DIVA - GIS ( Annapurna

)
Version 6.0.3 A geographic information system for the analysis of biodiversity data

Manual
January 2007

I

Manual Diva

Table of Contents
Part I Introduction 1
1 Spatial analysis and biological distribution data ................................................................................................................................... 1 2 What is DIVA-GIS? ................................................................................................................................... 1 3 What can DIVA-GIS do for you? ................................................................................................................................... 2 4 Installing DIVA-GIS ................................................................................................................................... 3

Part II Welcome

4

1 Getting Started ................................................................................................................................... 5 2 Official Website ................................................................................................................................... 6 3 Workbench ................................................................................................................................... 7

Part III Some Basic Concepts
The Data view .......................................................................................................................................................... Changing......................................................................................................................................................... Styles Modifying the Lines ......................................................................................................................................... Modifying the Fill ......................................................................................................................................... Modifying the Markers ......................................................................................................................................... Editing Labels .........................................................................................................................................

8
8 11 11 12 13 14

1 The DIVA-GIS................................................................................................................................... 8 desktop

2 File Types and Formats ................................................................................................................................... 15
Shapefiles Gridfiles Image files DBF files .......................................................................................................................................................... .......................................................................................................................................................... .......................................................................................................................................................... .......................................................................................................................................................... 15 15 16 16

3 Geographic coordinates ................................................................................................................................... 17

Part IV The File Menu
1 Projects 2 Imports

18

................................................................................................................................... 19 ................................................................................................................................... 20
21 24

Import Molecular Data .......................................................................................................................................................... Import to Grid files ..........................................................................................................................................................

3 Export Grid files ................................................................................................................................... 25

Part V The Edit Menu Part VI The Navigation Menu Part VII The Layer Menu Part VIII Tools Menu
Analysis Selected Features ..........................................................................................................................................................

25 26 27 27
29

1 Diva Box Selection ................................................................................................................................... 28

© 2007 International Potato Center

Contents

II

2 Information ................................................................................................................................... 31 3 Point ................................................................................................................................... 32 4 Data Grid Info ................................................................................................................................... 33

Part IX Analysis Menu
Grids .......................................................................................................................................................... Defining Grids .......................................................................................................................................................... Using the parameters of an existing grid .......................................................................................................................................................... Output Variables .......................................................................................................................................................... Richness ......................................................................................................................................................... Rarefaction (to be filled in) ......................................................................................................................................................... Estimators of Richness ......................................................................................................................................................... Chao 1 ......................................................................................................................................... Chao 1 Corrected ......................................................................................................................................... ACE ......................................................................................................................................... Michaelis-Menten ......................................................................................................................................... Rarefaction ......................................................................................................................................... Diversity indices ......................................................................................................................................................... Beta Diversity ......................................................................................................................................................... Reserve Selection ......................................................................................................................................................... Statistics .........................................................................................................................................................

34
36 38 39 40 40 40 41 41 41 42 43 44 44 45 45 47

1 Point to grid ................................................................................................................................... 35

2 Select Records ................................................................................................................................... 48
Select Records by Values .......................................................................................................................................................... Select Records by Query .......................................................................................................................................................... 48 50

3 CheckCoordinates ................................................................................................................................... 52
Checking Coordinates .......................................................................................................................................................... 54

4 Distance

................................................................................................................................... 55
55 56

Distance Statistics .......................................................................................................................................................... Distance Matrix ..........................................................................................................................................................

5 Climate
Ecocrop Map Extract

................................................................................................................................... 57
.......................................................................................................................................................... .......................................................................................................................................................... .......................................................................................................................................................... 58 62 64

6 Autocorrelation ................................................................................................................................... 65
Point .......................................................................................................................................................... 66

7 Exports

................................................................................................................................... 67

Part X Data Menu

70

1 Text to DBF ................................................................................................................................... 71 2 DBF to Shapefile ................................................................................................................................... 73 3 Text to Shapefile ................................................................................................................................... 74 4 Structure to Shapefile ................................................................................................................................... 77
Convertion to.......................................................................................................................................................... Shapefile 78

5 Assign Coordinates ................................................................................................................................... 82
Direction Codes .......................................................................................................................................................... Possible codes and Comments .......................................................................................................................................................... 84 85

© 2007 International Potato Center

II

........................................................................................................................................................................................................................ Downloading .......... 99 100 101 102 Diva Features ............................................................................................................................................................................................................................................................................................................................................................... plugins 89 89 94 1 Updating DIVA .............................III Manual Diva Part XI Tool Menu Batch Option ................................................................................................................................................................................................................................................ 3 Videos .......................................................................................................... 89 2 About ........................................................................................ 87 Part XII Help Menu Registration of the update site ...................................................................................................................................................................................................................................................... Features Details ......... 86 88 1 Geo Calculator ............................................................... 103 © 2007 International Potato Center ..................................................................................... Plugins Details ......

Typically.1 Introduction Spatial analysis and biological distribution data DIVA-GIS can be used to map and analyze biological distribution data. Peru).2 What is DIVA-GIS? DIVA-GIS is a free and open source Geographic Information System (GIS) application for the analysis of the biodiversity data from CIP (International Potato Center.g.Introduction 1 1 1. Spatial analysis with DIVA-GIS can also be used to identify geographic areas of interest. or genetically). environmentally. the distribution data would refer to locations where different species. and analyze these data using grids. taxonomically. These data can be analyzed to identify areas of high diversity. Luis Avila and Reinhard Simon are developing version Annapurna. 4 Currently under-represented in conservation efforts. 4Highly diverse (e. to predict the chance of finding a species in areas that have not been explored. Magna Schmitt. and other partners including FAO. Edwin Rojas. SGRP and USDA. 4 Threatened with genetic erosion. 4 Likely to be suitable as in situ conservation sites. 4 Well represented. to study the distribution of certain traits of interest. such as can be provided by natural history collections and genetic resources collections. and to select and design of sites for in situ conservation. DIVA-GIS was specifically developed for use with genebank data such as available through national or international genebank documentation systems and SINGER. 1. and perhaps collected.g. You can use it to make maps of species distribution data. areas rich in biodiversity but with relatively few common taxa). The DIVA-GIS software was originally developed at CIP and further enhanced in collaboration between the International Potato Center and the International Plant Genetic Resources Institute. 4 Complementary (e. phenotypes or genotypes have been observed. or not in current collections. © 2007 International Potato Center . for example those are: 4 Likely to contain habitats of interest.

and more than the fun part of using DIVA-GIS. given the climate of the locations were it was observed. Such mapping and spatial analysis of biological distribution data can of course be carried out with commercial geographic information system (GIS) software. This complicates their analysis and makes the results uncertain. DIVA-GIS can also provide estimates of the climate of the collecting locations (or any other location on earth). or even days and weeks in case of a major database. It may take more of your time than you wanted to spend on the whole project. These include maps showing the number of observations. using the latitude and longitude fields. Even so. DIVA-GIS can help in assigning the most likely coordinates. you would do better not to get involved in this type of work at all! When the data have been imported.2 Manual Diva 1. and produce maps of likely distribution of a species. the number of distinct classes of observations. More interestingly.3 What can DIVA-GIS do for you? DIVA-GIS can import biological distribution databases. there is a lot that can be done to improve the quality of the data. DIVA-GIS can be used to map the locations where samples were collected or other observations were made. which for most people is mapping and analysis. but locality information is available (such as department. the main commercial programs do not provide options specifically aimed at the rapid and uncomplicated analysis of biological distribution data. and checked for errors. © 2007 International Potato Center . But if you are not prepared to spend many hours. the high cost of some of these software packages can preclude their use by small research programs or institutes. and DIVA-GIS includes tools that can make this task easier. unlike DIVA-GIS. to assign. If latitude and longitude are unknown. Coordinate data are sometimes inaccurate. verify and improve coordinate data. and the value of diversity indices for an array of grid cells. Moreover. and place name). completed. DIVA-GIS can also be used to analyze point distribution data and produce maps that can be used to develop plans and strategies for future conservation activities. However. However. the whole process of getting data into shape for spatial analysis is a tedious and time-consuming exercise. province.

exe .cgiar.Introduction 3 1.4 Installing DIVA-GIS If you don't have the CD.zip file that contains sample files(Shapes. DBF's) to use with DIVA. you can download the installer from http://research.cip. After to download the installer double-click on install. you will install the full version. © 2007 International Potato Center . if you install DIVA-GIS from CD.org/confluence/display/divagis/Home and you will download the lite version. After to install DIVA-GIS. you can download the Tutor.

4 Manual Diva 2 Welcome © 2007 International Potato Center .

Welcome 5 2. © 2007 International Potato Center .1 Getting Started Clicking on the blackboard icon. the DIVA-GIS tutorial appears.

© 2007 International Potato Center .6 Manual Diva 2.2 Official Website Clicking on the Star icon the Official Website appears.

Welcome 7 2. © 2007 International Potato Center .3 Workbench Clicking on the Arrow icon call the workbench.

e. Analysis. and Help. Layers. is where you will do most of your work. Window.1 The Data view The Data view is taken up by a map and. a map of the World may be up of the following layers: national boundaries. A single click on a layer in the Layer view makes it the “active layer”. The ‘Data’ view. A map consists of geo-referenced databases called layers (sometimes also referred to as 'themes'). 3. Layers can be made (in) visible on the map using the checkbox next to their name on the Layer view. You can change the order of the layers by dragging them up or down (move your mouse while keeping the left button pressed). Data. Each layer on the map is listed in the Layer view. a layer higher in the Layer view will cover a lower one). its associated Map view. to its left.1. and printed or used in another application. Navigation. main rivers. Edit. The Image view is used to produce a graphical representation of your data that can be saved as a graphics file..1 Some Basic Concepts The DIVA-GIS desktop The DIVA-GIS window consists of one part. and capital cities. indicated by an uplifted layer bar. The order in which different layers are drawn on the map is from the bottom up (i. Tools. altitude. For example. © 2007 International Potato Center . The content of the map is managed or analyzed via functions that are spread over nine menus: File.8 Manual Diva 3 3.

.. Displays all data services known to the application along with the names of the layers within them. Quick access to some commonly used functions.Layers view 5.Menu bar 2... Lists known projects and the maps contained within each project. Lists all the layers on the map The map you are working on..Toolbar 3.Some Basic Concepts 9 1.Catalog view Provides access to DIVA-GIS functions. © 2007 International Potato Center .Map view 6.Project view 4..

10 Manual Diva Right click on a layer brings up a view that allows changes to be made to some of the Layer's properties (such a color) on the map. © 2007 International Potato Center .

1 Changing Styles 3.1 Modifying the Lines If the checkbox is not selected the layer won't have lines. This combo permits to select the opacity of the line.1.1.Some Basic Concepts 11 3. This combo permits to select the wide one of the line. © 2007 International Potato Center .1.1.1. This button permits to select the color of the line.

This combo permits to select the fill opacity.1.1.12 Manual Diva 3. This button permits to select the color of the layer.1.2 Modifying the Fill If the checkbox is not selected the layer won't have color. © 2007 International Potato Center .

This combo permits to select the type of marker. only we should select the checkbox.1. This combo permits to select the size of the marker.3 Modifying the Markers In shape files of points we can modify the markers.1.Some Basic Concepts 13 3. © 2007 International Potato Center .1.

font style.1. This button calls a window where we can select the font.4 Editing Labels By defect this checkbox is not selected. and the color.1. This combo permits to select the type of label that will be shown. but when is selected names appears in the layer.1. © 2007 International Potato Center .14 Manual Diva 3. size.

3. and do not contain data.g. Components of the gridfile. and used for display.g. however. DBF). A gridfile consists of four separate files. gridfile and image file formats for spatial databases and the dBaseIV (DBF) format for reading and writing external (non spatial) databases. you should export them to a suitable format. They were initially developed for use in ArcView.1 Shapefiles Shapefiles are so-called vector databases. The most important are the shapefile. © 2007 International Potato Center . Unlike in DIVA-GIS. in which an area is divided into equally sized rectangles. countries). but now nearly all GIS programs can either directly use them. This files describes the GRI file. GRI GRD PNG PGW The file with the grid database. The PNG and PGW files can also be used to visualize gridfiles in ArcView and in ArcExplorer (as images).2. There are some shapefiles with additional files (extensions SBN and SBX). but these are not essential and are not used in DIVA-GIS. The PNG (image) derived from the GRI file. but they are treated as one file. the data are not accessible in these programs. 3. because the other two are derived from them. a leading GIS software company. but DIVA-GIS again treats them as if they were one file. Only the GRI and GRD files are essential. SHX. The shapefile format was developed by ESRI. and are only needed for visualization. soil types.g. e.. polylines (e..Some Basic Concepts 15 3.2. and their legend categories cannot be changed meaningfully. The documentation files. If you want to use the data in gridfiles. or import them. that georeferences the BMP files. DIVA-GIS creates these files when opening a gridfile. DIVA-GIS gridfiles are used. The "world-file".. A shapefile actually consists of three separate files with the same name but with different extensions (SHP.2 File Types and Formats DIVA uses files of various types and formats. describing the location of points (e. If the BMP and BMPW are absent. collecting locations).2 Gridfiles For grid databases. roads) or areas (or polygons.

The field names (variable names) should be in the first row. In Excel. you should do something like insert a new column and multiply the values in the text column by the numeral one. there must be a number in the first cell (i. © 2007 International Potato Center . in the second row). Make these changes before you save the file as DBF (version 4).3 Image files Image files are a special kind of grids that can be displayed but not used for analysis. DIVA-GIS uses it to import and export tabular data. may not start with a number.2. DIVA . you should NEVER insert or delete rows.e. The names may not be repeated. use Insert to add columns or rows.4 DBF files DBF (version IV) is a commonly used database format. To avoid losing decimal places. These will not be saved. the field will be saved as text. and should only consist of letters and numbers. PNG and mrSID. Otherwise. particularly not to lose precision (decimals) of the coordinate data. or to create a DBF file with unsupported characteristics. and only there. The field names have a maximum length of 10 characters. However. A typical example of such a file would be one of an air photo or satellite image. it is fine to add or delete columns. as the data associated with the different colors in the file are not accessible. do not add columns to the right or rows at the bottom of an existing DBF table. A common problem is that fields with numbers are saved as text fields. 3.16 Manual Diva 3. It does not help to use Format/Cells/Numeric in Excel. you must take care not to lose data. Field names should not contain characters such as * ^ % ? / . select the column and set the number of decimals to 5 (or any desired number) using Format/Cells. That transforms the text values to numeric values (when possible). JPEG. or to change their content. For numeric fields.>. or from a spreadsheet program such as Excel. When a DBF is associated with a shapefile. That will not change the format to numeric. Instead.GIS supports these formats for images: TIFF. If you use Excel. You can create DBF file by exporting it from a database program such as Access. Each column with data should have a field name. Instead.2. Always save the file in the native Excel format (XLS) first so that you do not lose your data should they not be saved correctly as DBF.

At the equator. and no letters describe latitude and longitude. d is the degrees (º). (2004) for a thorough discussion of coordinate precision. m the minutes (’). a single number each. See Wieczoreck et al..g. – 12. A decimal system is universally used in geographic computing. 12°34’15” S (12 degrees.57083). 30º30’0’’ S = -30. and between 90° North and 90° South. © 2007 International Potato Center . You can do these calculations in a spreadsheet program or in the DIVA-GIS “Geo-calculator”. the following formula is used: Where DC is the decimal coordinate. This system worked fine in the days paper maps. For example. Southern hemisphere). with the sign indicating the hemisphere (+ = N or W. For example. h = 1 for the Northern and Easter hemisphere and -1 for the Southern and Western hemisphere. but it is not very suitable for the digital age. one unit of the fourth decimal (0. That should be precise enough for most applications. The most commonly used are degrees of longitude and latitude. A location on earth can be between 180°West and 180°East. and s the seconds (’’) of the sexagesimal system.. Decimal degrees should normally be recorded with 4 or 5 decimals. minutes. 34 minutes. not affected by longitude).Some Basic Concepts 17 3. and seconds to decimal degrees. – = S or E) (e.g.500 and 30º15’55’’ N = 30. If you are using high-precision GPS (with differential correction). 5 decimal places would be warranted. 15 seconds.3 Geographic coordinates There are several ways to describe a location on earth. 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). latitude can be described as e.0001 degrees) equals about 10 meters (less at other latitudes.265. To convert longitude and latitude in degrees. In this decimal system.

Creates Map. Saves the change of the current Map. Saves the changes of all Maps. Opens existing Project. Outgoing sync. It includes the functions for the management of a DIVA project. Short explanation © 2007 International Potato Center . Creates a page for printing based on the current map. A project consists of a number of geo-referenced databases (maps) that are called "Layers".18 Manual Diva 4 The File Menu The File Menu is very similar to the File menu of many Windows programs. Creates Project. Imports to DIVA-GIS files Export DIVA-GIS files. Icon Name New Layer New Map New Project Open Project Save Save All Commit Rollback Redraw Create a page to be printed Import Export Creates Layer. Rollbacks and clears current changes Redraws the current map.

A project file can be closed.1 Projects A DIVA-GIS project is a description of a DIVA-GIS map: it includes a collection of layers and their display properties. \diva\myshp. if you delete. Relative paths (e. Project files have the extension DIV.shp). as well as some general parameters describing the map’s scale and center. and stores map properties (such as scale). a data file. select New Project. The project file does not contain the actual data. To create a new project. in the folder structure. or rename. all your data will be still being available.. c:\mydata\diva\myshp. 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. However. saved with a new name. It is also possible to use network paths (e. © 2007 International Potato Center . This allows for sharing projects over a network. are below the project file. and opened again using commands from the File menu. This means that if you delete a project file.. a project file will not be able to find it anymore.g.g.shp) are stored for data files that.g. \\network\share\shape.shp).The File Menu 19 4. it only points to the files of the different layers. For all other files. or saving them on a CD-ROM (different drive letters can be used). the absolute path is stored (e. You can save a project by clicking on Save. This creates an empty Project that can be filled by adding layers using Layer/Add. and DIVA-GIS will show a message indicating this.

2 Imports Some data we have as molecular data file y we cannot visualize them in a Layer. DIVA-GIS has implemented a tool that converts the molecular data file in a shapefile. Select File menu/ Import/ Import Molecular Data.20 Manual Diva 4. © 2007 International Potato Center .

The File Menu 21 4. © 2007 International Potato Center .1 Import Molecular Data First select the file that contains the molecular data.2. The columns' field name must have 10 characters maximum.

22 Manual Diva Then select the shapefile with the one that is going to compare and to assign the respective attributes. © 2007 International Potato Center .

To view the results close the window and view the map.The File Menu 23 Select the output file. © 2007 International Potato Center .

2. © 2007 International Potato Center .24 Manual Diva 4.2 Import to Grid files With this module you can import single o multiple files to DIVA-GIS files like as grid files.

Icon Undo Redo Name Short explanation Allow user to undo last action. 5 The Edit Menu The Edit menu permits undo or redo the changes in the Map Editor. Allow user to redo last action. © 2007 International Potato Center .The File Menu 25 4.3 Export Grid files In this module you can export single o multiple DIVA-GIS files to IDRISI or ESRII Binary files.

Navigation command restoring a map location changed using the back command. Icon Back Forward Show all Zoom In Zoom Out Name Short explanation Navigation command returning to previous map location. show the full map. increase the Map scale by a fixed amount © 2007 International Potato Center .26 Manual Diva 6 The Navigation Menu The Navigation menu permits go back and forward. decrease the Map scale by a fixed amount. also you can show the entire layer or zoom in it and zoom out it. A navigation command. A navigation command. A navigation command.

A navigation tool providing control of a Map location. A navigation tool providing control of Map scale. An edit tool permits to selection a point of the Map Permits to selection a point of the Map to do Analysis. Request information for content at an indicated location. Icon Stop Zoom Pan Box Selection Diva Box Selection Information Point Polygon Edit Tool Data Grid Info Name Short explanation Cancel the current rendering. Calls a window with the attributes of the Layer. Shows environmental data for a location when you click on the map with the mouse. © 2007 International Potato Center . 8 Tools Menu The Tools menu permits change the properties of the map scale. also you can see a summary of the Layers. Permits view the Grid value. Icon Add Delete Layer Summary Feature Count Name Short explanation Permits add layer in the Map. Permits edit polygon geometries.The Navigation Menu 27 7 The Layer Menu The Layer menu permits add and delete layers. Permits delete layers. Calls a window with the number of the features in the Layer.

Select the area. © 2007 International Potato Center .1 Diva Box Selection This tool permits select an area to do Analysis.28 Manual Diva 8.

in the button Options click on Get Rectangle.1 Analysis Selected Features Select Point to Grid .Tools Menu 29 8. and this get the coordinate of the area selected with Diva Box Selection tool.Richness Analysis. © 2007 International Potato Center .1.

30 Manual Diva © 2007 International Potato Center .

2 Information This tool permits get the information of the accession. © 2007 International Potato Center .Tools Menu 31 8.

DIVA-GIS will show data for that location .32 Manual Diva 8. monthly average minimum and maximum temperature (°C) and monthly precipitation (mm). It also shows 19 Bio climatic variables derived from the monthly data. i. both as tables and graphs.e.3 Point When the Point button is pressed. © 2007 International Potato Center . The Point window shows the altitude (in meters above sea level) and climate data. if you then click on the map (on land!) with your mouse.

Tools Menu 33 8.4 Data Grid Info This tool permits view the values of the Grid. © 2007 International Potato Center .

The points represent location where a specimen was collected.34 Manual Diva 9 Analysis Menu This chapter describes the methods for analysis of biological distribution data available in DIVAGIS. a shapefile or a database file(DBF). Calculates distribution statistics from point data. distance. These analyses are all based on location (latitude and longitude) and additional attributes of point data. which highlights it. The output of the analysis routines can be a gridfile. Exports features. Includes tools to access climate data and to do climate related data analysis. Compares locality descriptions in a point shapefile with those in a polygon shapefile file. © 2007 International Potato Center . or where any observation of the presence of a specific biological unit was made. Name Point to Grid Select Records by Query Check Coordinates Distance Climate Autocorrelation Point Export Short explanation Creates a gridfile with different indices(diversity. or related) or statistics from a points shapefile Selects records from the active layer (shapefiles only) that comply with a specific condition (layer). Assesses the presence of spatial autocorrelation from point data. These points should be in the active (shapefile) layer in the DIVA-GIS project (a shapefile is made active by adding it to the map and clicking on its legend entry once).

Analysis Menu 35 9. the Point to grid window will open. When you select one of the output options.1 Point to grid The principal analytical functionality in DIVA-GIS is found in the Analysis/Point to grid menu. The output of the functions in this window is a grid. © 2007 International Potato Center .

© 2007 International Potato Center . The advantage of using grids over areas such as countries or other administrative units is that grid cells of the same size allow a more objective comparison. For instance. A grid divides (a part of) the world into equal-sized cells. the number of observations (points) in each cell can be calculated.1.36 Manual Diva 9. A calculation is then preformed on each of the cells.1 Grids Grids are central to the analytical capabilities of DIVA-GIS.

Analysis Menu 37 © 2007 International Potato Center .

a geographic reference system.38 Manual Diva 9. Because maps are flat. but could be different. As a grid is rectangular. you must specify whether you want the number of columns to adapt. For example. in the case of the latitude/longitude system. On the window that appears you can change the default grid extent (as defined by the coordinates of the four corners). or map projection. The vertical and horizontal resolutions of a grid are usually the same. © 2007 International Potato Center . when this would lead to less than 10 or more than 100 rows or columns. two opposite corners. its geographic reference system must be specified and then its extent and resolution. You can also define the grid extent by drawing a rectangle on the map after pressing the Draw rectangle button.g. while the Earth is not. You can either specify this from scratch or copy the parameters from an existing gridfile. or the grid extent (resolution). a resolution of 1 means that each cell is 1 by 1 degree. if you want to change the resolution. the resolution can be calculated when the other variables are known.. the default resolution is adapted accordingly. e. If the grid extent and resolution are known. As these parameters are all interrelated. You can use any projection in DIVA-GIS (see Chapter 10 for a discussion of projections). A grid has an “extent. Alternatively. The “resolution” is the area of each grid cell. DIVA provides default parameters for the output grid that are calculated on the basis of the extent of the active points shapefile layer. the upper left and the lower right corner. To define a grid. resolution and number of columns/rows. you need to specify which other parameter should also change . When you want to adapt the grid extent . and by setting the resolution to 1 (in the units of the reference system). has to be used that renders the three-dimensional reality in two dimensions (a flat map) with minimal distortion. However.2 Defining Grids The first step is to define the extend and resolution of the grid that will be used to make the calculations. can define it. using the Fix corner box. You can change the default parameters by selecting any statistics from the Point to grid/Define grid/Options menu under Analysis. For example. you can fix one corner of the grid.” which refers to the geographic area it covers. the number of rows and columns in the grid can be calculated.1. Resolution is always expressed in the units of the geographic reference system.

1.Analysis Menu 39 9. You can just the parameters from a gridfile produced in a previous analysis (use the scroll bar in the Define grid option of the Point to grid window and then press Options to choose an existing grid). or should get special treatment in the case of the Inverse Distance Weighted method (see section 4. © 2007 International Potato Center . The part of the gridfile that should be ignored can be indicated using numerical values or ranges. An existing gridfile can also be used as a “mask” to indicate what part of the grid should be ignored.3).3 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.

g. The Number of observations option calculates the number of points present in each grid cell. 9.4. the different species names in a dataset covering a genepool) present in each grid cell.1.4. Number of different classes counts the different classes of a variable (e. and associated with a number of options that can be set on the Parameters tab to the right of the Main Tab. and then you can exclude one or more of the values of that variable. The Parameters tab must be used to indicate which variable in the shapefile should be considered. In that case. Output variables are grouped.2 Rarefaction (to be filled in) © 2007 International Potato Center ..1. you may want to exclude these. 9. and optionally to exclude irrelevant values. Number of observations and Rarefaction.4 Output Variables There are a number of different output variables that can be calculated for a grid. you must select a variable from the genebank database on the Parameters tab (Figure 10).1.1 Richness In the Richness group there are three distinct output variables: Number of different classes. As there may be points in the shapefile that are not relevant. The appropriate output variable can be selected under the Point to grid menu.40 Manual Diva 9. The different output variables are discussed in the following sections.

Various different approaches have been proposed to estimate Smax. F2 the frequency of doubletons) © 2007 International Potato Center .1 Chao 1 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: S1 = SOBS + (a2 / 2b) SOBS is the observed number of species in a sample. The corrected version is less biased.1. a is the number of observed species that are represented by only a single individual in that sample.1. in most cases only a sample of an area is usually surveyed. An important problem that then arises is to estimate the total species (or other taxon) number.3.3 Estimators of Richness The number of species (or other units) observed in an area depends to some extent on the effort invested in recording there. SChao1 = Sobs + F12 2(F2 + 1) F1F2 2(F2 + 1)2 Where Sobs is the total number of species observed and F1 is the number of species that have exactly i individuals (F1 is the frequency of singletons. for the area. This estimate can give both a measure of the completeness of the inventory and also allow for better (i.4. less biased by the number of observations) comparison with the species richness of other localities.4. 9.3. b is the number of observed species represented by exactly two individuals in that sample 9. An estimate of the maximum species number is also useful when assessing if the further information to be gained from continued sampling justifies the cost.. Because a complete census is rarely feasible.2 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).1.e. Smax.4.Analysis Menu 41 9.

which estimates the coefficient of variation of the Fi's.3. © 2007 International Potato Center . is Where: Sobs Total number of species observed in all samples pooled Srare Number of rare species (each with 10 or fewer individuals) when all samples are pooled Sabund Number of abundant species (each with more than 10 individuals) when all samples are pooled Nrare Total number of individuals in rare species Fi Number of species that have exactly i individuals when all samples are pooled (F1 is the frequency of singletons. Cace Sample abundance coverage estimator. This estimator uses the proportion of all individuals in rare species that are not singletons. Cace = 1 .1.42 Manual Diva 9.3 ACE Abundance-based Coverage Estimator of species richness (Chao and Lee 1992). F2 the frequency of doubletons).F1 Nrare where 10 Nrare = S iF i =1 i Then the ACE estimator of species richness is Sace = Sabund + Srare + F1 g2 ace Cace Cace where Gamma-ACE.4.

but a higher number may be better for some data).e-kn) Equation 1 Where k is a fitted constant and n the number of samples. favored by (Raaijmakers 1987). The asymptotic behavior of the accumulation curve can also be modeled as the hyperbola: S(n) = Smax n B+n Equation 2 Where Smax and B are fitted constant This is Michaelis-Menten equation used in enzyme kinetics and thus there is an extensive literature discussing the estimation of its parameters.Analysis Menu 43 9. The number of species is estimated from this generated species accumulation curve. presents considerable statistical difficulties.4. © 2007 International Potato Center . is to calculate Smax and B using their maximum likelihood estimators as follows: if Xi = S(n) and Yi = S(n) then n Equation 3 Where Syy.4 Michaelis-Menten This estimator is calculated by repetitive random sampling and fitting an asymptotic model. This asymptotic model assumes that the probability that the next individual captured will be a new species declines linearly with species number. For each sample size (from 2 to number of observations -1). which unfortunately. and thus the species accumulation curve is the negative exponential function: S(n) = Smax (1 . the average number of species in the samples is calculated over the random samples (the default is 100 samples for each sample size. Sxx and Sxy are the sums of squares and products of the derivations Y Y i and X X i . following the method of Raaijmakers (1987). The method implemented in DIVA-GIS.3.1.

Ni = Number of individuals in the i .1. © 2007 International Potato Center . D. You must select a variable (field) from the input database for which you want to calculate this index. in the sample to be rarefied.S ln ni!) / N S = number of unique classes (species) per cell N = number of observations per cell ni = number of individuals in the i-th class pi = proportional abundance of the i th class = ni / N The Simpson index. and hence it is usually expressed as 1-D or 1/D. 9.44 Manual Diva 9. N = Total number of observations per cell.4. Index Margalef Menhinick Shannon Simpson Brillouin Formula DMg = (S .4 Diversity indices A number of diversity indices can be calculated for each grid cell.th class. See Table 5 for the mathematical description of the different diversity indices. The formulas for all indices were taken from Magurran (1988).1.S pi ln pi D = S (ni (ni . in the sample to be rarefied.4. who provides a detailed description of their properties. n = User specified standardized sample size.3.5 Rarefaction The rarefaction technique estimates the number of classes (species in this case) that would have been observed given a number of observations that is specified by the user. In DIVA-GIS it is expressed as 1-D. Equation (4) E(S) = Expected number of classes in the rarefied simple. decreases with increasing diversity. A disadvantage of this method is that the estimate can only be calculated for those cells in which the real number of observations is higher than that for which the estimate is calculated.1) / ln(N) DMn = S / vN H' = .1) / N / (N -1)) HB = (ln N! .

The procedure is based on the algorithm described by Rebelo (1994). The procedure is less straightforward than it might seem. With the "Equal weight" option. this procedure can lead to slightly different results every time it is run. 9. i. Hence.1.4.6 Reserve Selection The Reserve Selection procedure aims to identify sets of grid cells that are complementary to each other. been used to determine priority areas for in situ conservation of species in a particular flowering plant family in South Africa. The first step is to select a variable. If there are two or more cells with the same “value”. There are two options: "Equal weight" and "Rarity". one is selected at random. but one with different species in all its grid cells and another with the same species in all its grid cells. This is because the species in the cell with the second highest number of species may also be present in the first cell. species) has the same weight. but any multi-state variable could be used. The following discussion refers to species. © 2007 International Potato Center . and this is what has been implemented in DIVA-GIS.Analysis Menu 45 9. It indicates how different a number of nearby areas are. that capture a maximum amount of diversity in as few cells as possible. the second area a low turnover. for example. To maximize the total number of species selected in as few cells as possible is a non-linear optimization problem. and in relation to the observations in the cells already selected.g. In each iteration. an adjustment can be made in which rare observations get a higher weight. Imagine two large areas with similar numbers of species overall. Rebelo (1992) developed a procedure that calculates an approximate optimal solution. missing values) from the analysis. the cell with the second highest number of species may not contribute very much to the overall number of species selected. and possibly exclude some of the values (e. based on the observations in that cell. The rarity value equals the number of observations of a category divided by the total number of observations.4. The first area would have a high turnover. the “value” of each grid cell is calculated. each category (e. An iterative procedure is used. Instead of using simple richness. With the "Rarity” option. It has.1.5 Beta Diversity Beta diversity or Turnover is a measure of the rate at which species assemblages change in space. 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(s) depends on the previously selected cells.. the value of a cell is calculated using the “rarity value” for each observation. Several options need to be selected.g.e. The second step is to choose a scoring approach. In other words.

by changing the Values in selected cells option.e. i. for your purposes. you can indicate the iteration number or the number of categories? per grid cell on the grid. When the process finishes. © 2007 International Potato Center . When using the last option.46 Manual Diva There are two ways in which you can limit the number of iterations. Alternatively. too low a number of observations. only the "useful" observations. those that were not selected before. a "Process Report" appears. It allows you to exclude cells with what is. 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. This value should be 1 or higher. You can indicate the "Minimum number of records per cell". You can create a boolean (true/false) image in which the selected cells get the value "1" and the other cells the value "0". The results can be stored in different ways. This is important because the procedure can take a long time with large databases (or a grid with a many cells). You can also indicate the maximum number of iterations that you want the procedure to go through. are included..

1.7 Statistics If a numerical variable is selected. for each grid cell. straightforward statistics can be calculated for that variable.4. Min Max Mean STD CV Range Range / Mean Median Mode Minimum value Maximum value Mean value Standard deviation Coefficient of variation Difference between Max and Min Range divided by the mean Median value Mode (most frequent) value © 2007 International Potato Center .Analysis Menu 47 9.

48

Manual Diva

9.2

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 meets 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. Only Layers that are made from shapefiles can be selected from.

9.2.1

Select Records by Values
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.

© 2007 International Potato Center

Analysis Menu

49

Then select the values to include in the selection. When you are ready, click 'Apply'.

© 2007 International Potato Center

50

Manual Diva

9.2.2

Select Records by Query
Using selection by query, you must select a variable, a criterion and the value. Use the 'Add' button puts the query in the dialog box.

Continue adding additional conditions using 'AND' , 'OR'.

© 2007 International Potato Center

© 2007 International Potato Center .Analysis Menu 51 When you are ready. click 'Apply'.

The columns' field name must have 10 characters maximum. and any mismatches probably reflect errors (or name or boundary changes!). a new (temporary) database is created. (1999). By simultaneously querying the accessions database and an administrative boundaries database. this new database contains the location information according to both the genebank database and the administrative boundaries database. using a method described by Hijmans et al.3 CheckCoordinates The Check coordinates facility helps you to verify the correctness of the coordinates. For each accession. © 2007 International Potato Center .52 Manual Diva 9. The Check coordinates tool helps you identify errors. This information should be the same.

B. according to the genebank database. pointing at accessions 2. Six accessions have been collected and stored in a genebank. The co-ordinates of the collection locations. By querying the two databases. and C. have been plotted on a map of the provinces.Analysis Menu 53 A simple example for an imaginary island that has tree provinces called A. Genebank database Accession 1 2 3 4 5 6 Province B B B E C C Administrative Boundaries Province B A B C C © 2007 International Potato Center . the nest table is generated. 4 and 6 as possible errors.

© 2007 International Potato Center . select the longitude and latitude.3.1 Checking Coordinates To check coordinates right click on a layer. select the relations.54 Manual Diva 9.

1 Distance Distance Statistics With the Analysis/Distance/Statistics procedure. Distances are expressed in meters. you can calculate statistics for each unique class of a multi-state variable. and MinD. The output is written to a DBF file. for each species in a database of wild relatives in a genepool. maximum. for example. you must specify whether the shapefile is in decimal degrees or projected (with meters as unit). MaxD. and average distance between two points of each class). To allow correct calculations. the following statistics area available: number of observations. Currently.4. © 2007 International Potato Center .Analysis Menu 55 9. and AverageD (respectively the minimum.4 9.

2 Distance Matrix The same calculation can be followed for all points (i.4. and a complete distance matrix will be the output (Analysis/Distance/Matrix).56 Manual Diva 9. without distinguishing among classes). © 2007 International Potato Center .e.

© 2007 International Potato Center . (2) Yes – data were present.214 2.75 x 3. No – data were absent. but initiated from different points on the control run). All scenarios used assume an increase of 1% atmospheric CO2 per annum (ISO92a).2060. These data are stored in a special format (CLM files) to allow quick access and reduce storage space requirements. A global grid with a 10 minute resolution by New et al. Future climate refers to 2041 . excluding for major water bodies(oceans) and Antarctica.8125 x 2. If minimum and maximum temperature were absent these were calculated from mean temperature (see text).75 I II III IV V VI Canadian Centre for Climate Modelling and Analysis Australian Commonwealth Scientific and Industrial Research Organization Australian Commonwealth Scientific and Industrial Research Organization German Climate Research Centre UK Hadley Centre for Climate Prediction and Research UK Hadley Centre for Climate Prediction and Research (1) Climate change model forcing details: GG = Greenhouse Gas. Parameters for these calculations were taken from the current climate in a grid cell. DIVA-GIS comes with a default climate data set for the whole world. Scenario Institute / Model Code CGCM1(3) CSIRO-MK2 CSIRO-MK2 ECHAM4 HadCM2(3) HadCM2(3) Forcing details(1) GS GG GS GG GG GS Original Resolution in degrees 3.75 3.75 x 2. Their original dataset was re sampled (interpolated) to a 10 minute grid. You can also use your own climate data in DIVAGIS Data are included for current climate and also for projected future climate.625 x 3. The data were estimated from a number of different climate models and model runs provided by the intergovernmental Panel on Climate Change Data Distribution Center (1999).214 5. Current climate data refers to 1961-90. (2002) was used.5 Climate The Climate menu includes tools to access climate data and to do climate related data analysis. If solar radiation data were absent these were calculated from extraterrestrial radiation and cloud cover.Analysis Menu 57 9. GS = Greenhouse Gas and Aerosols.625 x 3.75 x 2. Climate scenarios used to calculate an average predicted climate for the 2041-2060 period. (3) Mean of four ensembles (identical model experiments performed with the same historical changes and future changes in greenhouse gases.8125 3.75 5.

1 Ecocrop This module uses the Ecocrop database of crop requirements from FAO. for any growing season. If this is not the case. minimum average temperature at which the plant will grow. on average. The length of the growing season is defined as the average of Gmin and Gmax. If the average minimum temperature in one of these months is 4 °C or less above KTMP. minimum average temperature at which the plant will grow optimally. Relation between average monthly temperature data and calculated suitability values for that month. To determine the suitability of a growing season for a certain crop.5. maximum average temperature at which the plant will cease to grow. © 2007 International Potato Center . The parameters are for maize. the temperature suitability is evaluated for that month using the other temperature parameters. it is assumed that. the following temperature parameters are used: KTMP : TMIN : TOPMN : TOPMX : TMAX : absolute temperature that will kill the plant. (In DIVA-GIS. we implement Ecocrop to predict the adaptation of a crop over geographic areas. In DIVA-GIS. maximum average temperature at which the plant will grow optimally. See the example for maize for how this is done. The temperature suitability of that month is 0%. Ecocrop can be used to assist in the identification of candidate crops to grow in defined environments. starting on the first of each month.58 Manual Diva 9. In Ecocrop. Currently only temperature and precipitation data are used to make this prediction. and the crop will die. The overall temperature suitability of a grid cell for a crop. KTMP will be reached on one day of the month. 12 possible growing seasons are considered. is the lowest suitability score for any of the consecutive number of months needed to complete the growing season. the growing period is defined in days between Gmin and Gmax (start of growth and end of growth respectively). The suitability of a location (grid cell) for a crop is evaluated for each of the 12 potential growing seasons. expressed in months.

You can search for crops using the options in Filter by. and for temperature. The changed parameters will be used. optimal maximum rainfall (mm) during the growing season. To run the module you must first select a crop in the Select tab. or for both. the following rainfall parameters are used: Rmin : Ropmin : Ropmax : Rmax : minimum rainfall (mm) during the growing season.Analysis Menu 59 To estimate the suitability of the rainfall in an area for a certain crop. The output is the highest suitability score (percentage) for a growing season starting in any month of the year. optimal minimum rainfall (mm) during the growing season. You can run the Ecocrop module for rainfall. but not saved. the minimum value of the two for each growing season is used to compute the suitability. On the next tab. except that there is no "killing" rainfall and there is one evaluation for the total growing period (a number of months defined by Gmin and Gmax) and not for each month. maximum rainfall (mm) during the growing season. © 2007 International Potato Center . Parameters. The evaluation for rainfall is similar as for temperature. Then select the crop you want by clicking on it (the selected record becomes blue). you can inspect the temperature and rainfall parameters and change them if you want. In the last case.

If you do not do this. the program will do it when you press Apply © 2007 International Potato Center .60 Manual Diva You can select the area for which you want output by filling the upper text boxes on the Predict tab. You can do this by pressing the Adjust coordinates button. You can also use the extent of a shapefile or gridfile by making it active in the legend and then pressing the Read coordinates button. The coordinates need to be adjusted to those of the climate grid cells.

Analysis Menu 61 © 2007 International Potato Center .

62

Manual Diva

9.5.2

Map
Climate/Map provides a tool to map a specified climate variable over a specified areas When you press the Read from layer button, the dimensions of the active layer will be copied to the minimum and maximum coordinates of the Climate data to Map window. 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 (Draw rectangle button). Choose the variable that you need and whether you want a gridfile for the current or for the projected future climate.

© 2007 International Potato Center

Analysis Menu

63

© 2007 International Potato Center

64

Manual Diva

9.5.3

Extract
The Extract tools assigns environmental data to locations in a points shapefiles. This allows socalled "retro-classification": climatic characterization of collecting sites after, rather than during, collecting. This can be useful because the distribution of species and traits cam be related to the value of ecological variables at the places where they occur.

© 2007 International Potato Center

data are clustered. at random. Geary 0<c<1 c=1 c>1 Moran i>0 i=0 i<0 Interpretation Autocorrelation exists.6 Autocorrelation Autocorrelation exists when the values of nearby geographical objects are more similar than objects further away. Independent. the Geary and Moran indeces. Negative autocorrelation. The autocorrelation option in DIVA-GIS calculates this relationship by using two common statistics.Analysis Menu 65 9. For example. an altitude grid has a high spatial autocorrelation. You can calculate the autocorrelation on a gridfile or a points shapefile. © 2007 International Potato Center . The spatial autocorrelation functionality implemented in DIVA-GIS is based on the “Rookcase” software by Sawada (1999).

To determine a reasonable lag distance. and you need to define which neighboring points to consider. max. You must select a quantitative field from the shapefile’s database to calculate autocorrelation. because you do no longer consider all points. © 2007 International Potato Center . a number of statistics are shown in the Options tab of the Point autocorrelation window. After selecting a field you can deselect individual values that you want to exclude. which will have changed. These statistics include the number of observations (points) and statistics describing the distances among all pairs of points (min.1 Point Autocorrelation for points is calculated point by point.6.66 Manual Diva 9. median and first and third quartile). mean. The results will appear on clicking Apply. This is done by specifying the lag (or neighborhood) distance. Only points within the lag distance are considered for calculation. If you do that you need to recalculate the statistics.

© 2007 International Potato Center .Analysis Menu 67 9.7 Exports Select the features to export.

© 2007 International Potato Center .68 Manual Diva Click on Export Selected Features.

Analysis Menu 69 Add the layer created to see the features exported. © 2007 International Potato Center .

Creates a shapefiles of lines or polygons from a text file.70 Manual Diva 10 Data Menu The Data menu has a number of functions that help you to manage your data. Creates a shapefile from DBF. Name Text to DBF DBF to Shapefile Text to Shapefile Structure to Shapefile Short explanation Creates a DBF from a text file. Assign Coordinates © 2007 International Potato Center . like checking or preparing coordinate data. The Structure to Shapefile Wizard allows the importation of an output report from the software structure Assigns coordinates to records based on the locality description.

these are sometimes also called ASCII files. DIVA will figure out what type of data is present in each column of the database: text. but this has proved to be difficult for many users. If your data are in a different format. we have included a simple import facility in DIVA-GIS to create DBF files from TXT files. from Microsoft Access). or can be exported to that format (e. © 2007 International Potato Center . such as Microsoft Excel.g.1 Text to DBF The Text to DBF function allows you to create a DBF files from a text (TXT or ASCII) file. However. The TXT files must have a header row containing the variable names. Some databases are in a DBF format already. but you may change this setting. you can create DBF files with a number of software programs. the data will be truncated (cut off at the position that you indicated). If you indicate fewer spaces than are actually used. Using commas as separators is problematic when you have a field with locality descriptions. Therefore. Same for the maximum number of spaces that a value of the variable will need.Data Menu 71 10. ‘tab-separated’ is probably best. or integer (whole). 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 appropriate box. TXT files are plain text files. which may well include commas .

72 Manual Diva The columns' field name must have 10 characters maximum. © 2007 International Potato Center .

the record is copied to the DBF table of the shapefile. By default.Data Menu 73 10. an “empty” record is created. DIVA-GIS will attempt to transform the text values to numbers. And you must provide an output filename that is different from your input filename The program then reads the input file and allows you to select the fields that have the X and Y coordinate data. That is.2 DBF to Shapefile With Points (DBF) to shapefile you can make a shapefile of points from a DBF file if that DBF contains fields with latitude and longitude (both in decimal degrees). you must indicate the filename of your DBF file. © 2007 International Potato Center . First. Where this is not possible. but no associated point is created. The columns' field name must have 10 characters maximum. or where there is no entry at all. If you use a text field for the X and Y coordinates. only numerical fields are listed for you to choose from.

) x y END ID x x y (.. A polyline is a line consisting of various parts. put END.. A polygon describes an area. At the end of the file there should be an additional END.) x y END END y y © 2007 International Potato Center . (.3 Text to Shapefile Here you can create a shapefile of lines or polygons from a text file(for example with coordinates obtained with a GPS. After the last node of an object.74 Manual Diva 10. the first line should have an ID (number) followed by a pair of coordinates (x and y .typically longitude and latitude). or read from a map). For each object (polyline or polygon) in the text file. all separated by spaces. An example of a TXT file that can be imported to a (poly)line or polygon. On the following rows are coordinate pairs for the nodes of the object. ID x x y (...) stands for any number of additional pairs of x and y.. and start again for the following object..

Data Menu 75 First select the input file. Then select the geometry type. in this case is Polygon. © 2007 International Potato Center .

76 Manual Diva Select the output file © 2007 International Potato Center .

From the structure webpage: "The program structure is a free software package for using multi-locus genotype data to investigate population structure. and estimating population allele frequencies in situations where many individuals are migrants or admixed. RFLPs and SNPs.4 Structure to Shapefile The Structure to Shapefile Wizard allows the importation of an output report from the software structure by Jonathan Pritchard. This method was described in an article in Genetics 2000 (155: 945-959). studying hybrid zones. Its uses include inferring the presence of distinct populations. including microsatellites. William Wen. assigning individuals to populations." © 2007 International Potato Center . Collaborators: Matthew Stephens. Extensions to the method were published in Genetics 2003 (164: 1567-1587). It can be applied to most of the commonly-used genetic markers. Peter Donnelly. Daniel Falush.Data Menu 77 10. identifying migrants and admixed individuals.

78 Manual Diva 10.1 Convertion to Shapefile The first step for importing structure output data into Diva is copying the output report we get from Structure (text) in the text window of the wizard.4. © 2007 International Potato Center .

For that purpose we need to select a dbf file and choose de Accession ID Field and the fields with latitude and longitude values.Data Menu 79 For the creation of a Shapefile we need to assign coordinates to the accessions used with structure. © 2007 International Potato Center .

coordinates are assigned and the following preview report is shown.80 Manual Diva The wizard search for matches between the accessions listed in the structure report and the provided ones in the dbf file. The preview report will be then used to create a shapefile of points © 2007 International Potato Center . When a match is found.

Data Menu 81 © 2007 International Potato Center .

DIVA-GIS uses the database of foreign geographic feature names from the U. with the coordinates of their locations and other information.5 Assign Coordinates The Assign coordinates function can help you to give coordinates to records that only have a locality description. particularly for older collections. The columns' field name must have 10 characters maximum. Fortunately. However.82 Manual Diva 10. there are digital gazetteers available to facilitate searching.S. Coordinates can be assigned to such records by searching for the locality names on maps or in gazetteers. © 2007 International Potato Center . Coordinate data are often absent in biological distribution databases. most records are accompanied by a locality description of some kind. National Imagery and Mapping Agency's (NIMA). A gazetteer is a list of names of geographic features.

If. BOL for Bolivia) If you do not want to use that. you must have a field with the name of the country. This name should be the 3-letter ISO code for the country (e. first and second administrative subdivision (ADM1 and ADM2) and up to two locality names. or ADM2 or locality field. you can use another name. This file should ideally have the field indicating where the accession was found: country. If you have more gazetteer in the same directory.Data Menu 83 To have DIVA-GIS search for the coordinates of localities. Distance should be expressed in kilometers. © 2007 International Potato Center . For the second location (B). the narrative locality description should be summarized in a number of well defined fields. but must then assure that the field name and the gazetteer filename are the same. The locality is then looked up in the digital gazetteer and its coordinates assigned to the accession. and only if. For both locality names you can indicate the distance (in a straight line) and direction from the collecting to that locality. In other words. 20 km east of B". Obviously. go to the Analysis / Assign Coordinates window or right click on the shapefile in the Layer view. the coordinate assignment will be very imprecise. A should be the first locality and B the second. B will be searched for and. by renaming the gazetteer file (by default. Not all fields are obligatory. if it is found. if you only have ADM1. the collecting site will be estimated as 20 km east of B. all they will be shown in the combo. As a minimum. the data on distance (20 km) and direction (east) should be indicated. A is not found. In this case. The "Open Gazetteer" button permits to load your gazetteer located in different directories. There are two locality fields because the narrative description of a collecting location often looks something like "collected in A. these have been given the ISO county codes).g. Your database must also have an ADM1 (first administrative division of the country).

you must locate the files you need on the DIVA-GIS website.southeast Southeast South .5.northeast Northeast East . You can check which files are present by clicking on the gazetteers list-box on the Assign coordinates window.southwest West .1 Direction Codes Direction must be expressed in text.southwest Southwest West West . © 2007 International Potato Center . The default location for these files is the <divadir>\gazet folder.northwest Northwest North-northwest N NNE NE ENE E ESE SE SSE S SSW SW W WSW WNW NW NNW CODE The gazetteer is divided into country files. These files are not all automatically installed with DIVAGIS.northeast East East . If the countries you need are not included.southeast South South . using the codes in Table DIRECTION North North .84 Manual Diva 10.

(x. y) Place name (abc) not found (used ADMn = ) Warning: distance from locality name was xxx km (>50km) Country (= xxx) not found (no coordinates assigned) ADM1 (=xxx) not found (no coordinates assigned) ADM2 (=xxx) not found (no coordinates assigned) Impossible angle © 2007 International Potato Center . CODE 1 2 3 4 5 11 12 13 14 COMMENTS Assigned Assigned to a similar name (San Francisco = San Francizco). You have to go over the comments in the output window carefully to decide which coordinates you want to accept. (x. LONGITUDE. CODE and COMMENT.Data Menu 85 10. y). You can also include all the other fields that may be present in the input database.2 Possible codes and Comments DIVA-GIS will generate a new output file that contains the input data (such as COUNTRY and ADM1) and four additional columns: LATITUDE. y). and which you do not want to use. which you want to verify. n duplicate locality names found (x.5.

© 2007 International Potato Center . Calculates the distance between two points. Name Geo Calculator Short Explanation Transforms geographic coordinates in degrees/minutes/seconds to decimal degrees. These functions allow you to classify you grid data. resize or combine your grid files and filters or recalculate the values of the grid cells.86 Manual Diva 11 Tool Menu A number of practical and analytical functions are available in the Grid menu.

seconds) system to a decimal system.1 Geo Calculator With the Geo-calculator you can convert coordinates in the sexagesimal (degrees.Tool Menu 87 11. This can be done for one location or for a file with many locations (use the Batch option). minutes. © 2007 International Potato Center . You can also calculate the distance between two points.

1 Batch Option With this tool you can convert the coordinates in the sexagesimal (degrees. also you can save the file as a Text file.88 Manual Diva 11. you have to click on Apply Changes button. When you set the Longitude and Latitude parameters. minutes. seconds) system to a decimal system.1. © 2007 International Potato Center .

1 Help Menu Updating DIVA 12.Tool Menu 89 12 12.1. © 2007 International Potato Center .1 Registration of the update site To download new plugins from the DIVA-GIS update site: Select Help->Updates and Extensions options...

© 2007 International Potato Center . Select “Search for new features to install” radio button and press “Next”. an instant wizard will guide you through the process of accessing the update site and downloading plugins.90 Manual Diva Then.

Help Menu 91 If you do not have any sites included then you have to register the DIVA-GIS Update Site © 2007 International Potato Center .

A small dialog box will appear and then fill the text boxes by writing a name to recognize the site and then its URL.92 Manual Diva Press the button “New Remote Site”. Name : DIVA-GIS Update Site URL : http://research.cip.cgiar.org/diva/software/diva-gis/update © 2007 International Potato Center .

Help Menu 93 Afterwards. Press “Finish” to finish the registration. the DIVA-GIS Update Site will appear in the list of registered sites. Wait a few seconds until DIVA-GIS finishes accessing the update site. (Fig6) © 2007 International Potato Center .

2 Downloading plugins The results of available plugins will appear in a new window where you can select one or various plugins to install.1.94 Manual Diva 12. © 2007 International Potato Center .

Help Menu 95 Read the license agreement and accept the terms by selecting the first radio button. © 2007 International Potato Center . Then. press “Next” to continue.

© 2007 International Potato Center .96 Manual Diva The selected feature will be ready to be installed. Press “Finish”.

A final dialog box will recommend you to restart the workbench © 2007 International Potato Center .Help Menu 97 A verification dialog with information about the plugin that is about to be installed will wait for your confirmation. Press the “Install” button.

you will see how the new plugin took place in DIVA-GIS as part of its functionalities.98 Manual Diva After that. © 2007 International Potato Center .

2 About © 2007 International Potato Center .Help Menu 99 12.

GIS Application appears.100 Manual Diva 12.2. © 2007 International Potato Center .1 Diva Features Clicking on the Diva icon a windows with the features of the DIVA .

2 Features Details Clicking on Features Details button a windows with the DIVA-GIS features details appears.Help Menu 101 12. © 2007 International Potato Center .2.

Version and Plugin Id.3 Plugins Details Clicking on the Plugin Details a DIVA-GIS Plugin Details appears. Plugin Name. that contain the Provider.2.102 Manual Diva 12. © 2007 International Potato Center .

© 2007 International Potato Center .cgiar.3 Videos The videos are located in http://research.Help Menu 103 12.cip.org/confluence/display/divagis/Videos .

Sign up to vote on this title
UsefulNot useful