarkSim total divided by the rain days Unfortunately the main sources of monthly climate data used in the interpolated climate surfaces rarely contain the number of rain days We therefore have to estimate these from the model The probability coefficients used in the model are transition probabilities They are the probability of the system passing from one triad state
46. erent and need a different order of model to fit them I eventually showed that this requires at least a third order model where a first or second order would produce a good fit in temperate climes I pursued these investigations as a minor part of my studies in CIAT One could almost say it was a hobby until Phil Thornton noticed what I was doing in the early 1990s He saw its application to crop modeling and pushed me to publishing the first paper Jones and Thornton 1993 We have been strong collaborators ever since producing a series of papers and working to craft MarkSim as a part of the CIAT Climate Database tools The MarkSim beta release written for DOS operating systems went to over 20 scientists in 1998 The response was good indeed Jeff White of the International Maize and Wheat Improvement Center CIMMYT used it to produce a rainfall reliability map for the whole of Africa It has taken a disappointing number of years to go from there to this release for Windows A lot of work has gone on in the meantime The basic model has been revised The database to which it is fitted has grown and been substantially cleaned The station algorithm has been rewritten to incorporate difficult climates where rotation on rainfall pattern is not valid We have incorporated new batch processing options that will greatly facilitate its use with geographic information systems GIS I am writing this introduction but MarkSim would not have ha
47. es from which to extract the filename Since the object of the exercise is to create CLX files this seems a roundabout way to do it It does however have some use when you might wish to recreate a set of CLX file or correct location data This could possibly be of use if you change from one climate grid to an updated one and you wish to recreate a set of CLX files with the new data Note that the latitude and longitude are in decimal degrees Go to the GLF editor and type in all or part of the GLF shown above Tutorial 15 Save it and run it by selecting the GLF panel option Open the file and run with the run clxgen button Y Check that all the CLX files were created and that the missing elevations were filled in from the climate grid S If you used the GLF in the example above you will have noticed that it finishes with an error If you look in the log you will see that almost all of the CLX files were created correctly ITAPEVI CLX however was not produced There is a warning in the log but MarkSim carried on to process the rest If you look at the coordinates for ITAPEVI you will notice that this point actually falls in the middle of the Atlantic Ocean Itapevi is actually in the state of S o Paulo in Brazil Unfortunately the validation routine in the GLF editor can only cope with checking if the latitude and longitude are possible It cannot check if they are correct Someone has left off the negative sign That is
48. f Port au Prince in the eighth record Next comes the random number seed This must be an integer with four or less digits It can be zero see records 3 4 and 5 in which case MarkSim will assign a random number seed calculated from the system clock and report it in the rungen log file The output type is c for MarkSim calendar style output or d for DSSAT 3 5 format output You can mix types of output throughout the XBF If you have a large number of CLX files to run the drag and drop feature will allow you to form the XBF with the minimum of effort Click on the drag and drop icon and the following window will appear CLX wn files 3 F L s n X i KT ORLE 2 CLG 7378 10 c S hE O CLXH 3074 10 pawa CLX popan CLX tusa CLX Clear selected Select files Move cursor Select all Set rAr F am F des path gt B Qar Save gt MatkSen Exit I Select L ees fe drive P laeci C Progam Fies CAT Wak Siniouputi oma nt cw we Select files individually in groups or all from the list of CLX files in the left hand window The list that you see initially is of all the CLX files in the MarkSim default output directory To select from CLX files in other directories change the path or drive in the windows provided Each line of the XBF must contain sufficient 42 MarkSim information for the simulation run This can be entered in the panel at the top right If D
49. fault 37 display 72 features 21 layer 33 erase 33 34 move 33 load layer 34 navigate 21 35 set up 10 14 window 20 22 Markov model 20 Markov98 ctr See MarkSim control file MarkSim calendar format 20 control file Markov98 ctr 32 67 MarkSim ctr 32 67 Rungen ctr 67 data source directory 35 directory 31 editor 6 24 40 43 66 file structures 65 73 input file 34 operation overview 20 operational function 77 parameter file See CLX theory 44 64 MarkSim ctr See MarkSim control file maximum likelihood method 45 Mediterranean climate 52 56 menu bar 20 21 pull down 21 right click 20 21 mode batch 40 model elevation 51 input format DSSAT 20 lapse rate 51 Markov 20 parameter 22 38 48 65 parameter estimation 20 rainfall 44 48 Monte Carlo simulation 75 monthly rainfall normals 61 move map layer 33 multiple georeferenced point data 14 15 multiple simulations 40 multiple site run 17 19 N navigate climate grid 10 map 21 35 Notepad 28 30 Oo operation overview MarkSim 20 operational function MarkSim 77 output calendar 19 39 41 directory 36 DSSAT 42 file WTG 39 option DSSAT 3 5 38 type 41 42 P pan 32 panel GLF 14 select button 39 panel select button 27 parameter estimates 48 derive 58 model 22 38 48 65 set 57 set of surfaces 44 variability 48 50 weather generator 44 parameter estimation model 20 pixel
50. h the layer control tool Y Set the fill to transparent and the outline on in the color of your choice This will show you the exact position of the grid pixels Note however that at small scales the grid will completely cover the continent with outline color To see the pixels you have to zoom in considerably The Main Menu Service Icons The figure shows the main service icons We will explain them each in turn moving from left to right Ejea point tool Spatial input tool Layer information tool Zoom in a bit tool Zoom out a bit tool Zoom to area tool raphics tool gc diagram Select a latitude Pan tool 8 ail OO Telefe ox lpi 3 we extent too JUR Zoom out to full Generate data tool tie Layer control tool Configuration tool User Reference Section 23 Certain of the MarkSim operating files have climate data associated with them These data can be shown graphically from various windows The graphic tool provides direct access to these graphics The CLX files are used to transfer model parameters from the parameter estimation phase clxgen to the stochastic weather generation phase rungen The DAT file is a method of presenting climate data to the clxgen phase The WTG files are DSSAT standard weather files produced in the rungen phase and the CLI files are DSSAT files associated with the generated data files and are necessary to run a DSSAT model See Appendix A for the file format definitions
51. hange the site name and save it as another file In this way you can use the base data in one file as a template for another Only make sure that you have changed all the data necessary to completely define the new file 8 MarkSim Running multiple DAT files It often happens that you will want to simulate a lot of points at a time Using MarkSim along with a GIS is a good way of testing model results over a study area It is also a good way to be left handling very large quantities of data For this reason we have included a number of batch processing options The Climate Batch File CBF is one example The CBF is a sequential ASCII file containing in each record the FULL path to a DAT file It looks like this C Program Files CIAT MarkSim dat K9238003 dat C Program Files CIAT MarkSim dat Mex07160 dat C Program Files CIAT MarkSim dat Hendersn dat CBF File Selection Climate ee eo SEE e hee Select View Drag and panel file drop You can construct a CBF in many ways You can type it in to an ASCII editor construct it from the DOS DIR instruction or you can use the handy drag and drop facility provided in MarkSim Y Select the CBF panel on the spatial input window Y Click on the drag and drop icon at the right of the panel You will see the DAT files available in the DAT directory displayed in the top left window You can search for DAT files in other directories or on other drives by altering the path and driv
52. he intermediate model parameter file known as a CLX file This needs User Reference Section 27 the climate data from a point on the interpolated climate surface as input The process uses two control files that can be viewed from the window after the CLX file has been created A record of the run is kept in the log file that can also be viewed after the run The log file can contain a full informative listing of the various operations in the process or can contain just error messages Once you are sure that everything is correct with a run or set of runs we recommend that you set the error reporting control to errors only because the log file can become large on long runs that create many CLX files t When viewing a file you are offered the option of editing it or viewing the data as graphics You may edit a CLX file but we highly recommend that you do not do so The parameters are interlinked and editing one without adjusting the set may result in serious errors The CLX file must be given a name of up to eight characters and the point to be simulated or the climate data for a simulation point must be provided This can be done in four different ways Use the panel select button to choose between the options 1 Georeference point entry The simplest form of spatial entry is controlled in the upper panel of the climate input screen Latitude and longitude are shown in degrees minutes and seconds and as decimal degrees If
53. ize minimize maximize close You can also control the window with the standard window control icons The menu bar consists of pull down menus that will activate the various services and tools All of these except help are available directly from the service icons The about box gives you information about the authors and about various copyright considerations for the software used in MarkSim development The right click menu gives you an alternative route to some of the tools that are found in the main menu service icons On the CD ROM you will find a range of shapefiles that you can overlay on the map using the layer control tool You can find these in the directory coverages They are not placed automatically on your hard disk at installation because you may not want to use them all They will supply map features such as roads rivers and towns to help you navigate about the map Beware They are for use with the map zoomed well in to present sufficient detail If you apply them to the map at full extent they will be so dense that they will practically color the map The map in the illustration is composed of sammunicip shp samcountry shp samtowns shp samrivers shp and samroads shp and shows the area around CIAT You will not find CIAT in the shapefiles I just put it there to let you know where we are The layer control tool allows you to color the map to your liking Go to the layer control tool and choose the layers you need
54. like to see the log file This is a file to record the process of the runs If you want the full information on the run choose full on the panel clxgen log Selecting errors will give you a minimal output with only the error messages It is best to change to this option once you are processing large quantities of data Now to practice entering the data with the MarkSim editor Y Select the DAT panel Da This editor icon will light up on the right of the panel i Aere Tutorial 7 Type in the data from the Mexican station given in the example above Type 500 for the January rainfall and try to save the file We have included some rudimentary data checks to trap errors If you want to check your typing as you progress use the cloud question mark icon to do a running check on the file Correct the January rainfall save the file and run the job Check with the log and have a look at the CLX file You will find a detailed description of the file contents in Appendix A IS When viewing a file you are offered the option of editing it W T amp or viewing the data as graphics You may edit a CLX file but we highly recommend that you do not do so The parameters are interlinked and editing one without adjusting the set may result in serious errors You can also use the DAT editor to correct files Enter the editor Select open a file Browse to find the Mexican file you have just made Open it and change the data C
55. ly with two of the parameter types rainfall event averages av and correlation matrices see below Derivation of parameter estimates The parameters for which we need regression submodels fall into two classes B ps and se have 12 monthly values the lag Theory 59 parameters d are single valued for each station or pixel We therefore created two sets of independent variates for their estimation The sets were derived from the basic station information and scaled as follows B ps and se d d d rm monthly rainfall 200 ra annual rainfall 200 tm monthly temperature 15 10 ta annual temperature 15 10 dm monthly diurnal temp range 11 4 da annual diurnal temp range 11 4 srm sqrt monthly rainfall 14 rar annual range rainfall 200 tmsq tm tar annual range temp 15 10 rmsq rm dar annual range diurnal temp 11 4 dmsq dm rasq tasq dasq ra ta da lat station latitude 90 rarsq tarsq darsq rar tar dar elev Ln station elevation 10 5 3 lat station latitude 90 sra sqrt ra The scaling was designed to place regression parameter estimates within a reasonable range for the subsequent selection process We ran a five stage stepwise regression for each cluster for B ps and se and a six stage stepwise regression for the d lag parameters Inspection of the results showed that correlations between the independent variates often resulted in large r
56. m tool and click on the Climate western pixel diagram tool Z Now click on the eastern pixel Tutorial 13 The first climate diagram will disappear behind the map window You will have to shift the map window to pick it up I am sorry about this it is a glitch that we have not been able to fix as yet You will notice that there is very little difference This is because the National Oceanographic and Atmospheric Administration NOAA digital elevation model DEM to which the climate grid is fitted holds the modal elevation not the average so it is approximating well to the valley floor The small difference you will notice is that the valley floor western pixel is slightly drier This is actually masking a larger effect that we would expect in this valley The Valle del Cauca is a large tropical valley and exhibits the typical large tropical valley circulation where there is a predominance of descending air in the valley center because of differential solar heating at the sides This results in a rainfall gradient that is wetter at the sides and drier in the middle MarkSim will shortly be linked to high precision 1 km or 20 arc second grids but we have to fix some problems of data storage and access before this can be implemented Choose which pixel you want and select the select a latitude longitude point tool point at the relevant pixel and left click Select The spatial input window will appear with the a coo
57. m wet winters hot dry summers Northville could be somewhere in California and Southville might be in Chile The August rainfall in Southville is received in January in Northville Figure 3 3 If we plot these rainfalls in polar coordinates we can readily see that to compare them we need to rotate them to a standard time Theory 53 Apr May Jul Aug Sep Oct Nov Northville 137 27 78 92 Southville 18 2 45 137 120 87 160 160 140 140 120 120 100 100 80 80 60 60 40 40 20 20 0 0 S 9 gt Ss gt RY FF KF FT KF S KF KF TF K LY Northville monthly rainfall Southville monthly rainfall Figure 3 3 Monthly rainfalls for Northville and Southville How do we do this automatically The answer is the 12 point Fourier transform This is fortunately the simplest of all the possible Fourier transform algorithms It is highly computationally efficient and fast In fact it is the basis of nearly all Fast Fourier transform algorithms that break the problem down sequentially into the simple 12 point case It takes the 12 monthly values and converts them to a series of sine and cosine functions The one used in MarkSim has a modification to make it conserve the monthly total values Jones 1987 The equation produced is 6 r a a sin ix b ix 5 i This can be rewritten as a series of frequency vectors each with an amplitude and a phase angle 8 t T a Ei N a a b 0 sin cos 6 Oo Oo j t If we s
58. mat 20 modifications 50 output 42 site field 17 site name 41 42 weather generator 50 DSSAT 3 5 output option 38 E edit 35 CLX file 7 DAT file 7 XBF 18 editor ASCII 6 14 17 28 30 35 40 66 DAT 7 GLF 14 icon 6 MarkSim 6 24 40 43 66 XBF 18 42 elevation model 51 enter data 66 erase all map layers 33 map layer 30 error 15 log 13 messages 6 report 31 reporting control 27 response 37 standard 48 term 45 estimates parameter 48 Euclidean distance 58 example CBF 8 DAT file 5 GLF 14 28 WTG file 16 XBF 18 40 F file ASCII 14 40 68 batch 17 68 CBF 68 construct 8 example 8 select 31 GLI 23 38 69 climate grid 37 climate normal select 30 31 CLX 14 17 29 65 batch run 39 construct 12 26 edit 7 multiple input 40 43 recreate 14 run 40 select 41 single run 39 correct 7 DAT 5 8 23 30 66 single 6 8 DAT directory 35 DBF 72 directory 35 DSSAT 23 format 30 65 73 GEN 71 log 6 13 27 31 MarkSim control search 17 WTG 23 XBF 17 40 41 68 editor 42 example 40 filename CLI 39 climate 16 39 CLX 27 28 41 format file 30 65 73 Fortran format 66 Fourier transform 48 53 function probit 44 functions 74 78 G gamma distribution 46 gamma shape parameter 46 74 GEN file 71 generate data tool 15 38 39 georeference list file See GLF georeference point entry 26 27 GLF 14
59. models Most users will not have much use for this output style For the format see Appendix A 40 MarkSim Multiple CLX file input A batch mode of operation is provided for the user who wishes to run many CLX files at once This is the mode to use where multiple simulations will be run to cover a geographic region or to simulate many points such as a set of regional trials The XBF is a list of CLX filenames with all of the data needed for each CLX file XBF name Browse to find View Drag and Create XBF and drop to XBF edit create in XBF XBF editor BUENAVEN BUEN 423 c CALI CALI 271 d CLXFILEO CLXF 0 c CLXFILE2 CLXG 0 c CLAFILE3 CLXH 0 c Example of an XBF MAYPEN MAYP 8135 d PALMIRA PALM 231 d PTAUPRINC 6868 c TULUA TULU 8971 c Output type Random number seed CLI filename CLX filename Here is an example of an XBF It is a sequential ASCII comma delimited file that can be prepared in any ASCII editor in the MarkSim editor or by drag and drop from a list of CLX files in one User Reference Section 41 or more directories The first field is the CLX filename This must start with an alphabetic character contain no special characters and be eight or less characters long The next field is the DSSAT site name This must start with an alphabetic character contain no special characters and be exactly four characters long This field can be blank if calendar output is requested see the case o
60. n a seed will be calculated from the system clock This will be reported in the log file so you can exactly duplicate the run at a later date by entering this seed If you specify DSSAT 3 5 output then you must also specify a site CLI filename The CLI file is not used in this simulation but is required for running DSSAT models User Reference Section 39 so one is constructed for you if it does not exist See Appendix B for the file structure As with the spatial data entry there are options for running a single CLX file or a batch run of many Use the panel select button to choose between these options Single CLX file input When running a single CLX you enter the data required directly in the upper panel Type in or browse for the filename of the CLX file from which you wish to run If your output option is DSSAT 3 5 then you must specify a four character DSSAT site name in the window under climate filename This is used to name the CLI file and also the sequence of WTG output files View or graph the CLX file Graph the WTG output files Select output type View the output file set The view weather files panel is not activated until you have run the simulation Once the run is complete you can look at the output file list Select a file and you can inspect it with the TeeChart graphics Calendar style output cannot be viewed graphically It is a shorthand output of rainfall data in the format used to create the MarkSim
61. ncluding Asia and southern China below 34 N Grid Independent Climate Data This form of input depends on the DAT file to input data to MarkSim A DAT file looks like this mex07160 17 130 92 720 70 471 471 471 42 43 23 47 115 264 188 236 275 172 86 56 18 0 18 2 20 8 22 4 22 8 22 1 21 7 21 5 21 1 20 8 19 5 17 9 10 4 141 1 23 0 13 3 12 39 11 7 21 6 13 6 16 5 9 6 10 3 9 9 See Appendix A for a full description of the format You can produce this fixed format ASCII file in a number of ways If you have 6 MarkSim data tabulated and wish to write out a series of DAT files the FORTRAN format for the file is a8 218 3 i6 12f5 0 12f5 1 12f5 1 Running single DAT files If you have only a few files to prepare you may type them in directly in an ASCII editor or use the MarkSim editor For grid independent data entry you do not need to load a map although if you have one displayed by default there is no harm in leaving it there Y Select the spatial input tool to bring up the spatial input window If you wish to enter data as a single DAT file select the DAT option in the third panel If the DAT file exists you can browse for it in the DAT directory We have placed palmira dat there for you to try Browse for palmira dat Y Open it Create the file palmira clx by clicking on Run MarkSim in the lower left corner of the window If there were no errors MarkSim will tell you so and ask if you would
62. nd drop facility The CLX files that are in the output directly will be displayed You can search for other files by changing the drive and path You can construct an XBF with CLX files drawn from various sources Y Select files to be incorporated and transfer them to the file building window on the right You have various options You must choose a number of years and output type but the other fields are optional If you leave the DSSAT site field blank the first four characters of the CLX filename will be used However the site name must be unique so if duplicates exist the name is incremented alphanumerically Thus if two fields result with the site name CLXF as in the example the second is incremented to CLXG the third to CLXH If you enter a site name then that is used as the first site name in the file and all 18 MarkSim subsequent ones are derived by incrementing If you leave the random number seed blank or zero then the first is derived from the system clock and subsequent ones from the random number generator ee Selected Fies ol type CLX to construct a XBF file Toj DSSAT Ste Name RandomSesd 0 J Yeas Ouipat Typa d o f SRAT MARI aie Ane g i ct FILES CLAT MARKSIM OUTPLIT CARIMAGU CLX Pass selected files Pass all files Construct and save file gt MarkSen Y Select DSSAT output enter 8 years leave the DSSAT name blank and the random number seed at zero Y Y Hit
63. no problem now that you have found it Y Go into the editor correct it and run the job again with just Itapevi because all the others ran correctly Running the Simulation Running a single site Once you have created your CLX files you need to move to the rungen phase to run the simulation and produce your simulated daily data output files The generate data tool will take you there or if you are in the climate input window merely switch to the second page The top panel will allow you to runa simulation from a single CLX file Use the browse key to find one of the CLX files that you created in the first part of the tutorial 16 MarkSim We will choose to generate DSSAT 3 5 style output for use with a DSSAT crop growth model Y Select the CLX file CARIMAGU CLX from the output directory Type in a climate filename of four characters or less This will be the name of the DSSAT i PS CLI file that will be produced In this Re 2 Run Rungen example it will be called CARI CLI and each Ses AMN year of the daily data output will be called CARInnO1 WTG where nn is the number of years Set the random number seed to 1243 Set the number of years you require and hit the run button Check the log to ensure that everything worked correctly You can now select the output file to check the data The start of the file CARIO101 WTG should look like this WEATHER cari From Interpolated Surfaces
64. nsion Davis CA USA Hutchinson M F 1997 ANUSPLIN Version 3 2 Users guide The Australian National University Centre for Resource and Environmental Studies Canberra AU 39 p Jones P G 1987 Current availability and deficiencies in data relevant to agro ecological studies in the geographic area covered by the IARCS In Bunting A H ed Agricultural Environments CAB International Wallingford GB p 69 83 Jones P G 1991 The CIAT Climate Database Version 3 41 Machine readable data set Centro Internacional de Agricultura Tropical CIAT Cali CO Jones P G 1996 Climate Database for Haiti Machine readable data set Centro Internacional de Agricultura Tropical CIAT Cali CO Jones P G Thornton be 1993_ rainfall ggnerator for licati ns agricultural app in the tropics Agric Forest Meteorol 63 1 19 Jones P G Thornton P K 1997 Spatial and temporal variability of rainfall related to a third order Markov mogel Agric Forest Meteorol 86 127 138 i tAr APET A ee Theory 63 Jones P G Thornton P K 1999 Fitting a third order Markov rainfall model to interpolated climate surfaces Agric Forest Meteorol 97 213 231 Jones P G Thornton P K 2000 MarkSim Software to generate daily weather data for Latin America and Africa Agron J 92 445 453 Marsaglia G Bray T A 1964 A convenient method for generating normal variables SIAM Rev 6 3 260 264 NOAA National Oceanographic an
65. of six records the title with site name latitude longitude and elevation TAV is the average temperature and AMP the monthly temperature amplitude The reference height REFHT and wind measurement height WNDHT are always set to missing values in MarkSim generated files The header is followed by 365 daily weather records 366 in leap years The date field is year day the data are solar radiation maximum and minimum temperatures and rainfall in millimeters SHP SHX DBF SBN SBX coverage files are ESRI shapefiles that are provided with MarkSim to give background detail to the map displays They are not used in MarkSim operations but allow the user to identify features when looking for a particular place There are files of country boundaries roads rivers towns contours and municipal boundaries Many of the coverages have been reworked from the Digital Chart of the World and are not complete In addition a set of shapefiles shows the grid cell bounds for the climate grids Because the climate grids are quite coarse they Appendix A 73 cannot match coastlines exactly and in mountainous areas are only an approximation to the relief detail Displaying the grid bounds on the map can help in choosing a site position or explaining why in some cases the error message appears saying no climate data are available for a point that appears to be on land near a coastline e7va wee Sew TS Appendix B Functions for Correcting the Cen
66. ol for Cali which appears directly below the A in the city name Left click 12 Oe u The map will redraw and a small blue dot will appear where the cursor was placed Y Track the cursor along the road to Palmira the Recta in local parlance until the distance at the lower left of the map window registers 23 km You have now arrived at the front gates of CIAT and the coordinates in latitude and longitude appear at the lower right of the window You are nearly ready to construct the CLX file for the location However the climate grid you are working from has pixels of 10 arc minutes on the side about 18 km at this latitude The valley at this point is only about 30 km wide check this with the MarkSim measuring tool just like you measured the distance down the Recta from Cali There is therefore one last check to make Go to the layer control tool and select america_grid from the shapefiles This contains the pixel boundaries of the climate grid You will have to go to the layer properties tool to set the fill to transparent because it is a polygon shapefile and you will need to see the map through it The grid pixel boundaries show that CIAT is almost exactly on a pixel boundary The eastern pixel includes some of the foothills of the Cordillera Central whereas the western pixel is almost all valley floor Check on the climate data to which you will be fitting Y Select the climate diagra
67. on MarkSim is a daily weather generator based on a third order Markov model for rainfall that is especially adapted to the tropics It runs off interpolated climate grids to estimate the parameters of the model It runs two parts that can be operated separately The model parameter estimation is the first part This produces an intermediate file known as a CLX file that contains the model parameters The LX file is then used as input to the second stage where the simulated daily data are produced The system offers a variety of input forms including an option to choose a point from the map The output comes in two standard forms the MarkSim calendar format and the DSSAT model input format See Appendix B for descriptions of the file formats The Map Window The basis window of MarkSim is termed the map window Although you do not need to load a map in order to use MarkSim this is the first window that appears when you fire up the software The window contains the menu bar and the service icons that you will use to do the job You can also access SOME gine bar Niii bis Service icons of the service functions through eA the right click menu eau Place the cursor anywhere on the Pee map window sonal 7 and right click SU This small B Rich menu will Wie click ES a menu appear Sa 4 Background User Reference Section 21 A right click on the title bar will give you the standard Windows control move s
68. or the present lets leave it as default Select the layer control tool to display the layer control window Use the zoom in tool to zoom into a window in western Colombia p ws We are going to add layers until you can see h a detailed map that you can navigate to find the relevant pixel for CIAT 4 zoom in as we go because the layers we are going to add will Layer Propierties Tool Load layer wn ee eee which is situated 23 km northeast of Cali on the road to Palmira We will cover the continent with a clutter of information Set layer properties Y Zoom in again as at right V Select the load layer icon in the layer properties tool You will be shown the layers available in the ire coverages directory E ein sa Y Select samroads shp and change the color to red Zoom to the window shown on the right then select the coverages samrivers and change the color to blue Select samtowns use set layer properties to set on the name in the labels fields Now we can see where we are CIAT lies in the Valle del Cauca or valley of the river Cauca between two large Andean mountain ranges the Cordillera Central to mL Ad iG the east and the S INA A Cordillera Occidental Te ES apt to the west also called iy ce CO ts gta W the Farallones or cliffs a S MIG of Can Y Make sure you have the zoom in tool selected and place the cursor over the place symb
69. ore details on the methods used in MarkSim can be found in Jones and Thornton 1993 1997 1999 and 2000 We summarize these below The Rainfall Model Rainfall is modeled using a two stage third order Markov chain First it is determined whether any particular day is wet this depends on whether there was any rainfall on the 3 previous days If so then the amount of rainfall is determined Probability of a wet day The probability of day i being wet is defined as P W D D D b a d a d a d 1 where is the inverse of the normal probability probit function b is the monthly baseline probit of a wet day following 3 consecutive dry days a are binary coefficients for rain 1 or no rain 0 on day m and d are lag constants Thus for example the probability of a wet day following 3 dry days is b and the probability of a wet day following 3 wet days is b d d d This part of the model is thus specified by 15 parameters The baseline probabilities b derived for each month and three lag constants d d and d which are unchanging from month to month Theory 45 The model uses a binomial error term and a probit link function The occurrences of rain on day i l day i 2 and day i 3 are treated as the independent variables and the monthly total as another variable This allows us to test the significance of the lag constants by using a chi squared statistic The results showed conclusivel
70. orm of display for the CLX file data This is the climate diagram tool which is described in the next section User Reference Section 25 The climate diagram tool Select the climate diagram tool and click on any point on the map The diagram will be displayed with maximum minimum and mean temperatures and monthly mean total rainfalls There are options for Cartesian or polar coordinates and for standard or rotated displays See Theory section for explanation of the rotation Under rotation the month names are meaningless so the months are merely numbered Lat Polar normal Polar rotated 26 MarkSim The tools to input spatial coordinates Two icons control this function They both bring up the same window but by different operations Select latitude longitude point tool Spatial input tool The select latitude longitude point tool does exactly what it says The spatial input tool brings up the climate input window directly to allow you to choose the form of entry you require Point and click on the map The climate input window will appear with the selected coordinates and elevation showing in the georeference point entry section of the window Check the climate for this point Open and view the GLP This button is used to view other files when selected Log for process control and error Panel select button Control error reporting The climate input window controls the creation of t
71. p and start from scratch with the X button lt gt NOTE The default map is defined with the complete paths to the map layers If you change the position of these files then delete them or do not have the CD ROM in the reader if that is where they reside MarkSim will not be able to complete the map MarkSim can handle any ESRI shapefiles that are in geographic coordinates latitude longitude It cannot handle projected layers because it does not pretend to be a full GIS The software is provided with a range of shapefiles to use as guides as to where you are in the areas selected In many cases these have far too much information for displaying at very small scales i e continental or world levels We are working on providing a range of products for use as you change scale but these will not be fully implemented until a later version You may however import any coverage you like as long as it is a shapefile in geographic coordinates The climate grids are not a complete match for the continental land coverages supplied with MarkSim This is partly because the grids have square pixels but also because some gaps occur where there are large lakes or wide rivers It is therefore possible that when you ask for a point that appears to be on land you may get an error response saying that there are no data for that point To make this explicit the shapefiles of the climate grid pixels are supplied on the CD ROM You can use these to
72. ply estimates obtained from sometimes short data sets have associated standard errors To introduce sufficient variability into the model any random sampling should be based on the uncertainty of the parameter estimates themselves The 12 monthly baseline probabilities b are autocorrelated because of the yearly progression of weather even in the tropics thus a resampling scheme must take these correlations __ Theory 49 into account This is done by randomly sampling from a 12 variate normal distribution The resampling scheme can be represented by b s RN b i 1 12 2 where b is the sampled value of b the baseline probability of rain s is the standard deviation of b and RN is a random normal number The resampling algorithm involves the Cholesky square root decomposition of the correlation matrix of monthly rainfall The correct correlation matrix to use would be that of the baseline probabilities in their probit transform In practice however this is difficult to calculate with short data sets We thus assumed a surrogate correlation matrix and used the standard errors per year obtained in the original GLIM analysis multiplied by the square root of n 1 where n is the number of years The pseudo random normal number generator of Marsaglia and Bray 1964 is used for rapid resampling of the 12 monthly baseline probabilities in their probit transform The algorithm then adds in the lag constants and produces a new matrix
73. ppened without Phil Thornton It has been done with remarkably 2 MarkSim little outside funding John Lynam of the Rockefeller Foundation has given us a couple of small but incredibly useful grants We would like to thank Paul Wilkens of the International Fertilizer Development Center IFDC for his programming in Delphi of the first version of the Windows interfacer Paul you will recognize some parts of it William Diaz as my system analyst and programmer has born the brunt of my quixotic decisions on the look and feel of the software for over a year now This version works I am sure that the next will be better but as it is already 2 years late this is what you get Peter G Jones Getting Started MarkSim is a Windows application that will be installed from the CD ROM and registered automatically The program files will normally be installed in the directory C Program Files CIAT and unless you have a good reason for installing in another directory we strongly recommend that you let the install package go ahead and do so Y Insert the CD ROM in your CD drive Go to the run prompt and type X setup where X is the drive letter of your CD drive The MarkSim system comes with large data files The first window of the install procedure shows an analysis of the disk space available on your system and subsequent windows will allow you to tailor the installation to make best use of this space Note
74. ranslate the software Upon loading the software into your computer you may retain the program CD ROM for backup purposes In addition you may make one copy of the software for the purpose of backup in the event the program CD ROM is damaged or destroyed You may not copy the user manual or parts of the user manual Except as authorized under this paragraph no copies of the software or the user manual may be made by you or any person under your authority or control LIMITED WARRANTY CIAT MAKES NO WARRANTIES INCLUDING WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ANY REMEDY UNDER THIS WARRANTY IS LIMITED TO RETURN OF THE SOFTWARE AND USER MANUAL TO THE DEALER OR TO CIAT FOR REPLACEMENT OR REFUND THIS WARRANTY IS VALID FOR 30 DAYS FROM YOUR DATE OF PURCHASE CIAT EXCLUDES ANY WARRANTY COVERAGE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES SOME STATES DO NOT ALLOW LIMITATIONS ON IMPLIED WARRANTIES SO SOME OF THE ABOVE LIMITATIONS MAY NOT APPLY TO YOU
75. rdinates and elevation of the pixel filled in for you ang se point too Type in a name for the CLX file Choose full reporting in the clxgen log panel Y Hit the run clxgen button You should see a message saying no errors were encountered and asking you if you would like to see the log Z Say yes and check what MarkSim has done for you When you are more confident about what is happening you can change the reporting option to errors only to save creating a large log file i a Multiple georeferenced point data If you are a power user perhaps running with a GIS system to simulate points sampled over an area or along a transect you will want a batch running system where all you do is specify the latitude longitude A perhaps the elevation and a name for the point The Georeference List File GLF is designed to do just that Y Select the spatial input tool and go to the GLF panel GLF name View Drag file and drop You can prepare the GLF as a comma delimited sequential ASCII file with any ASCII editor use the drag and drop facility or the MarkSim GLF editor A GLF could look like this spaces are not significant and missing elevation is recorded as 999 23 602 46 948 853 ITAPEVI 3 460 16 525 1523 CALI 4 340 12 3148 213 CARIMAGU 32 918 68 854 1219 CLXFILE3 3 893 77 073 999 BUENAVEN The drag and drop facility is of relatively limited use here because it searches for CLX fil
76. rict level that is to say zoomed in to large scales The icon erase all map layers clears the map completely for you to start anew It only removes them from the display map and does not affect the files themselves The move map layer up and move map layer down icons shift the selected layer up and down in the layer stack When the map layers cover different regions this has no effect on the map However when the layers are displayed over the same area the stack order matters The upper layers will obscure the lower layers This has a variety of effects depending on the type of layer you are displaying Closed polygon layers such as samcountries the country shapes for Latin America will obscure everything beneath them Obviously line 34 MarkSim and point files sit happily on top of closed polygon files but would be completely obscured if they were underneath 03 NOTE You can also drag and drop layers up or down with the cursor and mouse However this does not result in redrawing the image so you may not see a layer appear or disappear by this method until the map is redrawn The erase a map layer icon does precisely that and removes the selected layer from the map It does not delete the shapefile file Load a map layer will load a shapefile You will be cued to browse for the file to load It can be any shapefile that is appropriate to the map and anywhere that is accessible to the application Be careful that it is compatibl
77. rkspace However the MarkSim editor does not know which site name random number seed years or type of output you would like so it will leave these fields untouched If you add the record without modifying these they will contain the same information as the last selected record This will be OK for the last three fields because they can be the same throughout the file but the site name will be duplicated and will cause problems when you run the file with DSSAT output the previous outputs with that name will be overwritten We strongly recommend that you use the validation functions before you save and run the file You can do this record by record with the icon D Or you can validate the complete file with the icon a 44 MarkSim 3 Theory In essence there are two parts to MarkSim One is a reliable stochastic rainfall generator to drive a weather simulation model This is all very well when the user has the required parameters to generate synthetic weather records But what about the situation normal when one does not The second part of MarkSim is a set of surfaces of parameters that can be sampled by the user More correctly the parameters of the weather generator are not stored themselves but rather an intermediate set of parameters is stored that can be used to reconstitute a full set of weather generator parameters The reasons for this intermediate set of parameters are primarily to save space and to enhance efficiency M
78. rnal temperature range This makes 36 climate variates in three groups of 12 We use a simple interpolation algorithm based on the inverse square of the distance between the station and the interpolated point For each interpolated pixel we find the five nearest stations Then the inverse distance weights are calculated and applied to each monthly value of the data type being interpolated Thus for five stations with data values x and distances from the pixel distance d XY es ixel 5 2 i d 4 Temperature data are standardized to the elevation of the pixel in the DEM using a lapse rate model Jones 1991 Using this simple interpolation has various advantages First it is the fastest of all the common methods Second it puts the interpolated surface exactly through each station point because the weight 1 d 2 becomes infinite as d approaches zero Third the interpolation is highly stable in areas of sparse data It approaches the mean of the nearest stations while they all become equally distant Fourth it is relatively stable against errors in station elevation only the local region of that station is affected On the other hand laplacian spline techniques and co Kriging both propagate these errors more extensively This is one advantage of using a proven lapse rate 52 MarkSim model instead of fitting a local one as do both of these latter techniques The method has two small disadvantages First the derivative
79. sored Gamma Distribution The functions pc and ave approximate a stable value for the gamma shape parameter and mean as calculated from daily rainfall data censored below 1 mm from the relationship with mean monthly rainfall mm Sdf give an estimate of the standard deviation of the betas These functions are used as a check for the validity of the censored values NOTE As m tends to O pe tends to 35 31 this leaves reality behind by quite a long way Do not expect a reliable estimate below m 1 whereas avc is stable right down to m 0 real function pcir real m q xX m 1000 q m 10 0 return end real function ave m real m x x m 1000 ave 5 967 39 714 x VLLA x 2 return end real function sdf m real m if m eq 0 m 1 sdf 0 22757 0 02638 m 500 1 4238 1 057 0 503 m sm m sdf amin0O sdf 1 0977 return end Appendix B 75 The functions pu and avu give the uncensored gamma shape parameter estimated from the monthly rainfall calculated from the censored rain data The function pu is valid only for m ge 1 0 Below this value the function has no meaning because m is log transformed However monthly rainfalls below 1 mm may exist in fact they do not in the censored datasets It is truncated below 1 125 where it starts to climb to an infinite limit These functions are used to produce a stable estimate for the uncensored values when the parameters are out of range for the better correction
80. t av now requires only the baseline probabilities the lag parameters and the monthly rainfall normals The rain day probabilities are found by summing S Sor Sio and s and are divided into the monthly rainfall normals This eliminates 12 unwanted degrees of freedom and we have constrained the model to simulate actual long term monthly rainfall normals Correlation matrices As noted in Jones and Thornton 1997 we can see distinct patterns in the correlation matrices of many climate clusters These patterns can however be highly complex We therefore decided not to try to refine the estimate of the correlation matrices by fitting submodels 62 MarkSim within climate clusters but to accept the correlation matrix calculated from the pooled variance covariance matrices of the cluster members as being representative of all pixels allocated to that cluster References Bristow K L Campbell G S 1984 On the relationship between incoming solar radiation and daily maximum and minimum temperature Agric Forest Meteorol 31 159 166 Donatelli M Campbell G S 1997 A simple model to estimate global solar radiation PANDA Project Subproject 1 Series 1 Paper 26 International Symposium on Computational Intelligence ISCI Bologna IT 3 p Geng S Auburn J Brandstetter E Li B 1988 A program to simulate meteorological variables Documentation for SIMMETEO Agronomy Report No 204 University of California Crop Exte
81. ted Nations Food and Agriculture Organization FAO the Ford Foundation Fundaci n Polar the International Fund for Agricultural Development IFAD the Kellogg Foundation the Nippon Foundation the Rockefeller Foundation the Wallace Foundation and the World Bank CIAT also receives funds for research and development services provided under contract to a growing number of institutional clients Information and conclusions reported in this document do not necessarily reflect the position of any donor agency ISBN 958 694 046 2 MarkSim A Computer Tool That Generates Simulated Weather Data for Crop Modeling and Risk Assessment Version 1 2002 P G Jones P K Thornton W Diaz and P W Wilkens Edited by Annie L Jones U ADE 1EFOIMA ANY AGIAN pojema 1 DIC 2007 Manual Copyright 1998 2002 Software Copyright 1978 2002 MarkSim is written using MapObjects LT and Delphi MapObjects LT is a trademark of the Environmental Systems Research Institute Inc Copyright 1999 Environmental Systems Research Institute Inc All Rights Reserved Delphi is a trademark of Borland International Inc Copyright 1983 1999 Inprise Corporation Centro Internacional de Agricultura Tropica International Center for Tropical Agriculture Apartado A reo 6713 Cali Colombia Fax 57 2 4450000 E mail p jones cgiar org CIAT Publication No 330 ISBN 958 694 047 0 CD ROM ISBN 958 694 046 2 manual Press run 50
82. th an ASCII editor or more easily by drag and drop from a list of DAT files The drag and drop window is identical to that described above to form the GLF The only difference is the format of the file created In this case it is the name of each DAT file including the full path Error reporting The clxgen process produces a file called clxgen log as it runs At the end of a run a window will be displayed asking if you wish to see the log file You can also open it at any subsequent time by clicking on the log file button It is overwritten each time you run the process so if you wish to keep the information it should be renamed It is produced in the c program files ciat MarkSim directory This directory holds sensitive files so observe caution when accessing it with software other than MarkSim At the foot of the spatial input window two buttons select the type of reporting Errors will give a short report including only error messages and 32 MarkSim warnings Full yields a complete listing including all control file records and the resulting CLX output When processing large numbers of points this can result in a large log file It is best to use full only when you encounter difficulties Other mysterious files MarkSim ctr and Markov98 ctr are control files that are used to transfer information to the stochastic weather generation process You usually only need to view these files for debugging purposes their structure is given f
83. thly average C Temperature minimum all days monthly average C Rainfall total mm month Rainy days month Daily sunshine duration monthly average percent In this file missing data In this file dummy data S S See Appendix A 71 Calendar format simulated rainfall file GEN consists of a header followed by 31 records for each year and a final trailer record at the end of file The header is two records the year number filename latitude longitude and elevation followed by a record of month labels The trailer is similar to the first header record but with the word END in the first three characters 0001 buenaven Interpolated 3 895 77 073 60 JAN FEB MAR APR MAY JUN JUL AUG SEP OCT NOV DEC 1 7 118 0 109 244 253 60 42 230 32 207 124 2 191 S500 286 193 23 100 171 14 207 67 19 16 3 226 0 95 21 22 30 252 61 78 70 33 39 lt 0 5 495 47 8 50 145 641 164 53 120 5 94 0 50 0 120 181 60 202 284 196 142 120 6 227 338 158 0 227 407 94 86 131 105 154 32 7 0 116 6 120 340 0 140 37 262 151 443 189 8 0 61 50 170 336 id 132 0 0 7 105 313 9 0 Q 329 243 36 153 0 88 198 109 0 259 10 0 0 204 190 83 209 0 0 91 374 26 256 11 252 0 0 313 106 393 G 264 179 T16 122 125 12 22 0 19 56 173 37 154 LS FS 396 257 110 13 88 0 30 437 54 70 52 TA 57 ATS 370 98 14 300 0 245 0 900 237 50 150 229 0 52 75 15166 65 100 108 50 0 4 88 41 0 S34 TA 16 76 22 167 2 278 186 250 133 28 0 247 70 17 40 248 98 la 351 37 82 124 35
84. throughout the world Theory 47 We therefore needed a way to correct for the effect of censoring because we could not disregard it We ran 182 14 x 13 Monte Carlo simulations producing 100 000 samples from each of the gamma populations on the intersections of the rectangular lower grid in Figure 3 2 We calculated the mean and shape factor for each simulation to check the sampling We had to use a censoring to 0 000001 mm to avoid taking logs of very small numbers For some of the populations typically one sample in 100 000 was rejected because of this and the sample parameters matched the population parameters within 0 001 for the shape parameter and about 0 02 for the mean We then censored the sample data to 1 mm and recalculated the parameters Censoring to mm shifts the parameters by 15 distorting the projection 2 saa UNI NSL ASS SSS i NN SSS SS R 2 10 SSS SEE se a eee SSS Ser SES ns SDE ae led as ee a co i _ HE pT ston distribution Na i i parameters 3 0 9 0 15 0 21 0 27 0 Mean rainfall event size mm Figure 3 2 Distortion produced in the gamma distribution parameters by censoring to 1 mm 48 MarkSim The distorted upper grid shows the distortion introduced by the censoring As can be seen it is a monotonic distortion of the plane like a map projection The arrows at the corners show the movement needed at those points to undo the distortion We can therefore correct for it b
85. to alter the climate data or model parameters as the results can be unpredictable If you wish to adjust the climate information use the DAT file format described below You can simply cut and paste the data records from the foot of the CLX file to construct a DAT file a palmira Interpolated 3 544 76 306 1005 0 wep OR 9 966 0 050 90 53 0 65S O l 14 0 084 0 072 06 09 03 101 0 074 056 059 0 072 0 U6 093 0 091 1 000 0 16 0 114 0 083 0 064 0 066 O 082 0 116 t2 106 0 092 D103 0 336 1 000 Q TF3 8 097 0 8971 0 076 0 896 0 138 0 140 0 221 O 090 O 202 Totla 0 333 1 000 6 3095 0 071 8 078 C 993 6 23354 addi 8129 0 066 0 074 6 083 097 90 095 1 000 6 054 6 057 0 068 80 099 0 101 0 088 0 050 0 056 0 0644 071 0 0 1 0 054 1 000 09 043 0 0598 G 071 0 075 9 066 SS 0 066 7 OG 057 43 0 054 0 0 78 0 069 Q 5 2 0 082 i 6 0 8 050 4 0 T 098 0 085 9 iE 16 138 0 134 999 71 26 4 122 0 094 6 186 2320 0 740 8 147 0 202 0 075 0 078 6 098 O 142 1 000 V 925 0 083 0 093 O TOG 2212 0 179 6 6888 O 066 0 069 0 085 g bh22 0 525 1 800 MONTH AV P BETA RAINDAYS Sis 6 6 0 2353 1 736 0 316 0 76106 Z f Ai Y 4 33 4 9 329 i 500 43 965 4 B F 4 342 25 2518 8 8 0 327 435 65 5641 3 369 802 29 544 6 9 0 484 L176 150 23316 8 E Oars fe Bik 0 952 0 220 1 27601 4 6 66 7 30 gt 2612 0 9 0 ja 0 308 0 q 95 1 8 4 34 0 5 0 429 g2 12 0 344 0 60 0 38 0 25 H F 0 5750 WLIS 2075 N 2 luster 132 Phase 0 452 rain
86. tory They can be edited there using an ASCII editor e g Notepad but will not be applied until you leave MarkSim and restart the application Changing them through the configuration window will make them valid_for the current session Sources Ouilputs Others 3 Output Directory c Program fles Ciat MarkSim output 7 RE Biowse i The output directory should definitely be moved to another disk if at all possible MarkSim can produce voluminous data files which will often be used onwards in modeling applications These are best kept separate from the disk partition used for the program files because filling the disk space may mean that your applications no longer run The default map layers define those shapefiles that you require to be loaded automatically when you fire up MarkSim R Configuration Sources Outputs C Program Files CIAT Mark Sim coverage seacountries shp k Detaut maplayer C Program Fies CIAT MarkSim coverage samcountnes shp C Program Files CIAT MarkSim coverage afrcountnes shp sty Zr eee LS r A n ET TO a AN eee ee a arna aa e a m eene e oe een eye User Reference Section 37 To compile a set for the default map use the browse facility to open shapefiles into the top window Use the plus button to add the latter to the default map To delete a layer select it with the arrow keys or by clicking on it in the list and using the minus button You can clear the complete ma
87. ual variance 48 50 ASCII comma delimited file 40 68 editor 6 14 17 28 30 35 40 66 file 14 Asia climate grid 5 background coverage 35 batch file 17 68 batch mode 40 batch processing options 8 batch run CLX file 39 batch running system 14 binomial error term 45 C calendar format MarkSim 20 simulated rainfall file See GEN file calendar output 19 39 41 Cartesian coordinates 25 CBF 68 construct 8 example 8 select 31 censoring 45 distortion 47 effect 46 change scale 37 check data 7 16 sampling 47 validity of censored values 74 choose layer 21 CLI file 23 38 69 available data 24 filename 39 climate available data 24 data 23 grid independent 5 diagram tool 25 entry window 26 filename 16 39 grid 12 37 Africa 27 Asia 5 file 37 interpolated 5 20 22 Latin America 27 navigate 10 pixel boundaries 12 input window 26 Mediterranean 52 56 normal file select 30 31 surface 59 51 62 interpolated 58 spatially interpolated 51 world 56 climate batch file See CBF climate date standardization See rotation climate definition file See DAT file cluster algorithm analysis 58 clustering data 58 CLX batch file 17 See XBF file 14 17 29 65 available data 24 batch run 39 construct 12 create 26 edit 7 recreate 14 run 40 select 41 single run 39 filename 27 28 41 multiple file input 40 43 clxgen 29 31 run 15 coefficient r
88. ubtract the first phase angle from all the other vectors in the set then we have produced a rigid rotation of the vectors This is the rotation that we are seeking It puts the maximum of the first frequency at a phase angle of zero and places the rest in positions equivalent to their angular separation in the original data We then use the first phase angle for rainfall to rotate the data for temperature and diurnal temperature range and these variates are rigidly rotated along with the rainfall 54 MarkSim Jul Jul Northville Southville Southville rainfall rotated to coincide with timing of Northville This explanation works well for the tropics There was a small chance of the procedure going off the rails if the rainfall record did not have a seasonal peak This was the case in some records from tropical desert regions in these cases the rotation was ambiguous and sometimes resulted in pixels allocated to the wrong cluster The beta release of MarkSim went out with this type of rotation algorithm as did the first release of FloraMap When the climate grids of the latter were extended to Europe the case arose where annual climate pattern was dominated by temperature and not rainfall We therefore have the possibility of rotating on rainfall or temperature but when to decide which is the dominant We tried many combinations of rules but unfortunately came to the Theory 55 conclusion that none were acceptable
89. ude is decimal degrees with longitudes west of Greenwich negative A DAT file can be created using an ASCII editor such as Notepad However in this case too we have included an input facility to help with the formatting Y Click on the page symbol at the right of the panel and the DAT data entry window will appear You may use this to enter a new DAT file or if you have selected one with the browse facility you can use it to edit the file and validate the data At present MarkSim merely checks that the site name is valid and that coordinates elevation and data are within real world limits In later releases we will be including more sophisticated checks User Reference Section 31 i Create DAT File SteName fendersni owe aa OR S gt A Elevation 1292 January February March April May June July August Sept October Nov Dec Monthy Total Raestall imr CO Cn ec SC Monthly Mean Temperature a far fe fe fe RE fs fer fas fee a a Monthy Dumat Tersperature Range ie fine fe fa fer iar fe fis fe a fe Make sure that the DAT file is in the MarkSim data entry directory defined in the configuration window 4 Climate batch file selection You may have a large number of DAT files to use to create CLX files These may be in the MarkSim data entry directory or they may be elsewhere The climate batch file selection panel allows you to select a CBF that gives the names and paths to these files It may be created wi
90. ully in Appendix A They are also found in the c program files ciat MarkSim directory The zoom tools Zoom in a bit tool Zoom out a bit tool Zoom to area tool Pan tool Zoom out to full extent tool v The zoom and pan operations are reasonably standard Zoom in by drawing the desired window on the display map Pan by pushing the map with the hand cursor The zoom out feature is a map reset it will zoom out to the full extent of the map For a gradual zoom in or out the zoom in a bit and zoom out a bit tools are available User Reference Section 33 The layer control tool Move selected map Erase selected map layer layer up or down Erase all Layer control tool Set layer characteristic map layers Set map layer Selected map colors layer Load a map layer Set map background color Each map layer is an ESRI shapefile representing geographic features that will help you to identify the points you want to choose on the map Shapefiles are described in Appendix B A number of files are included on the CD ROM MarkSim will however accept shapefiles from any source provided that they are in geographic coordinates latitude longitude and are at a scale appropriate for the window in which you wish to work NOTE The files of roads and rivers included with MarkSim v1 00 are not suitable for display at the scales of the full map extent However they are useful when displaying at the department or dist
91. y the Mediterranean climates are at moderately high latitudes and we can afford to have the rotation dominated by temperature without losing generality in the rotations and comparisons We therefore need to increase the weighting for the temperature vector smoothly as we approach the Mediterranean climates in order to avoid a sudden swing The following weightings were found to work well p rainfallmm t temperature x 2 x abs latitude Theory 57 There is a potential trap when the two vectors almost cancel each other This could result in wild swings of the rotation angle for small changes in the rainfall and temperature vectors This becomes more likely as the situation passes from that in A above to B and beyond The dashed arrows are the rotation vectors as before but calculated on the weighted rainfall and temperature vectors Where the rotation vector is the vector sum r t the counter diagonal vector is the difference r t It can be readily seen that the dangerous areas will be when r t is much greater than r t We can therefore use a handy index of stability s 8 s arctan This will be zero for stable states where the rotation angle is dominated by rainfall by temperature or by both acting in concert It will approach n 2 as the vectors tend towards canceling their effects Because we can map this index we can check for areas where this indeterminate rotation might occur Areas of relatively high s
92. y that a third order Markov rainfall model was necessary because the chi squared statistic related to the inclusion of the third order lag in the model was highly significant for 92 of the tropical locations that we have studied This method of fitting the model also allowed us to test the significance of any interaction between the lag constants and the probabilities for the 12 months Although certain data sets did show small interaction effects this was generally not the rule and it was concluded that under a probit transform the lag effects could be considered additive to the monthly effects see Equation 1 The residual deviance tested as a chi squared statistic was insignificant in almost all cases Rainfall on a wet day Rainfall is modeled by using the censored gamma distribution restricted below 1 mm to determine daily rainfall amounts on those days that rainfall is experienced Sterne and Coe 1982 The method of maximum likelihood is used to estimate the mean and shape parameters of this distribution for each calendar month thus giving rise to 24 additional model parameters The censoring of the gamma distribution means truncating the lower part of the distribution This is especially important in the case of the gamma distribution because if the shape parameter is low then there is a large proportion of small values small rainfall events Differences in the rainfall measurements or reporting mean that these small events
93. y working out the projection functions We used Genstat to fit stepwise regressions to the complete set of 6 order polynomial variables These are x 38 y y plus all cross products The fitted functions are shown in Appendix B Now we know that by censoring the rainfall we have eliminated all the events with less than 1 mm rainfall so we have to adjust the frequency of events also if we just use the corrections above the overall amount of rain per month will fall in the model The answer is to divide the rainfall probability by the probability of gamma p av exceeding 1 mm after reconstituting the probabilities from the probits Interpolating Back to Daily Data In generating rainfall records the monthly baseline probabilities the probability of rain after no rain for 3 successive days are interpolated to daily probabilities by using the 12 point Fourier transform described in Jones 1987 The lag effects are then added to each day s probit transform of the baseline probability to produce a matrix of 365 or 366 days by eight states wet or dry conditions on 3 successive days The inverse probit transform is then used to transform this matrix to normal probabilities Similarly the monthly mean and shape parameters of the gamma distribution of rainfall amounts are interpolated to daily values by using the 12 point Fourier transform Annual Variance and the Variability of Parameters The parameters of the model being sim

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