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DIVA-GIS Manual

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1. the selection window rectangle circle etc can be set in Tools General Options 26 DIVA GIS 7 Selections can be cleared using Clear Selection The selection can also be converted to saved as a new shapefile with Data Selection to New Shapefile The Filter facility also allows you to select features of a shapefile but only one field at the time and you can t save the result to a new shapefile 4 6 Copy and Paste The Copy and Paste functions can be used to copy and paste a layer in the legend This is useful if you want to use one layer more than once on the same map For example a layer of a country can be used as the lowest layer to give a background color and this time with transparent polygons as the highest layer to place departmental boundaries on top of all other layers 27 DIVA GIS 7 5 THE MAP MENU The Map menu includes functions for changing the properties of the map extent center and scale These are explained in Box 6 Box 6 The Map menu Icon Sect e ul gt 3 al a al al E E E Name Properties Measure Distance Map to Image Zoom to Full Extent Zoom to Active Layer Zoom to Selected Zoom In Zoom Out Previous Next Pan Overview Map Design View 5 1 Map to image Short explanation Sets map properties background color projection Measures a distance by clicking twice or more on the map double click to stop drawing Exports the map or
2. For example 28 50 0 0 28 50 174505 50 2769288 00 Some SID images do not need a world file In many cases these images already have world files e g the SID images that can be downloaded from https zulu ssc nasa gov mrsid If your image does not have a world file you will need to create one and you can use the Georeference Image tool for that You will need to know how many rows and columns your image has You can find this out with most graphics programs You then fill this in as well as the estimated coordinates of the extremes of the image By overlaying a shapefile of the same area you can see if the coordinates are correct You will probably need to change them little by little a number of times before the image is correctly located 10 5 Geo calculator With the Geo calculator you can convert coordinates in the sexagesimal degrees minutes seconds system to a decimal system This can be done for one location or for a file with many locations use the Batch option You can also calculate the distance between two points 10 6 Options The Options window lets you define a number of default settings including the font used and how map features are selected 68 DIVA GIS 7 On the second tab you can specify where DIVA should look for climate CLM files and you can inspect and edit the metadata associated with these files 69 DIVA GIS 7 REFERENCES Bonham Carter G 1994 Geographic informa
3. Map The map you re working on Overview Map Shows the location of what is visible on the map in a wider region Oo 09009 Status bar Indicates from left to right the location of the cursor x and y coordinates the scale of the map the value and position row column of a gridcell and the distance between two points 7 Data Design view tabs Figure 1 The DIVA GIS main window in Data view DIVA GIS 7 Double clicking on a layer in the TOC or clicking on Layer Properties brings up a small window that allows changes to be made to some of the layer s properties such as its colors on the map Figures 2 and 3 It is important that you explore these windows click on the different tabs See Section 5 2 for more details about them aio Alas PE_LDEPARTMENTS Source Jecipragram filestdiva gisttutoripe_departments shp Type Polygon 81 33 0 04 68 65 18 35 Single Unique Classes Field NAME Legend Colors Reset Legend Use color of single tab vi AMAZONAS wo E ANCASH rf E APURIMAC Voo AREQUIPA in i AYACUCHO he EJ CAJAMARCA Select Al Clear All Filename A Legend Info History Auto complete 0 200 f Edit values C Select rows 400 200 400 agg 400 S00 1200 800 1200 Select color scheme 1200 2000 1200 2000 000 694 2000 7694 Ramp cu Modata MoData Read From File Add or Remove Aow Ww NoData Transpa
4. ccccsccccccccescccccccessceescecesceeesceessceeess 39 6 2 6 Choosing complementary areaS oooocooocconccconcccnacconoccnncoconoccooo 40 6 2 7 A ON 41 Methods of converting point data to grid data oooooomooo 42 6 3 1 Circular MNEWNDOMNOO iia 42 PORE COLPOW GON ni idad 43 POMELO OWEN ai 44 SUMMA ZO POMS 2 da 44 DISTANCIA T IEE EE TEA EEE ad A at used oh E ena 44 Au tocorrelal ON aa 45 6 8 1 FOF DONS norr ia ANA 45 6 8 2 FOF ondel sna a 46 EIE 8 0104 2 0 y y POOE A AET TEE E E E E E E EEST 47 REOPCSSION as csc unicn saahcealeasveceatat E E A E saenetsoeeaoes 47 MUIDE REOTESSION etario 47 THE MODELING MENU sones a 48 BIOCUNT A DOMA eree a r S 48 7 1 1 MDU io craton lead ate sd 48 7 1 2 A cas EE E ew nen eee E EE 49 7 1 3 UC ns E 49 7 1 4 PUSTO OI sates Sorte gs eee a weal tech EE ta 49 7 1 5 ENVIO ocios 49 7 1 6 A edie E E E E eee uaa maw urea R 50 Externat Models a AS AA a 92 EVALUACION ncaatatewesd E E T O aa 52 Fe 9 ol PVC Dake DOIN S ornen E E eae amen saserdenewones 52 72332 Greate Fvalua Gon IlO in da 53 7 3 1 SNOW ROG ROD Da A peau toute eeeoanvansis 53 FOG POD ri toda 94 FAE GRIDIMENU rs so tad ose 9 DOSED ratio E EEEE PEE EE E ee cween aes 57 OV CHIOV ars tatoo OEE ENE 58 SCG GF css clvintscl ad 59 8 4 ROCOSAS 59 Oso NerOnDOURNOO las daass 99 8 6 Calculator Va ae 60 Bel ARBOL dis 60 00 DISGGClCOGlC iscas dacoxnstanatcuiacctecdiuesasasenleusteateneiastecsiacseessueaen 61 8 9 CU risa raless 61
5. 2 External Models Uses other models to predict the presence of species 7 3 Evaluation 7 5 EcoCrop Predicts the adaptation of a crop for a selected area 7 6 Terrain Modeling Creates grids of aspect or slope from an elevation grid 7 1 Bioclim Domain With the Bioclim Domain tool you can extract data from the climate database for point locations in the active points shapefile make graphs of these data and use the extracted data for predictive niche modeling using the BIOCLIM Busby 1991 Nix 1986 and the DOMAIN Carpenter et al 1993 approach You can only open this window when a points shapefile is the active layer on your Table of Contents There are six tabs in this window 7 1 1 Input Here you can choose to run a model with the standard climate data DIVA climate data or with a stack of layers of your choosing You can also choose to consider all points as one class or distinguish different classes e g species by selecting an appropriate field Duplicate points with exactly the same coordinates and species are removed from the analysis You can choose whether 48 DIVA GIS 7 you want to also remove points that fall within the same grid cell this is recommended 7 1 2 Frequency You can make cumulative frequency distribution plots for various climatic variables for up to two classes e g species which are shown in different colors on the graph This can be very useful in spotting outliers
6. Predict tab 7 2 External Models With this module you can export points from a shapefile to prepare input files for external distribution models i e ones not supported directly by DIVA GIS In some cases such as for MAXENT and GARP this is in fact not very difficult because they just use a list of species with coordinates However for programs that need a site by species matrix such as GRASP the preparation of input files is far from trivial For GRASP 3 files are made YYY XXX and XXXpred Some models will produce grids in a format that DIVA can import via the Data Import to Gridfile menu GRASP however produces LookUp Tables or LUT files that can be imported in this module You must select the LUTs you want together with the stack that was used to make the input files or another but compatible stack if you study climate change 7 3 Evaluation Using this menu you can evaluate the performance of a niche model It is a three step process as described below a sub menu for each step 7 3 1 Prepare points This tool allows you to split point distribution data into a number of subsets that you can use to test a distribution model You can specify what percentage of the points you want to use to train i e run the model as a percentage of the total number of points Sample size training data and how many separate times you want to do the sampling Repetitions You can also sample th
7. a project including all data to a DIVA GIS export file file with extension DIX E 2 2 Import Project Imports a DIVA GIS export file DIX 2 1 Her you can find a list of the 10 last used DIVA GIS projects E Closes the project and shuts down DIVA GIS 2 1 Projects A DIVA GIS project is a description of a DIVA GIS map it includes a collection of layers and their display properties as well as some general parameters describing the map s scale and center A project file can be closed saved with a new name and opened again using commands from the Project menu To create a new project select New This creates an empty map that can be filled by adding features using Layer Add You can save a project by clicking on Project Save Project files have the extension DIV The names of the last 10 projects you saved are listed at the bottom of the Project menu to allow quick access to these files You can open a recently used project by selecting it from this list It is important that you clearly understand the difference between a DIVA GIS project file DIV and the layers files that make up the map The project file does not 11 DIVA GIS 7 contain the actual data it only points to the files containing the data pertaining to the different layers included in the project and stores map properties such as scale Relative paths e g diva myshp shp are stored for data files that are below the project file in the folder st
8. and only there Each column with data should have a field name The names of fields may not be repeated may not start with a number and should only consist of letters and numbers Field names should NOT contain characters such as and gt Field names should not be longer than 11 characters Always make a backup copy of the DBF file and save the new file in the native format first so that you do not lose your data should they not be saved correctly as DBF DIVA GIS 7 1 5 Geographic coordinates There are several ways to describe a location on the Earth The most commonly used are degrees of longitude and latitude A location can be between 180 West and 180 East and between 90 North and 90 South Degrees are often subdivided using a sexagesimal system a calculus system with 60 as the basic number of minutes and seconds exactly as done with subdivision of hours For example a latitude can be described as e g 12734 15 S 12 degrees 34 minutes 15 seconds Southern hemisphere This system worked fine in the days of paper maps but it is not very suitable for the digital age A decimal system is universally used in geographic computing In the decimal system latitude and longitude are described by a single number each and no letters with the sign indicating the hemisphere N or E S or W e g 12 57083 for 12 34 15 S To convert longitude and latitude in degrees minutes and se
9. data in a grid against those Regression in two or more other grids _ o Lu 6 1 Point to Grid Some of the main analytical functionality in DIVA GIS is found in the Analysis Point to Grid menu As the name implies this menu allows you to take point data in a shapefile and create gridfiles where each grid cell takes a value calculated based on the points that are found within the cell The Point to Grid window is shown in Figure 8 29 DIVA GIS 7 Point to Grid Input Shapetile lc Shemp nes mar ship Define Grid Create a new Grid r Options Output Yarable Richness Number of different classes Richness Point to Grid Procedure Simple Output gy he Apply W Close Figure 8 The Point to Grid window 6 1 1 Defining grids The first step is to define the extent and resolution of the grid that will be used to make the calculations You can either specify this from scratch or copy the parameters from an existing gridfile A grid has an extent which refers to the geographic area it covers As a grid is rectangular it can be defined by two opposite corners e g the upper left and the lower right corner The resolution is the area of each grid cell Resolution is always expressed in the units of the geographic reference system For example in the case of the latitude longitude system a resolution of 1 means that each cell is 1 degree by 1 degree The verti
10. its TOC to the clipboard or toa graphics file Zooms to the extent of all layers included in the TOC Zooms to the extent of the currently active layer Zooms to the extent of the current selection if any Zooms in to a point by a mouse click or to an area by drawing a rectangle while holding the left mouse button down Zooms out from a point by a mouse click Goes back to the previous setting zoom pan Goes to the next setting zoom pan after Previous Moves the visible zone of the map by holding down the left mouse button and moving the mouse Show or hide the overview map Switch to design view from map view to create a map e g with legend text scalebar With Map to Image you can export either the current map or its table of contents to the clipboard or to a graphics file in BMP bitmap or EMF enhanced metafile format These images can subsequently be used as an illustration in other applications such as a word processor or presentation software BMP is a raster image format while EMF is a vector format You may want to convert these to JPG format using a graphics package to save space 28 DIVA GIS 7 6 THE ANALYSIS MENU This chapter describes the methods for analyzing biological distribution data available in DIVA GIS These analyses are all based on the location latitude and longitude and additional attributes of point data The points represent locations where a specimen e g herb
11. the sample is calculated over the random samples the default is 100 samples for each sample size but a higher number may be better for some data The number of species is estimated from this generated species accumulation curve This asymptotic model assumes that the probability that the next individual captured will be a new species declines linearly with species number and thus the species accumulation curve is the negative exponential function S ny S k is a fitted constant Equation 2 n the number of samples 36 DIVA GIS 7 The asymptotic behavior of the accumulation curve can also be modeled as the hyperbola Maj 2 H s n iii Equation 3 Smax and B are fitted constants This is the Michaelis Menten equation used in enzyme kinetics and thus there is an extensive literature discussing the estimation of its parameters which unfortunately presents considerable statistical difficulties Colwell and Coddington 1994 The method implemented in DIVA GIS favored by Raaijmakers 1987 is to calculate Smax and B using their maximum likelihood estimators as follows If A n and Y an then H _ XS s _ and FS Ad a Pe es Equation 4 Syy Sxx and Sy the sums of squares and cross products of the deviations Y Y and X X i S obs This is simply the actual number of species observed per grid cell 6 2 3 Turnover Turnover or beta diversity is a meas
12. the total number of species or whatever other units Smax for the area This estimate can give both a measure of the completeness of the inventory and also allow for better i e less biased by the number of observations comparison with the species richness of other localities An estimate of the maximum number of species is also useful when assessing if the further information to be gained from continued sampling justifies the cost Various different approaches have been proposed to estimate Smax Some of these have been implemented in DIVA GIS based on the review by Colwell and Coddington 1994 and later authors Chao 1 34 DIVA GIS 7 Chao 1984 derived a simple estimator S1 or Chao 1 of the true number of species in an assemblage based on the number of rare species in the sample S Sons a 2b Sobs the observed number of species in a sample a the number of observed species that are represented by only a single individual in that sample i e the number of singletons b the number of observed species represented by exactly two individuals in that sample the number of doubletons Chao 1 Corrected This corrected version replaces the original Chao estimator which is still included to allow for comparison with studies that have used this estimator The corrected version is less biased Ef E E Senant Sons SS Chaol obs 2 F 1 2 F 1 Sobs the total number of species o
13. then pressing the Read from layer button The coordinates need to be adjusted to those of the climate grid cells You can do this by pressing the Adjust button If you do not do this the program will do it when you press Apply You can run the EcoCrop module for current and for future climate see ROPmin ROPmax 100 75 50 Suitability 25 0 500 1000 1500 2000 Rainfall mm section 8 1 You must name an output gridfile Figure 13 Relation between rainfall during the growing season and calculated rainfall suitability values for that month The parameters are for maize 56 DIVA GIS 7 8 THE GRID MENU Various functions are available in the Grid menu which allow you to create new grids from one or more existing ones They are listed in Box 10 Box 9 The Grid menu Ilco Sect n 8 1 8 2 8 3 8 4 8 5 8 6 8 8 8 8 9 8 10 8 11 Name Describe Overlay Scalar Reclass Neighborhood Aggregate Disaggregate Cut Concatenate New Transect 8 1 Describe Short explanation Describes the contents and structure of a grid Carries out arithmetic on the values of corresponding grid cells in two grids Carries out arithmetic on a single grid Classifies the values of a grid in a new way Carries out neighborhood operations such as filter and pattern analysis Aggregates combines cells of a grid Disaggregates divides cells of a grid Cuts a specif
14. your own climate grids CLM files are used to store grids of monthly climate data in DIVA GIS All input files gridfiles must have the same number of rows and columns and the Same origin You must always provide a gridfile with altitude data If you do not have such a file you can replace it with any other file as long as it has data and nodata in the right places and of course the output altitude file should be discarded It is important to note that cells with nodata in the altitude file will not be stored in the CLM files The output of Make CLM files should always include the files index clm and a cli file without which the climate data files cannot be read properly Store all files in a single 19 DIVA GIS 7 folder Set the default path for the climate data to that folder in Tools General Options 3 9 Check Coordinates The Check Coordinates facility helps you to verify whether coordinates are correct The first time you make a shapefile of your database you are most likely to immediately spot some gross errors For example if you have a file of terrestrial bird specimen from the Solomon Islands it is likely that some dots will fall in the ocean and there might even be one in Siberia These impossible or unlikely locations are easy to spot and often also easy to correct They may well be just typing errors However it is likely that there will also be other errors that cannot be spotted so easily The Da
15. 0 10 CONANA O ii it nese E ERA 62 Ben NOW nia 62 A SE AAA O E EE OE tes mebeawencss 62 0 13 APC std tl dad 62 9 GHE 5 PACH MEN Unas da cabrera descritas deba das 63 9 1 MOKE STOCK loa 63 9 2 A A EE AS 64 9 3 CALCULA ai A NA A AA 64 DA A E EE REET 64 9 5 CUSCO ad pica eee 64 9 6 EXDOFE O TOXO ei asias 65 10 THE FOOLS MENU coscicirarinalad oia didas 66 UL PPO CCU caia iia 66 OZ Gr Otitis 67 es SIE SN rara EE 67 10 4 Georererence Mage catala 67 10 5 Geo ca culata A A a 68 100 OPENS esa seh da eee ee as 68 REFERENCES Suscrito te erent aR Ree ene see aie ates adie 70 vi DIVA GIS 7 1 INTRODUCTION This manual explains how to use DIVA GIS Additional information including an introductory tutorial exercises and examples of the use of DIVA GIS can be found on the DIVA GIS website http www diva gis org 1 1 Conventions used The following conventions are used in this manual Italics are used to refer to menusand sub menus and also to tabs and views A forward slash is used to relate a submenu to a menu Quotes are used to refer to buttons and boxes File types are referred to by their extension For example a dBase file like data dbf is referred to as a DBF file 1 2 Installing DIVA GIS If you downloaded DIVA from the Internet you will need to unzip the downloaded files first use e g 7 Zip Then you should click on setup exe to install DIVA GIS also click on this file if you are ins
16. AT document GIS Laboratory CIAT Cali Colombia Nix H A 1986 A biogeographic analysis of Australian elapid snakes Pp 415 in R Longmore ed Atlas of Elapid Snakes of Australia Australian Flora and Fauna Series No 7 Australian Government Publishing Service Canberra Raaijmakers J G W 1987 Statistical analysis of the Michaelis Menten equation Biometrics 43 793 803 Rebelo A G 1994 Iterative selection procedures centres of endemism and optimal placement of reserves Strelitzia 1 231 257 Rebelo A G and W R Sigfried 1992 Where should nature reserves be located in the Cape Floristic Region South Africa Models for the spatial configuration of a reserve network aimed at maximizing the protection of diversity Conservation Biology 6 243 252 Sawada M 1999 Rookcase an Excel 97 2000 Visual Basic VB add in for exploring global and local spatial autocorrelation Bulletin of the Ecological Society of America October 1999 231 243 Sanders H L 1968 Marine benthic diversity a comparative study American Naturalist 102 243 282 Smith E P and G van Belle 1984 Nonparametric estimation of species richness Biometrics 40 119 129 Wieczorek J Q Guo and R J Hijmans 2004 The point radius method for georeferencing point localities and calculating associated uncertainty International Journal of Geographic Information Science 18 745 767 71
17. DIVA GIS Version 7 5 Manual January 2012 Robert J Hijmans Luigi Guarino and Prem Mathur Conditions of use The DIVA GIS software can be used and distributed freely It is provided as is without warranty of any kind express or implied including but not limited to the warranties of merchantability fitness for a particular purpose and noninfringement In no event shall the authors or copyright holders be liable for any claim damages or other liability whether in an action of contract tort or otherwise arising from out of or in connection with the software or the use or other dealings in the software Portions of this computer program are owned by LizardTech Inc and are copyright 1995 1998 LizardTech Inc and or the University of California U S Patent No 5 710 835 All rights reserved Contributors DIVA GIS is maintained by Robert J Hijmans Edwin Rojas Rachel O Brien and Mariana Cruz have written parts of the code for previous versions DIVA GIS was improved thanks to bug reports and or suggestions made by many individuals particularly Luigi Guarino Prem Mathur Xavier Scheldeman and others including Vstein Berg Israel Barrantes Rachel O Brien Coen Bussink Arthur Chapman Dirk Enneking Catherine Graham Dave Hodson Andrew Jarvis Maarten van Zonneveld were also involved in the development of earlier versions Support for the early development has come from the Bioversity International the
18. L library See http www gdal org gdal_vrttut html for more info 3 13 Export Shapefile Save a shapefile to a Google Earth KMZ file a compressed KML file See above under Export Gridfile to export gridfiles rather than shapefiles 3 14 File Manager With the File Manager you can delete copy and rename shapefiles and gridfiles As both shapefiles and gridfiles in fact consist of more than one file this can be a very helpful utility 3 15 Download This launches your Internet browser and the webpage http www diva gis org data from which you can download geo referenced databases 23 DIVA GIS 7 4 THE LAYER MENU The Layer menu Box 5 allows you to add and delete a layer also known as theme to a project and change a layer s properties A layer can be a shapefile a DIVA GIS gridfile or a georeferenced image TIF JPG or SID but most functions in the Layer menu refer to shapefiles Gridfiles and shapefiles for all countries of the world are available from the DIVA GIS website Box 5 The Layer menu one symbol missing Icon Sect 4 1 4 1 4 2 Name Add Layer Remove Layer Properties Add labels Identify Feature Table Filter Select Records Select Features Clear Selection Copy Paste Hide Show Legend Short explanation Adds a layer to the map Removes the active layer from the map Changes the style color and size of lines of the active layer Adds labels to a
19. MIN minimum average temperature at which the plant will grow TOPMN minimum average temperature at which the plant will grow optimally TOPMX maximum average temperature at which the plant will grow optimally TMAX maximum average temperature at which the plant will cease to grow The suitability of a location grid cell for a crop is evaluated for each of the 12 potential growing seasons If the average minimum temperature in one of these months is 4 C or less above KTMP it is assumed that on average KTMP will be reached on one day of the month and the crop will die The temperature suitability of that month is thus 0 If this is not the case the temperature suitability is evaluated for that month using the other temperature parameters See the example for maize in Figure 12 for how this is done The overall temperature suitability of a grid cell for a crop for any growing season is the lowest suitability score for any of the consecutive number of months needed to complete the growing season 54 DIVA GIS 7 120 TOPmin TOPmax 100 O 00 O O Suitability 40 Fig 0 19 20 30 9 ure data and calculated Average temperature C are for maize To estimate the suitability of the rainfall in an area for a particular crop the following rainfall parameters are used Rmin minimum rainfall mm during the growing season Ropmin optimal minimum rainfall mm during the growing season Ropmax opt
20. On pressing the Apply button a graph will be drawn in which each point on the graph 49 DIVA GIS 7 represents the climate of a point on the map each axis representing one of the climate variable that you chose You can set a percentile value to find out which are the extreme observations in terms of climate The percentile is used to exclude the extreme values of all climate variables A box is drawn on the graph to indicate for the two climate variables selected which points are within and which points are outside the climatic envelope defined by the specified percentiles These points will be different for each pair of variables The points that fall within the envelopes for all the climate variables are colored green on the graph The points that fall outside one or more envelopes are shown in red All the points inside the two dimensional envelope shown on the graph are selected highlighted in yellow on the map You can of course save the graph to the clipboard in the usual way The Extract button saves a TXT file with the average values of each bioclimatic variable for each class 7 1 6 Predict This is the business end of this menu The extracted climate data can be used to predict where a species is likely to occur or would survive if it was brought there this could be on a different continent for example To select an area for mapping you can enter the coordinates manually or use Dra
21. UC Berkeley Museum of Vertebrate Zoology the International Potato Center CIP SINGER SGRP FAO and USDA We have benefited from the work of the following persons M Sawada Rook s case Gerald Everden and Frank Warmerdam PROJ4 Andrew Williamson Shapechk the contributors to Delphi Zip Version 1 70 http www geocities com SiliconValley Network 2114 Warning DIVA GIS is a relatively new program that is under continuous development and not all parts have been tested completely This means that you should never blindly believe the results of your analysis Rather you should always test if DIVA GIS works well for example by manually calculating the expected results for a small number of grid cells or by first doing the calculations with a simple sample data set for which you know the results If you find a possible error please be so kind as to report it Please send your comments to info diva gis org Abstract DIVA GIS is a free computer program for mapping and analyzing spatial data It is particularly useful for analyzing the distribution of organisms to elucidate geographic and ecological patterns It is aimed at those who cannot afford generic commercial geographic information system GIS software or do not have the time to learn how to use these often complicated programs and for anyone else who wants a GIS tailor made to analyze biological distributions DIVA GIS supports vector point line polygon image and gri
22. ap and with Transect you get a graph showing on the vertical axis the changes in grid cell values with latitude or longitude You can choose to fix the vertical axis so that different transects will be comparable A moving average will be displayed if you tick the appropriate box The results may be saved in a number of ways You can save both the graph and the data on which it is based in the clipboard You can also save the data to a file by going to the Data tab and specifying an output file 8 13 Area Area lets you create a new grid in which the value in each cell represents the total area of the class in that cell in an existing grid For example you have a grid with values 1 to 10 the classes A cell with input value 1 will have as output value the combined area of all cells with that value 62 DIVA GIS 7 9 THE STACK MENU A stack is a set of grids with the same dimensions number of columns and rows and resolution and location minimum and maximum X and Y coordinates which are handled together as a group Grouping grids in a stack makes it easier to process many files in the same way and allows a number of additional analytical procedures You can carry out the following grid operations i e from the Grid menu see chapter 8 on Stacks as well as on individual grids Scalar Reclass Neighbourhood Aggregate Disaggregate Cut Distance and Area A stack is stored in a file with the extension GRS A GRS file is no
23. ar Neighborhood as implemented in DIVA GIS for the Point to Grid analysis and described below 6 3 1 Circular neighborhood When the Circular Neighborhood option is chosen in Analysis Point to grid Main calculations are made based not on the observations within each grid cells but rather on the observation found within a circle of specified radius with its center in the middle of each grid cell The advantage of this method is that it produces a smoother surface To avoid some observations not being used at all the radius should not be smaller than the distance between the center of a square grid cell and its corners A disadvantage may be that a number of observations or even all if the radius is 42 DIVA GIS 7 sufficiently large compared to the size of the grid cells will used more than once in the calculations See Bonham Carter 1994 and Cressie 1991 for more information on circular neighborhoods When this method is used you must specify in the Options tab the size of the neighborhood i e the diameter of the circle and indicate if you want to scale the result Scaling means you correct the results for the difference between the size of the grid cell and that of the neighborhood 6 4 Point to Polygon Polygons or closed lines that enclose an area can also be used to summarize point distribution data For example you may want to make calculations for different countries Make a shapefile of points the act
24. arameter should also change For example if you want to change the resolution you must specify whether you want the number of columns to adapt or the grid extent When you want to adapt the grid extent you can fix one corner of the grid using the Fix Corner box You can also define the grid extent by drawing a rectangle on the map after pressing the Draw Rectangle button Grid Options Es Y Minimum E n 34 Masimum E 13 E Cell size 1 1 Fis Comer Lower Right H Columns H Rows Adjust with Rows Columnas Y Draw Rectangle Default Values x Cancel Figure 9 The Grid Options window 31 DIVA GIS 7 6 1 2 Using the parameters of an existing grid The alternative to defining manually the parameters of a grid is to use the parameters of an existing grid You can use the parameters from a gridfile produced in a previous analysis by scrolling down in the Define Grid bar of the Point to Grid window and then pressing Options to specify an existing grid An existing gridfile can also be used as a mask to indicate what part of the grid should be ignored or should get special treatment in the case of the Inverse Distance Weighted method see section 4 3 The part of the grid that should be ignored can be indicated using numerical values or ranges 6 2 Choosing output variables There are a number of different output variables that can be calculated for a grid The output variable you want can be sele
25. arium museum genebank was collected or where any observation of the presence of a specific biological unit e g species landrace genotype allele was made These points should be in the active shapefile layer in the DIVA GIS project to remind you a shapefile is made active by adding it to the map and clicking on its legend entry once which highlights it The output of the analysis routines can be a gridfile a shapefile or a database file DBF Box 7 The Analysis menu Icon Sect Name Short explanation 6 1 3 Point to Grid Creates a grid with different indices diversity distance or statistics from a points shapefile 6 4 Point to Creates a new shapefile either from an existing one or Polygon a rectangular or pentagonal grid with diversity indices from a points shapefile 6 5 Point to Point Calculates diversity indices for a neighborhood around each observation in a points shapefile 6 6 Summarize Calculates diversity indices for all the data in the Points database of a points shapefile Distance Calculates distribution statistics from point data la 6 8 Autocorrelation Assesses the presence of spatial autocorrelation from point or grid data Centroid Calculates the centroid for each polygon in a shapefile 6 9 Histogram Makes a histogram of the frequency distribution of the data in a grid 6 10 Regression Calculates a regression of the values in a grid against those in another grid 6 11 Multiple Calculates a regression of the
26. ata set for the whole world excluding major water bodies oceans and Antarctica These data are available at different spatial resolutions and can be downloaded from the DIVA GIS website The climate data are stored in a special format CLM files to allow quick access and reduce storage space requirements You can also use your own climate data in DIVA GIS With Climate Point you can click on the map on land and DIVA GIS will show climate data for that location The window shows the altitude in meters above sea level and monthly average minimum and maximum temperature C and monthly precipitation mm both as tables and graphs It also shows the values of 19 bioclimatic variables derived from these monthly data Climate Map provides a tool to map a specified climate variable over a specified area When you press the Read from layer button in the Climate Map window the dimensions of the active layer will be copied to the minimum and maximum coordinates By clicking Adjust the dimensions of the output gridfile are adjusted to the grid cells of the climate database You can also draw a rectangle on the map to define the area using the Draw rectangle button Choose the variable that you need and whether you want a gridfile for the current or for the projected future climate The result will be displayed automatically if you check Add to map In the Climate Make CLM files window you can construct CLM files from
27. ates the value of each grid cell according to the values of the cells in a 3x3 5x5 7x7 or 9x9 neighbourhood around that cell Mean median mode minimum maximum range CV or the number of distinct classes richness within the neighborhood may be calculated When the mean median or mode are calculated this is often referred to as a filter because it smooths the values on a grid Filtering is sometimes used after disaggregating a grid or to remove noise in a satellite image mode filter The number of distinct classes is an indication of the pattern of the grid in that area for example to what extent vegetation is heterogeneous Figure 14 How a 3x3 mean filter works Original cell values left and the new ES ojs O1 GO NO CO N CO Ol gt Q3 CO gl de DIVA GIS 7 cell values right 8 6 Calculate In the Calculate window you can do mathematical calculations with one or more grids The things you can do with Calculate can also be done with combinations of Scalar and Overlay The advantage of Calculate is that you can do several steps at once The disadvantage is that the calculations are much slower so if you have very large grids you re better off using Scalar and or Overlay Use the Add Grid button to choose the files you want to use insert the operator s you require between grid names and provide a name for the output grid As with Overlay to be able to use Calculate with multiple grids these
28. boxes before you press OK Another approach is to add a legend and use the Undo button if you do not like the place it gets and try again The width of the TOC in the Data view determines its width in the Design view Thus if it is too wide or narrow go back to the Data view change it and try again Design view Adding a scale North arrow and text to the image follows the same principles as outlined above for the legend You can set the color and font for any text that you add to the image To set the font for the TOC however you must go to the Tools Options Layer menu in the Data view change the default font Close the project and then Open it again in the Project menu To export your map from DIVA GIS you can print it copy it to the clipboard and paste it into another application or save it to a graphics file in bitmap BMP or TIF format 1 4 File Types and Formats DIVA uses files of various types and formats The most important are DIVA GIS 7 1 the shapefile gridfile and image file formats for spatial databases and 2 the dBaselV DBF format for reading and writing external non spatial databases 1 4 1 Shapefiles Shapefiles are so called vector databases describing the location of points e g collecting locations polylines e g roads and areas or polygons e g soil types countries A shapefile actually consists of three separate files with the same name but with diffe
29. bserved F the number of species that have exactly individuals F is the frequency of singletons F the frequency of doubletons Chao 2 Chao 2 is an incidence based estimator of species richness Chao 1987 Chao 2 and the Jacknife estimators are based on the number of samples for an area To create samples DIVA GIS divides each grid cell into 4 or 9 sub areas 9 Schao2 obs 20 2 Sobs the total number of species observed in all samples pooled Q the number of species that occur in exactly j samples Q is the frequency of uniques Q the frequency of duplicates Jacknife Jacknife 1 is the first order jacknife estimator of species richness incidence based Burnham and Overton 1978 1979 Heltshe and Forrester 1983 35 DIVA GIS 7 m 1 Sackt obs al 111 e Jacknife 2 is the second order jacknife estimator of species richness incidence based Smith and van Belle 1984 S 4 Q 2m 3 Q m 2 Jack aby m m m _ 1 Sobs the total number of species observed in all samples pooled Q the number of species that occur in exactly j samples Q is the frequency of uniques Q the frequency of duplicates m the total number of samples Michaelis Menten This estimator is calculated by repetitive random sampling and fitting an asymptotic model following the method of Raaijmakers 1987 For each sample size from 2 to the number of observations 1 the average number of species in
30. cal and horizontal resolutions of a grid are usually the same but could be different If the grid extent and resolution are known the number of rows and columns in the grid can be calculated Alternatively the resolution can be calculated when the other variables are known 30 DIVA GIS 7 To define a grid its geographic reference system must be specified and then its extent and resolution Because maps are flat while the Earth is not a geographic reference system or map projection has to be used that renders the three dimensional reality in two dimensions a flat map with minimal distortion You can use any projection in DIVA GIS see Chapter 10 for a discussion of projections DIVA provides default parameters for the output grid that are calculated on the basis of the extent of the active points shapefile layer and by setting the resolution to 1 in the units of the reference system However when this would lead to less than 10 or more than 100 rows or columns the default resolution is adapted accordingly You can change the default parameters by selecting any statistic from the Analysis Point to Grid menu and clicking on the Options button under Define Grid On the window that appears when you do so Figure 9 you can change the default grid extent as defined by the coordinates of the four corners resolution and number of columns rows As these parameters are all interrelated you need to specify which other p
31. cesesso 12 TAE DATA NENE 13 IMPOrt POIMES TO SNGDC ING nai AA 14 Import Text to Line POLYGON ccscccscncscucsvecscccssecsceccceccsecces 15 DOW SHODE indi rit ci eceessunied sauaaanes ae taweatets 17 POV COM OGIO essa e NO eames ceases 17 Points CO CONVEX POV SOI an 18 Selection to New Shape file ccscccncccncccncccnccenccesccescceecess 18 EXEFACE VALUES DY PONES lidia 18 CUO E TEE E EE ETE E E E N E EEA 19 CNECKCOOGINAl OS ii a TRA 20 EXDOFE ONAJ NG nuit a 21 IMPporE tO GIO cirios 22 WIO VRE TO ni a io 23 EXPDOFES NADO Oia as 23 ELO MANGO CN aa dana 23 DOWMOGG isc 23 TAE LAYER MENO sue ardor 24 Add Layer and Remove Layer oooooooccoocccoccnoccnaconaconoconoconoos 25 POD CIES ica 25 IG CREP RCOCUN OC Ii das 25 TADA 26 SOLO cl ROCOV OS ria ida dao eos EEA 26 CODY ANG POSO nas 27 5 1 6 1 6 2 6 3 6 4 EI CoN O Oo O Ov gt O O 7 1 7 4 CoO CO 00 Wn THE MAP MENU x2 one ncuuinnstecease en OEE AA 28 MADONNA A e 28 THE ANALYSIS MENU Sssaosinaiodansasod EEEN 29 POMETO GIO sia 29 6 1 1 cs A Seeccueaeneseedaivaneeaedeusetaseeuercseunes 30 6 1 2 Using the parameters of an existing Orid cee cece eect eee ceeeeeeesees 32 Ehoosine output VvanaDleSsacinasin is did dario 32 6 2 1 ICONOS idas 32 6 2 2 Estimators of Richness ssssssseecescesesesccsoeseeccsceceseroesorseeceeeeo 34 6 2 3 TUVO EATE EA 37 6 2 4 Diversi INCGIC ES iaa 38 6 2 5 Molecular marker data
32. conds to decimal degrees the following formula is used Dos hare 60 3600 Where DC is the decimal coordinate d is the degrees m the minutes and s the seconds __ of the sexagesimal system h 1 for the northern and eastern hemispheres and 1 for the southern and western hemispheres For example 30300 S 30 500 and 30 15 55 N 30 265 You can do these calculations in a spreadsheet program or in DIVA GIS using Tools Geo calculator Chapter 10 Decimal degrees should normally be recorded with 4 or 5 decimals At the equator one unit of the fourth decimal 0 0001 degrees equals about 10 meters less at other latitudes not affected by longitude That should be precise enough for most applications If you are using high precision GPS with differential correction 5 decimal places would be warranted See Wieczoreck et al 2004 for a thorough discussion of coordinate precision and uncertainty 10 DIVA GIS 7 2 THE PROJECT MENU The Project menu contains functions for the management of DIVA GIS project files and some related tasks Box 2 Box 2 The Project menu Icon Sect Name Short explanation oO 2 1 New Starts a new project map and associated image El 2 1 Open Opens an existing project file with DIV extension ri 2 1 Close Closes the current project 2 1 Save Saves the current project a 2 1 Save As Saves the current project with a new name gt 2 2 Export Project Exports
33. cted under the Point to Grid Main Output Variable menu Output variables are grouped and associated with a number of options that can be set on the Parameters tab to the right of the Main Tab The different output variables are discussed in the following sections 6 2 1 Richness In the Richness group there are four distinct output variables Number of different classes Number of observations Presence Absence and Rarefaction Number of different classes counts the different classes of a variable e g the different species names in a dataset covering a genepool present in each grid cell The Parameters tab must be used to indicate which variable in the shapefile should be considered and possibly to exclude irrelevant values The Number of observations option calculates the number of points present in each grid cell As there may be points in the shapefile that are not relevant you may want to exclude these In that case you must select a variable from the database on the Parameters tab Figure 10 and then you can exclude one or more of the values of that variable 32 DIVA GIS 7 Presence Absence simply gives cells in which a class is found the value 1 and cells in which it is not found the value 0 The Rarefaction technique estimates the number of classes species for example that would have been observed given a number of observations that is specified by the user Sanders 1968 Hurlbert 1971 Magurran 1988 Equat
34. d data types It can help improve data quality by finding the coordinates of localities using gazetteers and by checking existing coordinates using overlays spatial queries of the collection sites with administrative boundary databases Distribution maps can then be made Analytical functions in DIVA GIS include mapping of richness and diversity including based on molecular marker DNA data mapping the distribution of specific traits identifying areas with complementary diversity and calculating spatial autocorrelation DIVA GIS can also extract climate data for all locations on land Ecological niche modeling can be carried out using the BIOCLIM and DOMAIN algorithms lii Table of Contents di Wn 1 4 1 5 NM N N O a D XA OO COW A UO A Uy NN UA UN INTRODUCTION O es 1 CONVENTIONS USCG 6 ii vumeetes couse dscns 1 NStalline DIVA GIS icc ncsnsdccusacswandeatannc seth sckewetaesacetecsnentansetas ess 1 Tine DINA GIS desicion 1 1 3 1 THS Data View sack cast di wtewtt San vtidawsdeteelaeeaedcesecialaedeawsieeassdecedaueaehees 2 1 3 2 Te DESION VIS Wisteria 5 FING Types and FORMAUS airis 7 1 4 1 SAD EM A O A EEEIEE ane 8 1 4 2 o RDA 8 1 4 3 Maceta ARAN o 9 1 4 4 DBE TGS AAA AAA AS 9 Geographic coordinates sesseseesseseesesesoeseesorecesoreeesoreceeo 10 THEPROJECT MENU csoro iaraa EE a 11 PRO CCUS ee E EE EAE 11 Import project and Export project ssssssesesessseseesoesess
35. d from DIVA GIS and to check or prepare coordinate data for use Box 3 The Data menu Sect 3 1 Icon 3 2 3 3 3 4 3 5 3 6 3 7 3 8 3 9 Name Import Points to Shapefile Import Text to Line Polygon Draw Shape Polygon to Grid Points to Convex Polygon Selection to new shapefile Extract values by points Climate Georeference Check Coordinates Export Gridfile Import to Gridfile Write VRT file Export Shapefile File Manager Download Short explanation Creates a shapefile of points from a text file DBF file or Access database Creates a shapefile of lines or polygons from a text file Creates a shapefile of points lines or polygons by moving the cursor across the map Assigns values from a polygon shapefile to a gridfile Creates a convex polygon around all points in a shapefile Saves a selected part of a shapefile or indeed a complete gridfile to a new shapefile Extracts values from a grid or a stack for all points in a shapefile and produces different types of text files 1 Queries a location on the map for its climate 2 Creates grid files of climate variables 3 Creates CLM files There used to be a module Assign Coordinates for this Now this will take you to the BioGeomancer website Compares locality descriptions in a point shapefile file with those in a polygon shapefile file Exports a gridfile to a number of other grid data formats Imports a gridfile f
36. d may be made up of the following layers national boundaries altitude main rivers and capital cities Each layer on the map is listed in the table of contents TOC Layers can be made in visible on the map using the checkbox next to their name in the TOC If you click on a layer s checkbox while holding the Ctr1 key down all layers on the map will be made in visible depending on the state of the checkbox of the layer that you click on A single click on a layer in the TOC makes it the active layer indicated by an uplifted layer bar for example the countries layer in Figure 1 The order in which different layers are drawn on the map is from the bottom upwards so a layer higher up in the TOC will cover a lower one You can change the order of a layer by dragging it up or down i e by clicking on it and then moving your mouse while keeping the left button pressed DIVA GIS 7 o Y Y DIVA GIS 5 1 MyProject1 gt Project Data Layer Map Analysis Modeling Grid Stack Tools Help 0 gt ole 23 pee x almae 2 5 01 2 6 lw Countries ee iw CITIES o lw RIVERS Bol lw Annual precipitation WM o 200 200 400 E 400 800 E 800 1200 E 1200 2000 OY 2000 7604 wi 46 6624 Scale 1 195114398 Data Design Menu bar Provides access to all DIVA GIS functions Toolbar Quick access to some of the more commonly used functions Table of contents Lists all the layers on the map
37. e Evolution of Global Data Sets Third International Conference Workshop on Integrating GIS and Environmental Modeling Santa Fe New Mexico USA CD ROM and web publication http www ncgia ucsb edu conf SANTA_FE_CD ROM sf_papers greene_stephanie sgreene html Heltshe J and N E Forrester 1983 Estimating species richness using the jackknife procedure Biometrics 39 1 11 Hijmans R J M Schreuder J De la Cruz and L Guarino 1999 Using GIS to check coordinates of genebank accessions Genetic Resources and Crop Evolution 46 291 296 Hurlbert S H 1978 The non concept of species diversity a critique and alternative parameters Ecology 52 577 586 Intergovernmental Panel on Climate Change Data Distribution Center 1999 Providing climate change and related scenarios for impact assessment CD ROM Version 1 0 Climate Research Unit University of East Anglia Norwich UK Magurran A E 1988 Ecological diversity and its measurement Princeton University Press 70 DIVA GIS 7 Nabhan G P 1990 Wild Phaseolus ecogeography in the Sierra Madre Occidental Mexico aeorographic techniques for targeting and conserving species diversity Systematic and ecogeographic studies on crop genepools 5 International Board for Plant Genetic Resources Rome Italy Nelson A G LeClerc and M Grum 1997 The development of an integrated Tcl Tk and C interface to determine visualise and interogate infraspecifc bio diversity Internal CI
38. e background environment to create pseudo absence points Include Random Absence Data The output is 52 DIVA GIS 7 two shapefiles of points the name of one ending with _train the model training data and the other with _test the model testing data Use the training data to run a model see previous sections in this chapter and the test data to evaluate the models see below using the class e g species field and the presence absence field 7 3 2 Create Evaluation File Use a _test shapefile from the process described above to create a ROC file You must provide a shapefile that has a presence absence field The field name does not matter but the contents must be words that start with a p or with an a e g pres and abs A ROC file is a text file with values extracted for each species grid for the absence and the presence points You can calculate kappa and ROC statistics with these see below 7 3 1 Show ROC Kappa You can visualize the results of model testing here The input file is the ROC file generated above You can asses the quality of a prediction by inspecting the ROC curve and you can find the optimal threshold for presence absence by inspecting the kappa threshold plot The area under the ROC Receiver Operating Characteristic curve is commonly used to evaluate models in species distributional modeling A ROC curve is created by plottin
39. ep a record of the original coordinates and of the reason and way the data were altered 20 DIVA GIS 7 ef Figure 7 Imaginary island with three provinces A B and C and the location of six collecting sites Table 1 The location of six imaginary collecting sites according to the genebank database and according to the administrative boundaries database Genebank database Administrative Boundaries Accession Province Province 1 B B 2 B A 3 B B 4 E C 5 C C 6 C 3 10 Export Gridfile With the Export Gridfile function you can export DIVA gridfiles to a number of different formats listed in Table 4 You can either export a single file or a group of files all at once Table 2 Export formats Format File extension Text TXT Generic binary BIL and HDR Shapefile points or polygons SHP SHX DBF Google Earth KMZ 21 DIVA GIS 7 IDRISI v2 IMG and DOC GRASS ASCII GRS ESRI Arc Info ArcView shapefiles SHP SHX and DBF ESRI ASCII grids ASC ESRI binary grids FLT and HDR A Text File has lines with the number and value of each grid cell Cells are counted from the upper left to the lower right corner Nodata values are exported as 9999 When exporting gridfiles to the generic binary format BIL band interleaved by line a data file with the extension BIL is produced as well as a header file with the extension HDR These files can be imported into a number of GIS programs includ
40. g the true positive fraction against the false positive fraction for all test points across all possible probability thresholds Fielding and Bell 1997 The curve goes from 0 0 to 1 1 and a model that produces a curve with a high true positive fraction at low values of the false positive fraction is considered good This is commonly quantified by calculating the area under the curve AUC AUC ranges from 0 to 1 where a value of 0 5 indicates that a model is no better than random and a value of 1 indicates that the model can discriminate perfectly between presence and absence records 93 DIVA GIS 7 7 4 EcoCrop This module uses FAO s EcoCrop database of the environmental requirements of a long list of plant species whichcan be used to identify possible crops to grow ina particular environment In DIVA GIS we implement EcoCrop to predict the adaptation of a crop over geographic areas Currently only temperature and precipitation data are used to make this prediction In EcoCrop the growing period is defined in days between Gmin and Gmax start of srowth and end of growth respectively The length of the growing season is defined as the average of Gmin and Gmax In DIVA GIS 12 possible growing seasons are considered starting on the first of each month To determine the suitability of a growing season for a certain crop the following temperature parameters are used KTMP absolute temperature that will kill the plant T
41. grid cell location to compare in this way 9 3 Calculate Using Calculate you can produce a single grid from the multiple grids in a specified Stack the value in each cell of the output grid being the sum mean minimum maximum harmonic mean or sum of the reciprocals of the values in the grids in the stack If you select the Calculate Area option a text file is produced with the area of each grid expressed as number of cells with values above a certain specified threshold value If you select a grid to serve as a mask only the cells for which the mask has data i e not Nodata will be considered 9 4 Regression You can use this function to perform regression on a cell basis across a stack of n grids That is for each cell position linear regression is done using 1 n as X values and the values in the corresponding grids as Y values Make sure that the grids are in the right order e g the grids could be the result of running models with increasing values of a parameter You can open the stack file with a text editor and check 9 5 Cluster You may want to classify grid cells based on the values they have in different grids for example if the different grids represent the presence and absence of different species You can do this in the Cluster menu in three steps 1 In the Distance Matrix tab calculate a matrix of distances file extension DMT between grid cells by specifying a distance measu
42. ied section out of a grid Combines two grids into one Makes a new grid with the same parameters as an existing one but different cell values Makes a graph of the values in a given column or row of agrid Calculates the area of classes in a grid You can use this function to get the following information on the contents and Structure of a grid Structure 57 DIVA GIS 7 type of data integer real number of rows number of columns Contents across all cells number of cells with data number of grid cells without data minimum value maximum value sum of grid cell values mean of grid cell values median of grid cell values Mode of grid cell values standard deviation of grid cell values variance of grid cell values Describe operates on the active layer when the window is open or else on any layer selected using the Grid button Some of the information e g the number of rows and columns can also be obtained by double clicking on a grid layer in the legend and choosing the Info tab 8 2 Overlay Given two grids that have the same dimensions number of columns and rows resolution and location min and max X and Y coordinates Overlay allows you to place them on top of each other as it were carry out some arithmetic on corresponding grid cells 1 e cells directly above each other and place the results in a new third grid The arithmetical ope
43. imal maximum rainfall mm during the growing season Rmax maximum rainfall mm during the growing season The evaluation for rainfall is similar as for temperature except that there is no killing rainfall and there is one evaluation for the total growing period the number of months defined by Gmin and Gmax and not for each month See Figure 13 for an example The output is the highest suitability score percentage for a growing season Starting in any month of the year You can run the Ecocrop module for rainfall or for temperature or for both the boxes to tick are in the Predict tab In the last case the minimum value of the two for each growing season is used to compute the suitability To run the module you must first select a species in the Select tab You can search for Species using the options in Filter by Then select the crop you want by clicking on it the selected record is highlighted in blue On the next tab Parameters you can inspect the temperature and rainfall parameters from the EcoCrop database and change them if you want The changed parameters will be used but not saved If you want to make permanent changes you must edit the file faoecocrop dbf in the lt DIVA dir gt bin directory 59 DIVA GIS 7 You can select the area for which you want output by filling the upper text boxes on the Predict tab You can also use the extent of an existing shapefile or gridfile by making it active in the legend and
44. ing IDRISI Arc Info with the imagegrid command and ArcView where they can be opened as an image If you need a file in the similar formats BIP or BSQ you can rename the extension of the output file because these are the same when only one grid or band is stored in a file When exporting grids to IDRISI version 2 and earlier the result is a data file with extension IMG and documentation file with extension DOC Files in the GRASS ASCII format can be imported to GRASS using the command r in ascii Grids can also be exported to shapefiles with rectangular polygons This can be particularly useful when you want to use the data in ArcView but do not have the Spatial Analyst extension that allows you to visualize and manipulate grids or the grid module in Arcinfo In other cases it would be more appropriate to export the gridfile to an ASCII grid or a floating point grid extension FLT and HDR 3 11 Import to Gridfile With the Import to Gridfile module you can import one or many grid data files into DIVA GIS from the IDRISI IMG or RST generic binary BIL BIP BSQ and ESRI binary export formats 22 DIVA GIS 7 3 12 Write VRT file This option lets you create vrt header files for existing gridfiles such that they can treated like VRT Virtual grid raster format files These files can be read by ArcGIS Quantum GIS and other software that used the GDA
45. ion 1 gives the formula which is used to make this calculation A disadvantage of this method is that the estimate can only be calculated for those cells in which the actual number of observations is higher than that for which the estimate is calculated E S Y i a e a 0 Equation 1 E S Expected number of classes in the rarefied sample N Total number of observations per cell in the sample to be rarefied N Number of individuals in the th class in the sample to be rarefied n User specified standardized sample size 33 DIVA GIS 7 Point to Grid Main Parameters Si classes 5 acaule Bitter 5 acraglossum Juz 5 acroscopicum Ochoa 5 albicans Ochoa Ochoa 5 amapanum Ochoa 5 ambosinum Ochoa 5 anamatophilum Ochoa 5 ancophilum Correll Ochoa 5 ariduphilum Ochoa 5 augusti Ochoa 5 apacuchense Uchoa 5 aymaraesense Uchoa 5 bill hooken Ochoa 5 brevicaule Bitter 5 buesi Yargas electio All Clear Invert Cal Cal Cal Cal Cal Cal Cal Cal Cal Cal Cal Cal cal Cal v 5 AS Apply BL Close Figure 10 The Parameters tab in the Point to Grid menu 6 2 2 Estimators of Richness The number of species or whatever other units observed in an area depends to some extent on the effort invested in recording there Because a complete census is rarely feasible in most cases only a sample of an area is surveyed An important problem that then arises is to estimate
46. ions Sets general options file locations etc 10 1 Projection With the Projection option you can transforming the data in a shapefile from geographic coordinates i e lat long into any of a number of projections and back There is no single best map projection Some projections can be used for a map of the whole world other projections are appropriate for small areas only One of the most important characteristics of a map projection is whether it is equal area a grid cell anywhere on the map will always cover the same amount of area or conformal the shapes of the geographic features are as they are seen on a globe No map projection is both conformal and equal area and some are neither For our kind of work it is usually best to use equal area projections particularly when large areas are being analyzed see Table 8 This will assure that the grid cells are all of the same size and therefore comparable to each other Projections are defined using the PROJ 4 notation And example for longitude latitude is proj longlat datum WGS84 ellps WGS84 towgs84 0 0 0 Projection doesn t work on gridfiles yet If you want to project a gridfile you have to convert it to a shapefile first using Data Export Gridfile 66 DIVA GIS 7 Table 6 Horizontal resolution and area of a 10 minute grid cell by latitude The vertical resolution is 18 5 km at all latitudes Latitude Horizontal resolution km Area pe
47. isted in Table 6 Table 4 Statistics Coefficient of variation Coefficient of variation of values Maximum Maximum value Mean Mean value Median Median value Minimum Minimum value Mode Mode most frequent value Range Difference between Max and Min 41 DIVA GIS 7 Range Mean Range divided by the mean Standard deviation Standard deviation of values Sum Sum of all values Variance Vriance of values 6 3 Methods of converting point data to grid data At the core of DIVA GIS is the conversion of the point data represented by the accession localities to the raster data represented by the diversity and other values of the different grid cells Several GIS programs allow the conversion of point data to raster data However the way that this is generally done as in the Simple procedure in DIVA GIS has the following important shortcomings e A point that is on a border between grid cells is assigned to one of those cells arbitrarily e The value of a point that falls within a grid cell is assigned to that cell only irrespective of the proximity of the point to other cells e The origin of the grid i e its bottom left hand corner is arbitrary Given a coordinate system and resolution of the grid slightly different origins could lead to quite different results of the point to grid conversion e Uncertainty about the location of points is not taken into account These shortcomings can largely be overcome with the Circul
48. ive theme and click on Analysis Point to Polygon Diversity Then specify which polygons are going to be used to make the calculations You can either select an existent shapefile e g with administrative boundaries or ecoregions or define a new shapefile of squares i e a grid or hexagons Note that if you define a grid of squares you will get the same output as with Point to Grid except for minor differences due to the way points that fall on the borders between two cells are treated The output consists of a shapefile with the following fields DIVAID and ORDER these can be ignored QBS the number of observations SPP the number of different classes typically species four diversity indices Margalef Menhinick Shannon Simpson see section 7 3 3 Table 5 The value 1 in the Simpson column means missing value i e the index could not be calculated 43 DIVA GIS 7 As the size of polygons may vary unlike that of grid cells the results may need careful interpretation Nevertheless this can be an interesting option that allows Summarizing the data by pre defined and often well known areas 6 5 Point to Point An alternative to the use of grids is the kind of point based approach that was used by the Spatial Intra specific Diversity SID software described by Nelson et al 1997 The same procedure is also implemented in DIVA GIS Calculations are done for all observations lying within a
49. layer on the map using one the fields in the shapefile database undo by resetting in the Properties window Shows the attribute data of a geographic feature of the active layer on clicking on it Shows the attribute data of the active layer shapefiles only Displays a defined sub set of the records from the active layer shapefiles only Selects records from the active layer shapefiles only that comply with a specific condition query Selects point features by clicking or drawing a rectangle on the map Unselects the currently selected point features of the active layer Copies the active layer to the clipboard Pastes a layer from the clipboard to the map Hides or shows information on the active layer in the legend 24 DIVA GIS 7 4 1 Add Layer and Remove Layer Use Layer Add Layer from the menu bar to add a layer to the map window The new layer is added on top of the list of layers already in the legend To remove a layer from the project click on it once in the legend to make it the active layer and then click on Layer Remove Layer This will not delete the data it will only remove the link to it from the current project Multiple layers can be selected and then removed together by clicking on them in the legend while holding the down the Shift key 4 2 Properties Properties of the spatial objects of a shapefile such as the size and shape of points and the colour of polygons can be modified using Layer P
50. le From dBase IV file DBF you can make a shapefile of points from a DBF file if that DBF contains fields with latitude and longitude both in decimal degrees First you must indicate the filename of your DBF file And you must provide an output filename that is different from this input filename The program then reads the input file and allows you to select the fields that have the X longitude and Y latitude coordinate data By default only numerical fields are listed for you to choose from However you can check the Include Text Fields box to see text fields as well If you use a text field for the X and Y coordinates DIVA GIS will attempt to transform the text values to numbers Where this is not possible or where there is no entry at all an empty record is created That is the record is copied to the DBF table of the shapefile but no associated point is created 14 DIVA GIS 7 Create Shapefile from Text File Input File D Atemp maxent_input cev Output File D stempimasent_input shp Field Delimiter f Jab C Semilolon Comma f Space f Other Longitude x Text Qualifier i Ye Latitude y Field Options Field Hame species Data Type TEXT 42 599 Rows 3 Columns caule Bitter 5 acaule Bitter caule Bitter caule Bitter acaule Bitter caule Bitter Figure 5 Create Shapefile from Text File window 3 2 Import Text to Line Polygon Here you can create a sha
51. ll This is because the species in the cell with the second highest number of species may also be present in the first cell In other words the cell with the second highest number of species may not contribute very much to the overall number of species selected To maximize the total number of species selected in as few cells as possible is a non linear optimization problem Rebelo 1992 developed a procedure that calculates an approximate optimal solution and this is what has been implemented in DIVA GIS An iterative procedure is used In each iteration the value of each grid cell is calculated based on the observations in that cell and in relation to the observations in the cells already selected If there are two or more cells with the same value one is selected at random Hence this procedure can lead to slightly different results every time it is run Several options need to be selected under the Parameters tab The first step is to select a variable and possibly exclude some of the species e g missing values from the analysis The second step is to choose a scoring approach There are two options Equal weight and Rarity With the Equal weight option each category e g species has the same weight With the Rarity option the value of a cell is calculated using the rarity value for each observation The rarity value equals the number of observations of a category divided by the total numbe
52. must all have the same dimensions number of columns and rows and resolution and location min and max X and Y coordinates 8 Aggregate The Aggregate procedure allows you to lump together or merge cells of a grid and create another grid with a lower resolution larger grid cell size You must specify the aggregation factor which determines how many cells will be merged into one and thus how big the new cells will be For example with factor 2 the new cells will have two times the length and two times the height of the original cell In other words four cells will be merged into one The values in the cells of the aggregated grid will depend on the procedure chosen mean minimum maximum range sum mode median standard deviation 60 DIVA GIS 7 3 4 Figure 15 Grid values before left and after aggregation with procedure sum middle and aor pe If you choose the option Ignore Nodata aggregation is also done on groups of cells one or more of which has Nodata as value If you do not choose this option the value of the aggregated cells will become Nodata even if only one of its component cells has that value In some cases the aggregation factor is not a multiple of the number of rows or columns Say you have a grid of 3 by 3 cells that you want to aggregate with a factor two In this case the cells in the last column and row cannot be aggregated properly DIVA GIS gives you two option
53. n are shown 4 4 Table Table allows you to view the database of the active layer shapefile If you click on a record in the table the location of the corresponding geographic object will be highlighted You can also move the center of the map to that object 4 5 Select Records Records can be selected for various purposes For example to save a subset of a layer to a new file or to find geographic features that meet particular conditions The selected items will be displayed in a different color yellow is the default You can make a selection by either making a query in the Select Records window or by drawing on the map after clicking on the Select Features button Only layers that are made from shapefiles can be selected from In the Select Records window you can either select by values or by query The first option is useful for variables with a limited number of values which are typically non numerical Select the variable and all values will be listed Then select the values to include in the selection When using a query you must select a variable a criterion and the value Use the Add button to put the query in the dialog box and continue adding additional conditions using AND OR or condition parentheses When you are ready click Apply Selections can also be made using Select Features by clicking on a map item or drawing an area click keep your finger down and move the mouse The shape of
54. o be added to the Design view Copies the Design view to the clipboard Prints the Design view to a specified printer saves the Design view to a graphics file BMP or TIF Producing a nice map for presentation purposes is not very difficult but will take some trial and error Start by adding the basic map from the Data view Then decide if there is too much white space around the image If there is go back to Data view and zoom and or pan around to better fill up the area If there is too much white space at the right of the image you may need to remove a layer that causes this to happen for 6 DIVA GIS 7 example a layer that although perhaps invisible is mainly located to the east of the area of interest When you have the map the way you want it add a legend First click on the Add legend button A panel will appear on the left hand side of the window It includes a number of options and lists all the visible layers Decide what layers to include in the legend by unchecking the ones you do not want You can add the legend to the map by clicking on the image at the point where you want the legend to appear One approach is to keep clicking until you find the spot you like then press Clear All followed by Add Map then Add legend and finally OK The legend will be put where you last had it because the coordinates were saved in the text boxes You can also change these values in the text
55. pefile of lines or polygons from a text file for example with coordinates obtained with a GPS or read from a map For each object line or polygon in the text file the first line should have an ID number followed by a pair of coordinates X and Y typically longitude and latitude all separated by spaces On the following rows are coordinate pairs for the nodes of the object After the last node of an object put END and start again for the following object At the end of the file there should be an additional END Box 4 15 DIVA GIS 7 Box 4 The general format and an example of a text txt file that can be imported to a shapefile of lines or polygons stands for any number of additional pairs of x and y The map shows the result for the example data Format Example AAA Project Data Layer Map Analysis Modeling Grid Stack Tools Help Dill ejqjolalal gt 2 01 elaf x melo 310 Y Slo 18 Text to Line or Polygon Shapefle Type Polygon y AAA Seye l0 x Output File fo polygons shp IV Add to map A son j f x 75 1816 y 23 3139 Scale 1 6266135 16 DIVA GIS 7 3 3 Draw Shape You can use this function to create points lines or polygons shapefiles by drawing clicking directly on the map click on the Draw button For each point line or polygon that you have drawn you can add two attributes that identify or describe the object You can u
56. pped as false 0 Bioclim Most Limiting Factor For the cells that fall within the 0 100 percentile the variable for which the percentile score was lowest or highest is mapped The value in each grid square is a number that corresponds to the variables on the Predict tab Domain The Domain procedure calculates the Gower distance statistic between each cell on the map and each point using the values of the 19 climate variables The distance between point A and grid cell B for a single climate variable is calculated as the absolute difference in the values of that variable divided by the range of the variable across all points The Gower distance is then the mean over all climate variables 1 GIA B d az e NES p a rangek The Domain similarity statistic is calculated as D 1 d The maximum similarity between a grid cell and all points is mapped In DIVA this value is then multiplied by 100 A good match is thus a high number e g above 95 Domain Mean Distance This is the same as above but the mean distance to all points is used instead of the minimum distance 51 DIVA GIS 7 Domain True False All areas that are within the specified threshold are mapped as true 1 all other areas are mapped as false 0 Domain Most Limiting Factor The variable with the lowest score largest distance is mapped The value in each grid square is a number that corresponds to the variables on the
57. r grid cell km7 0 18 5 343 15 17 9 332 30 16 0 297 45 13 1 240 60 9 3 172 75 4 8 89 90 0 0 10 2 Graticule With this function you can make a shapefile of lines with fixed intervals e g 10 degrees in North South and East West directions Adding such a graticule to a map makes it easier for the reader to determine where an area is See Figure 4 for an example of a map with a graticule 10 3 Shift Shape Shift Shape helps you to move a shapefile in a vertical and or horizontal direction to cope with displacements of the data You can transform map units for example from feet to meters by multiplying 10 4 Georeference Image With Georeference Image you can create a world file for an image A word file is an attribute file associated with corresponding image file which allows the image to be imported into a GIS and located on the surface of the earth TIF mrSID and JPG are the supported image formats TIF and SID are commonly used to distribute satellite images The extension of the world file depends on the extension of the image It is SDW for a SID file and TFW for a TIF file A world file is a text file with 6 lines with a number on each line denoting 1 size of pixel in X direction 2 rotation term for row 67 DIVA GIS 7 rotation term for column size of pixel in Y direction X coordinate of centre of upper left pixel in map units Y coordinate of centre of upper left pixel in map units oO of KR Uy
58. r of observations 40 DIVA GIS 7 There are two ways in which you can limit the number of iterations This is important because the procedure can take a long time with large databases or a grid with many cells You can indicate the Minimum number of records per cell This value should be 1 or higher It allows you to exclude cells with what is for your purposes too low a number of observations You can also indicate the maximum number of iterations that you want the procedure to cycle through When the process finishes a Process Report appears that tells you how many iterations were used and hence the number of cells selected and how many distinct observations are present in those cells Three new grids are created and added to the project labeled Sequence Classes and Additional Classes The Sequence grid indicates in which order cells were selected The cell with most species is selected first and has a value of 1 The next cell has a value of 2 etc The Classes grid indicates how many different classes typically species are in each selected cells The Additional Classes grid indicates how many new classes species are in that cell These species were not present in any of the previously selected cells 6 2 7 Statistics If a numerical variable is selected some basic statistics can be calculated for that variable for each grid cell The statistics included are l
59. r of observations points and statistics describing the distances among all pairs of points min max mean median and first and third quartile You must select a quantitative field from the shapefile s database to calculate autocorrelation After selecting a field you can deselect individual values that you want to exclude If you do that you need to recalculate the statistics which will have changed because you do no longer consider all points The results will appear on clicking Apply Point Autocorrelation Oj x Point Autocorrelation 5 x Options Result Options Result Input File Global Summary Statistics c program files diva gistutoripe_cultsweetpot shp Observations 2206 H Pairs 596 fei t Neighbour Statisti arc Mean 847 42747 STD 836 29782 Observations 2206 Mean 0 10607 Ls Recalculatel Min 1st Quart Median 3rd Quart Max T Geary o fo 03606 0 0728 0 1 3928 0 92049 COO z Namal ET acord zea Field ALT y Var Normal 0 009132 Var Random 0 005199 Moran i 1 24382 z Normal 30 441 87 z Random 30 434622 War Normal 0 001671 War Random 0 001671 Apply SAS Aol Rl Close KLA Rl Close Figure 11 Autocorrelation Point window Options left and Results right 6 8 2 For gridcells No lag distance needs to be specified to calculate autocorrelation of grid
60. rations included are addition subtraction multiplication division and calculation of minimum and maximum In the operation Cover the values of the cells in the first grid are used unless the value of a cell in the first grid is Nodata in which case the value of the cell in the second grid is used 58 DIVA GIS 7 8 3 Scalar Scalar lets you create a new grid by applying an arithmetical operation to the values in each cell of an existing grid For the following operations you need to also specify a number add substract multiply divide raise to a power and take the the logarithm with a specified base Other functions include taking the absolute value rounding truncating and trigonometric operations 8 4 Reclass The Reclass option re classifies data in a grid according to class limits which you specify For example you may want to give all grid cells with values between 0 and 1000 the value 1 and all cells with the values 1001 2000 the value 2 Class limits can be adjusted manually Extra classes can be inserted with the button and deleted with the button DIVA GIS shows automatically the data type and minimum and maximum values of the input file to facilitate appropriate re classification You can save the new classification limits using the Save RCL button and then use them to apply the same re classification to another grid Read RCL 8 5 Neighbourhood This function re calcul
61. re 64 DIVA GIS 7 2 In the Cluster tab use the DMT file produced above to calculate a cluster file file extension DTR using either the weighted or unweighted UPGMA algorithm 3 In the Draw tab use the DTR file you just produced to draw a dendrogram of the distance relationships among grid cells decide at what level of distance to prune the dendrogram and finally produce a new grid in which the values of the grid cells will correspond to which cluster in the dendrogram the cells belongs to 9 6 Export to Textfile With the option Export to Textfile all the gridfiles in the stack can be exported together to a single TXT file Such a file can be used to make comparisons on a cell by cell basis e g in a spreadsheet program As an option any row that has a null value for one or more of the grids may be omitted in the output file 65 DIVA GIS 7 10 THE TOOLS MENU The Tools menu Box 11 has some additional miscellaneous functions Box 11 The Tools menu Icon Sect Name Short explanation Projection Projects a shapefile from geographic coordinates to a projection of choice Graticule Adds a latitude longitude graticule Shift Shape Shifts the position of a shapefile Georeference Provides tools to help you georeference an image image Geo Calculator Transforms geographic coordinates in degrees minutes seconds to decimal degrees Calculates the distance between two points Toolbars Shows or hide toolbars Opt
62. rent extensions SHP SHX and DBF but they are treated as one file There are some shapefiles with additional files extensions SBN and SBX but these are not essential and are not used in DIVA GIS The shapefile format was developed by ESRI a leading GIS software company They were initially developed for use in ArcView but now nearly all GIS programs can either use them directly or import them 1 4 2 Gridfiles Grids are central to the analytical capabilities of DIVA GIS A grid divides a part of the world into equal sized cells The advantage of using grids as opposed to areas such as countries or other administrative units is that grid cells of the same size and shape allow more objective comparisons For grid databases in which an area is divided into equally sized rectangles DIVA GIS gridfiles are used A gridfile consists of two separate files GRI and GRD but DIVA GIS treats them as if they were one file The GRI file has the actual data and the GRD file has metadata and a number of parameters that are needed to read the GRI file properly From these two files DIVA GIS creates two more files BMP and BPW These files are derived from the GRI and GRD files and are used to visualize the data on the map but are otherwise not essential If the BMP and BPW are absent DIVA GIS creates these files automatically when opening a gridfile The BMP and BPW files can also be used to visualize gridfiles in ArcVie
63. rent ha e Classify Y Figure 3 The Layer Properties window for grids DIVA GIS 7 1 3 2 The Design view The Design view of the main DIVA GIS window allows you to put together a map that you can save as an image file It is based on the layers that are visible in the Data view The resulting image can be exported from DIVA GIS for example to be used as an illustration in a document or presentation DIVA GIS 5 1 MyProject1 CIR peer a a OEA Overview Map wf OF Location ti 325 Y 2 Outline Annual precipitation MA o 200 P 200 400 C 400 800 O s00 1200 O 2000 1200 2000 O 2000 7694 kilometers Scale 1 98114398 were VIO Data h Design Figure 4 The DIVA GIS main window in Design view Map Legend Scale North arrow Overview map Add text Undo Redo Clear all Set color Set font Copy Print Save DIVA GIS 7 Box 1 The Design view buttons Short explanation Adds the map from the Data view to the Design view Adds the legend from the Data view to the Design view Adds a graphic scale to the Design view Adds a North arrow to the Design view Adds the overview map to the Design view Adds text to the Design view Un does last addition to the Design view Re does last addition after undo to the Design view Starts from scratch Sets the color for the text and lines to be added to the Design view Sets the font for text t
64. rillouin HB ln N 2 linni N S number of unique classes species per cell N number of observations per cell n number of individuals in the i th class pi proportional abundance of the i th class n N The Simpson index D decreases with increasing diversity and hence it is usually expressed as 1 D or 1 D In DIVA GIS it is expressed as 1 D You can use Grid Scalar to calculate D or 1 D from this see Chapter 9 38 DIVA GIS 7 6 2 5 Molecular marker data Molecular markers data associated with point localities can also be analyzed in DIVA GIS At this moment only absence presence data e g of bands on an electrophoretic gel can be analyzed Molecular distance molecular diversity and number of haplotypes can be calculated The fields that have the data must be selected using the Parameters window The values in these fields can be checked in the Values tab A band can either be present value 1 in the database absent value 0 in the database or missing any other value Average or maximum molecular distance between the observations in a grid cell can be calculated using either Jaccard s 1908 distance J Nei and Li s 1978 distance NL and Sokal and Michener s 1958 distance SM Equations 5 7 J 1 1 Equation 6 Ny FA thg 2xn NL Z A Equation 7 2 XN o tg n n SM 1 Y Equation 8 Ny FM t Ao Ngo Where ny the number of bands shared by
65. rom a number of other grid data formats Write a Virtual Raster header file to open gridfiles in e g ArcGIS or Quantum GIS Export Shapefile to Google Earth KMZ file Renames or deletes gridfiles and shapefiles Goes to the DIVA GIS website to download data needs an Internet connection 13 DIVA GIS 7 3 1 Import Points to Shapefile With this menu you can create a shapefile of points from a text file a DBF file or an Access database The TXT file must have a header row containing the variable names It does not matter whether the columns are separated by spaces or a symbol such as a comma or tab the importation wizard will read your data anyway when you tick the box which specifies the separator you are using Figure 5 However tab separated is probably best Using commas as separators causes problems when you have a field with locality descriptions which may well include commas this problem can be circumvented by using quotes around text DIVA will figure out for itself what type of data is present in each column of the database text integer whole or real decimal numbers But you may change this automatically generated setting if you wish The same goes for the maximum number of spaces that a value of the variable will need If you indicate fewer spaces than are actually used the data will be truncated cut off at the position that you indicated not rounded With Import Points to Shapefi
66. roperties You should first make it the active layer by clicking on it in the legend Double clicking on a layer in the legend also activates the Properties window There are three ways to change the symbols 1 you can change them all at once use the Single tab 2 you can give every unique entity a different symbol according to one of its attributes Unique or 3 you can classify the numeric attributes and give a different symbol to each class Use the reset button every time you choose a different attribute or number of classes Here s a useful tip if you want all polygons transparent except for one you should first make the polygons transparent in the Single tab and then go to Unique to change the one polygon you want with a solid fill 4 3 Identify Feature When you click on an item geographic feature on the map s active layer the Identify Feature window shows the variables in the database and their values for that item If you click on more than one item e g a number of points with nearly the same 25 DIVA GIS 7 location the data for all these items are shown The number of the visible record and the total number of records are indicated on top of the list of variables e g Rec 1 of 5 The 4 and VY buttons on the right of the list can be used to toggle between the selected records If the active layer is a gridfile the column row number and value of the grid cell that was clicked o
67. ructure This allows sharing projects over a network or saving them on a CD ROM different drive letters can be used For all other files the absolute path is stored e g c mydata diva myshp shp It is also possible to use network paths e g network share shape shp This means that if you delete a project file all your data will be still be available However if you delete or rename a data file the project file will not be able to find it anymore and DIVA GIS will show a message indicating this 2 2 Import project and Export project Another way to share a DIVA GIS project is to place all its contents into a DIVA GIS export file extension DIX In contrast to a DIV file the DIVA GIS export file contains the project file and all the layers data files You can send such an export file to another DIVA GIS user who can then import it into DIVA or you can use it to simply Store all files pertaining to a project in one location These files are compressed and they do not take up much disk space they can often be sent to another user via email To import a project file you must indicate where the data should be expanded and under which project name Typically you would make a new directory for this so that it is clear which files belong to a specific project that you imported 12 DIVA GIS 7 3 THE DATA MENU The Data menu will help you to manage your data It includeds functions to import and export data to an
68. s Only adjacent cells are considered either 4 horizontally and vertically adjacent cells Rook s case or also including the 4 diagonally adjacent cells King s case 46 DIVA GIS 7 6 9 Histogram With the Histogram option your grid data are arranged in classes The program offers you some common tools to improve the histogram titles show grid etc and the result can be copied to the clipboard 6 10 Regression With the Regression tool you can regress one grid against another cell by cell and plot the results Choose one gridfile for X and another for Y making sure that the grid extents and resolutions coincide You can use linear logarithmic or exponential regression For multiple regression and more advance statistical methods it is convenient to use the R program with raster package 6 11 Multiple Regression You can regress one grid against several others using the Multiple regression tool If you find a satisfactory statistically significant model you can use it to predict values for the same area or for another area by changing the independent variables 47 DIVA GIS 7 7 THE MODELING MENU The Modeling menu provides various options for niche modeling or the prediction of species distribution patterns Box 8 Box 8 Functions in the Modeling menu Icon Sect Name Short explanation l 7 1 Bioclim Domain Runs the BIOCLIM and DOMAIN models for predicting the presence of species 7
69. s to deal with this either ignore these cells and truncate the original grid in the example the aggregated grid would have one cell or expand the grid by adding another row and column with Nodata values in the example the aggregated grid would have four cells 8 8 Disaggregate Disaggregate divides the cells of a grid into smaller cells The value of the original cell is assigned to all of the smaller cells You need to specify the disaggregation factor which should be an integer greater than one 8 9 Cut Cut allows you to make a new grid consisting of a selected part of the area of an existing grid You can define the area to be cut and placed in the new grid by the column and row numbers or by coordinates These parameters can also be selected by drawing a rectangle on the map They can also be copied from an existing grid 61 DIVA GIS 7 8 10 Concatenate Concatenate combines the data of two grids with the same resolution and origin but with different extents For areas where both grids have values the value of the first grids is maintained as with Cover 8 11 New You can generate a new grid with this option using the parameters from an existing grid The grid cell values can be a single number consecutive numbers starting with 0 or random numbers from a uniform or a Normal distribution 8 12 Transect Choose a row or column in a grid either by specifying its number or by clicking on the grid on the m
70. se a numeric attribute value and or a text attribute Label by typing something in the box on the form When you are done press the Save button to save the results to a shapefile Figure 6b Create Shapefile by drawing on screen 3 4 Polygon to Grid This function creates a grid output file based on the features of a polygon shapefile input file If you do not select a particular field from the input shapefile the grid will have the value 1 for the area covered by the polygon and O otherwise If you select a numeric field each grid cell in the output file will be assigned the value of the polygon that covers the center of the cell Creating a grid from polygons can be useful to for example create a mask that can be used to remove cells set to NODATA from an existing grid that are outside of the 17 DIVA GIS 7 area of interest also see the Grid Reclass and Grid Overlay In this case you would convert the shapefile to a raster using the existing raster as template do not select a field such that you get a new grid with NODATA and 1 and then multiply overlay the two grids to only show values for the required region e g a country 3 5 Points to Convex Polygon This creates a bounding convex polygon around a set of points For example you can use this to make a range map from a set of points representing point localities for a species If you want to use all the points in
71. ta Check Coordinates tool helps you identify such errors using a method described by Hijmans et al 1999 By simultaneously querying the specimen database and an administrative boundaries database a new temporary database is created For each record this new database contains the location information according to both the specimen database and the administrative boundaries database This information should be the same and any mismatches probably reflect errors or name or boundary changes This is illustrated in a simple example for an imaginary island that has three provinces called A B and C Six germplasm accessions have been collected The coordinates of the collection locations according to the genebank s database have been plotted on a map of the provinces Figure 7 By querying the two databases Table 3 is generated pointing at accessions 2 4 and 6 as possible errors In addition it is possible to use altitude to spot likely errors in the coordinate data In many cases the passport data will include altitude This figure can be compared with an estimate of the altitude of the locality using Data Extract Values by Points This form of checking may not be particularly effective in highly dissected mountainous terrain because the estimated altitude will not be very precise More precise estimates can be obtained using the SRTM elevation database see the DIVA GIS website If coordinates are changed it will be necessary to ke
72. talling from a CD ROM You will be asked in what directory folder you want to install the program As you can install the program in any directory you like in this manual we will refer to this directory as the DIVA directory or lt DIVA dir gt By default DIVA GIS will be installed in the C program files DIVA GIS directory 1 3 The DIVA GIS desktop Once installation is complete you can click on the DIVA GIS icon which will launch the DIVA GIS program The program consists of two overlapping parts which we call views The Data view is where you will do most of your work The Design view is used to produce a graphical representation of the results of your work that can be saved as DIVA GIS 7 a graphics file printed or used in another application You move between views by clicking on the appropriate tab at the bottom right hand corner of the window 1 3 1 The Data view The Data view is taken up by a map and to its left its associated table of contents TOC Figure 1 The content of the map is managed and analyzed via functions that are spread over nine menus arranged across the top of the desktop Project Data Layer Map Analysis Modeling Grid Stack and Tools The menus are discussed in chapters 3 to 11 one chapter per menu There s also a Help menu but there is no on line help yet A map consists of geo referenced databases called layers sometimes also referred to as themes For example a map of the worl
73. the genotpyes x and y positive matching Nig the number of bands present in x and absent in y No the number of bands present in y and absent in x Noo the number of bands absent both in x and y negative matching Alternatively molecular diversity can be calculated using Nei s diversity index Equation 8 NDI Y x x NDI Equation 9 ij Where Xi the frequency of the i th allele in the population and NDI the number of allele differences per locus between the the i th and j th loci 39 DIVA GIS 7 6 2 6 Choosing complementary areas The Reserve Selection procedure aims to identify sets of grid cells that are complementary to each other i e that capture a maximum amount of diversity in as few cells as possible Instead of using simple richness an adjustment can be made in which rare observations get a higher weight The procedure is based on the algorithm described by Rebelo 1994 see also Rebelo and Sigfried 1992 It has for example been used to determine priority areas for in situ conservation of species in a family of flowering plants in South Africa The following discussion refers to species but any multi state variable could be used The procedure is less straightforward than it might seem Whereas the selection of the first cell is easy it is the cell with highest species richness or a random choice between ties if there are any the choice of the next cell depends on the previously selected ce
74. the shapefile use the Single tab If you want to create more than one range map use the Multiple tab and specify which field and which values in that field you want to use to distinguish the points that will be bounded Once you have the polygon defining the range of an organism you can use Polygon to Grid as described above to create a gridfile version of the range map 3 6 Selection to New Shapefile This saves a selected part records of the active elevated in legend shapefile to a new shapefile Parts of shapefiles can be selected graphically right on the map or by querying the database see the options available in the Layer menu as explained in Chapter 5 3 7 Extract Values by Points The Extract tool assigns values to the locations specified in the active points shapefile You can extract values from a polygon shapefile a gridfile a stack of gridfiles or a CLM file see below In all cases the result is a text txt file If you extract values from a stack you can select a field in the point layer that will be used to match the grids by class That means that it will only extract values from a grid when the attribute of a point for the selected field matches the name of the grid For example you can use this when you have a shapefile of points with a field with species names and a number of grids with filenames that match these species names 18 DIVA GIS 7 3 8 Climate DIVA GIS comes with a climate d
75. thing but a list of the grids that the stack contains Hence rather like a project or DIV file remember them it does not contain any of the actual data in the grids Rather it points to the existing files with the data Therefore if you delete rename or move one its constituent grids to a different directory the stack will become invalid Box 10 The Stack menu Sect Name Short explanation Make Stack Defines a stack by listing the grids it contains Plot Makes a histogram of cell values Calculate Carries out arithmetic on grids in a stack Regression Calculates regression on a cell by cell basis Cluster Classifies grid cells Export to Text Places all grid cells values in a single text file File 9 1 Make Stack You make a stack by adding grids to a list and then naming the output GRS file You can remove grids from the list individually or all at once if you make a mistake or change your mind DIVA tells you about the dimensions and location of each grid you add to the stack These must be identical for all grids in the stack If you forget which grids are in a stack or wonder whether it is still valid or why it isn t use the Check Stack tab to obtain a list of the grids included in a specified stack You can edit stack files with text editors such as Notepad 63 DIVA GIS 7 9 2 Plot With this you can make a histogram of the values of corresponding cells in all grids in a stack Click on the map to choose which
76. tion systems for geoscientists Modelling with GIS Computer Methods in the Geosciences 13 Pergamon Elsevier London U K Burnham K P and Overton W S 1978 Estimation of the size of a closed population when capture probabilities vary among animals Biometrika 65 623 633 Busby J R 1991 BIOCLIM a bioclimatic analysis and prediction system Pp 64 68 in Margules C R and Austin M P eds Nature Conservation Cost Effective Biological Surveys and data Analysis Melbourne CSIRO Carpenter G Gillison A N and Winter J 1993 DOMAIN a flexible modelling procedure for mapping potential distributions of plants and animals Biodiversity and Conservation 2 667 680 Chao A 1984 Non parametric estimation of the number of classes in a population Scandinavian Journal of Statistics 11 265 270 Chao A 1987 Estimating the population size for capture recapture data with unequal catchability Biometrics 43 783 791 Colwell R K and J A Coddington 1994 Estimating terrestrial biodiversity through extrapolation Philosophical Transactions of the Royal Society Series B 345 101 118 Cressie N A C 1991 Statistics for spatial data John Wiley amp Sons New York Fielding A H and J F Bell 1997 A review of methods for the assessment of prediction errors in conservation presence absence models Environmental Conservation 24 38 49 Greene S L and T Hart 1996 Plant Genetic Resource Collections an Opportunity for th
77. ure of the rate at which species assemblages change in space It indicates how different a number of nearby areas are Imagine two large areas with similar numbers of species overall but one with different species in all its grid cells and another with the same species in all its grid cells The first area would have a high turnover the second area a low turnover 37 DIVA GIS 7 At this point only Whittaker s 1960 measure of beta diversity is implemented in DIVA GIS Equation 9 It can be calculated for each grid cell considering its 8 neighbors 2 horizontal 2 vertical and 4 diagonal Queen s case or considering its 4 closest neighbors 2 vertical and 2 horizontal Rook s case B S a 1 Equation 5 S the total number of species over the grid cells considered a the average number of species in the grid cells considered 6 2 4 Diversity indices DIVA GIS can calculate a number of different diversity indeces for each grid cell You must select a variable field from the input database for which you want to calculate an index e g species name The formulas for all indices were taken from Magurran 1988 who provides a detailed description of their properties See Table 5 for the mathematical description of the different diversity indices Table 3 Diversity indices Index Formula Margalef Dug S 1 In N Menhinick Du S VN Shannon H p ln pi Simpson D n n 1 N N 1 B
78. user defined circle around each observation point The result is assigned to the location of the observation for which the calculation was done For such a point based analysis you have to specify the variable in the points shapefile to be used Unlike when creating a grid you cannot choose the output variable By default the following variables are included in the output file longitude latitude number of observations NOBS number of distinct values NDIST the diversity indices listed in Table 5 If you want you can add to these any of the fields that are in the input shapefile The results are stored in a shapfile 6 6 Summarize Points This calculates diversity indices diversity estimators and basic statistics for the whole dataset in an input shapefile 6 7 Distance With the Analysis Distance Statistic by Class procedure you can calculate distance Statistics for each unique class of a multi state variable for example for each species in a database Currently the following statistics area available 44 DIVA GIS 7 number of observations minimum distance between two points of each class MinD maximum distance between two points of each class MaxD average distance between two points of each class AverageD Distances are expressed in meters For correct calculations you must specify whether the shapefile is in decimal degrees or projected with meters as unit The o
79. utput is written to a DBF file The same calculation can be done for all points i e without distinguishing among classes and a complete distance matrix will be the produced Analysis Distance Matrix 6 8 Autocorrelation Spatial autocorrelation exists when the values of nearby geographical objects are more similar than those of objects that are further away For example an altitude grid has a high spatial autocorrelation The Autocorrelation option in DIVA GIS calculates this relationship by using two common statistics the Geary and Moran indices the values of which may be interpreted as in Table 7 You can calculate the autocorrelation on a grid or a points shapefile The spatial autocorrelation functionality implemented in DIVA GIS is based on the Rookcase software by Sawada 1999 Table 5 Autocorrelation statistics Geary Moran Interpretation O lt c lt 1 1 gt 0 Autocorrelation exists data are clustered c 1 i 0 Independent at random c gt 1 1 lt 0 Negative autocorrelation 6 8 1 For points When calculating autocorrelation for points and you need to define which neighboring points to consider This is done by specifying the lag or neighborhood distance Only points within the lag distance are considered for calculation 45 DIVA GIS 7 To determine a reasonable lag distance a number of statistics are shown in the Options tab of the Analysis Autocorrelation Points window These statistics include the numbe
80. w rectangle or you can press the Read from layer button and the dimensions of the active layer will be copied These may need to be adjusted a little to coincide with those of the climate database This is done automatically but you can also do it by pressing the Adjust button You can select the climate variables you want to use in the analysis The fewer variables you select the larger the predicted areas of suitability will be You can also choose either the current climate or the future climate If you selected Many classes on the Input tab you can use the Batch option under Predict to run the model for all different classes typically species Or you can select a single class and run the model for that only 50 DIVA GIS 7 You must select an output grid You have a choice of six different output variables for this grid Bioclim Four types of areas are mapped Areas completely outside the 0 100 percentile envelope for one or more climate variables get a code 0 The cells within the 5 95 percentile get a code 3 those outside this range but within the 2 5 97 5 percentile get a code 2 and the ones outside this but within the 0 100 percentile for all climate variables get a code 1 Bioclim True False All areas that are within the envelope described by the data points cut off beyond a certain user defined percentile are mapped as true 1 all other areas are ma
81. w and in ArcExplorer as images Unlike in DIVA GIS however the underlying grid data will not 8 DIVA GIS 7 be accessible in these programs and it will not be possible to change their legend categories If you want to use the grid data in another program you should export the gridfile to a suitable format Chapter 3 Gridfiles with the same extents and gridcell size can be manipulated together ina stack Stacks are discussed in Chapter 9 1 4 3 Image files Image files are special kinds of grids that can be displayed but not used for analysis as the data associated with the different colours in the file are not accessible A typical example of such a file would be an air photo or satellite image DIVA GIS supports three image formats TIFF JPEG and mrSID 1 4 4 DBF files DBF version IV is a commonly used database format DIVA GIS uses it to import and export tabular data You can create a DBF file by exporting it from a database program such as Access It used to be possible to easily do this from Excel but this is no longer the case although it may still be possible with some third party plugins Fortunately you can use the free and open source OpenOffice spreadsheet Calc If you use Calc you must take care not to lose data particularly not to lose precision decimals of coordinate data or to create a DBF file with unsupported characteristics The field names variable names should be in the first row
82. which may be due to errors in the data Click on a point on the graph for the second class only to see where the corresponding locality is on the map and display attribute and or climate data for that point You can show percentiles and the 1 5 inter quartile range IQR points within this range are not considered outliers on the graphs and change the size of the dots You can save the graph to the clipboard with the Copy button at the top left hand corner and then paste it into a document or presentation and counts of the number of observations per class to a TXT file Save Stats button in the bottom right hand corner 7 1 3 Outliers Here you can look for outliers in environmental space You can include 1 to n variables in the evaluation n being the number of variables in your stack if you use DIVA GIS climate files n 19 Suspect records are colored red as opposed to black You can click on a line on the graph to see where the corresponding locality is on the map and display attribute and or climate data for that point 7 1 4 Histogram Another way to explore the climate data for a points shapefile is to make histograms Select a class a variable and either an appropriate bar width or number of bars You can restrict the minimum and maximum values to be shown As usual you can save the histogram to the clipboard 7 1 5 Envelope In this menu you must choose a class e g species and two climatic variables

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