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DIVA-GIS Version 5.2 Manual

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DIVA-GIS
Version 5.2

Manual




September 2005





Robert J. Hijmans, Luigi Guarino, Andy Jarvis,
Rachel O’Brien, Prem Mathur, Coen Bussink
Mariana Cruz, Israel Barrantes, and Edwin Rojas




Conditions of use
The DIVA-GIS software can be used and distributed freely. The software 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 currently being developed by Robert J. Hijmans, Luigi Guarino, Andrew
Jarvis, Rachel O’Brien, and Prem Mathur. Edwin Rojas, Mariana Cruz, Coen Bussink,
and Israel Barrantes were involved in the development of earlier versions. Support for
the development has come from the International Plant Genetic Resources Institute
(IPGRI), the 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/)
DIVA-GIS was improved thanks to bug-reports and/or suggestions made by many
individuals, including Østein Berg, Arthur Chapman, Stefano Diulgheroff, Dirk
Enneking, Tito Franco, Catherine Graham, Stephanie Greene, Lee Hannah, Dave
Hodson, Roel Hoekstra, Andrew Jarvis, Ravish Kumar, Prem Mathur, Andy Nelson,
Andreas Ohr, Xavier Scheldeman, Victor Soto, Jeff White, Louise Willemen, Karen
Williams, and Brian Zutta.

ii

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. Instead, 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 to report it!
Please send your comments to info@diva-gis.org
Abstract
DIVA-GIS is a free computer program for mapping and for analyzing spatial data. It is
particularly useful for analyzing the distribution of organisms to elucidate geographic
and ecological patterns. It is aimed at persons who cannot afford generic commercial
geographic information system (GIS) software, or do not have the time to learn how to
use these, and for anyone else who wants a GIS tailor-made to analyze biological
distributions. DIVA-GIS supports vector (point, line, polygon) and image and grid data
types. DIVA-GIS 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 and 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; identification of areas with complementary diversity; and analysis of
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.


iii

Table of Contents
1.
INTRODUCTION......................................................... 1
1.1
Conventions used ............................................................... 1
1.2
Installing DIVA-GIS .............................................................. 1
1.3
The DIVA-GIS desktop .......................................................... 2
1.3.1
The Data view ........................................................................2
1.3.2
The Design view ......................................................................5
1.4
File Types and Formats ........................................................ 7
1.4.1
Shapefiles .............................................................................7
1.4.2
Grids ...................................................................................8
1.4.3
Image files ............................................................................8
1.4.4
DBF files ...............................................................................9
1.5
Geographic coordinates ......................................................10
2.
THE PROJECT MENU...................................................11
2.1
Projects .........................................................................11
2.2
Import project and Export project..........................................12
3.
THE DATA MENU ......................................................13
3.1
Import Points to Shapefile ...................................................14
3.2
Import Text to Line/Polygon.................................................15
3.3
Draw Shape .....................................................................16
3.4
Polygon to Grid.................................................................16
3.5
Points to Convex Polygon.....................................................17
3.6
Selection to new shapefile ...................................................17
3.7
Extract Values by Points......................................................17
3.8
Climate ..........................................................................17
3.9
Assign coordinates .............................................................18
3.10 Check coordinates .............................................................21
3.11 Export gridfile..................................................................23
3.12 Import to gridfile ..............................................................24
3.13 File manager....................................................................24
3.14 Download........................................................................24
4.
THE LAYER MENU .....................................................25
4.1
Add layer and Remove layer .................................................26
4.2
Properties .......................................................................26
4.3
Identify ..........................................................................27
4.4
Table.............................................................................27
4.5
Select records ..................................................................27
4.6
Copy and Paste.................................................................28

iv

5.
THE MAP MENU .......................................................29
5.1
Map to image ...................................................................29
6.
THE ANALYSIS MENU ..................................................30
6.1
Point to grid ....................................................................30
6.1.1
Defining Grids ...................................................................... 31
6.1.2
Using the parameters of an existing grid....................................... 33
6.2
Output variables ...............................................................33
6.2.1
Richness ............................................................................. 33
6.2.2
Estimators of Richness ............................................................ 35
6.2.3
Turnover............................................................................. 38
6.2.4
Diversity indices.................................................................... 39
6.2.5
Molecular marker data ............................................................ 39
6.2.6
Reserve selection .................................................................. 41
6.3
Methods of converting point data to grid data ...........................44
6.3.1
Circular neighborhood............................................................. 44
6.4
Point to polygon ...............................................................45
6.5
Point to point...................................................................46
6.6
Summarize Points..............................................................47
6.7
Distance .........................................................................47
6.8
Spatial autocorrelation .......................................................47
6.8.1
Points ................................................................................ 48
6.8.2
Grid .................................................................................. 49
6.9
Histogram .......................................................................49
6.10 Regression ......................................................................49
6.11 Multiple Regression............................................................49
7.
THE MODELING MENU .................................................50
7.1
Bioclim / Domain ..............................................................50
7.1.1
Input ................................................................................. 50
7.1.2
Frequency ........................................................................... 51
7.1.3
Outliers .............................................................................. 51
7.1.4
Histogram ........................................................................... 51
7.1.5
Envelope............................................................................. 51
7.1.6
Predict ............................................................................... 52
7.2
External Models ................................................................54
7.3
Evaluation.......................................................................54
7.3.1
Prepare points ...................................................................... 54
7.3.2
Create evaluation file ............................................................. 55
7.3.3
Show ROC / Kappa ................................................................. 55
7.4
EcoCrop .........................................................................55
7.5
Terrain Modeling...............................................................58
8.
THE GRID MENU.......................................................59
8.1
Describe .........................................................................59
8.2
Overlay ..........................................................................60
8.3
Scalar ............................................................................60

v

8.4
Reclass...........................................................................60
8.5
Neighbourhood .................................................................61
8.6
Calculate ........................................................................61
8.7
Aggregate .......................................................................62
8.8
Disaggregate....................................................................63
8.9
Cut ...............................................................................63
8.10 Concatenate ....................................................................63
8.11 New ..............................................................................64
8.12 Transect.........................................................................64
8.13 Area ..............................................................................64
9.
THE STACK MENU .....................................................65
9.1
Make stack ......................................................................65
9.2
Plot...............................................................................66
9.3
Calculate ........................................................................66
9.4
Regression ......................................................................66
9.5
Cluster...........................................................................66
9.6
Export to textfile ..............................................................67
10.
THE TOOLS MENU .....................................................68
10.1 Projection.......................................................................68
10.2 Graticule ........................................................................69
10.3 Shift shape ......................................................................69
10.4 Georeference image ..........................................................69
10.5 Geo-calculator .................................................................70
10.6 General options ................................................................71
REFERENCES ....................................................................72




vi

DIVA-GIS 5

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 menus and sub-menus and buttons. A slash (/) is used to
relate a submenu to a menu.
“Quotes” are used to refer to buttons.
Courier font is used for file and directory names and for special keys such as Shift;
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 need to unzip the downloaded files
first (use e.g. pkzip; www.pkware.com). Then you should click on setup.exe to install
DIVA; also click on this file if you are installing 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 dir>. By default, DIVA will be installed in the C:\program files\DIVA-GIS\
directory.

1


DIVA-GIS 5

1.3 The DIVA-GIS desktop
The DIVA-GIS window 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 a graphics
file, and printed or used in another application.
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 world 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 Ctrl 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 “cities” layer in Figure 1). The order in which
different layers are drawn on the map is from the bottom up, so a layer higher in the
TOC will cover a lower one). You can change the order of the layers by dragging them
up or down (move your mouse while keeping the left button pressed).


2


DIVA-GIS 5

1
2
3
4
5
6


1
Menu bar – Provides access to DIVA-GIS functions.
2
Toolbar – Quick access to some of the more commonly used functions.
3 Table of contents – Lists all the layers on the map.
4 Map – The map you’re working on.
5 Overview Map – Shows the location of what is visible on the map in a winder
region
6 Status bar –Indicates, from left to right, the location of the cursor (x and y
coordiates), the scale of the map, the position and value of a gridcell, and the
distance between two points.
Figure 1. The DIVA-GIS main window in Data view




3


DIVA-GIS 5

Double-clicking on a layer in the TOC (or clicking on Layer/Properties) brings up a
window that allows changes to be made to some of the layer’s properties (such as
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.

Figure 2. The Layer/Properties window for shapefiles.


Figure 3. Layer/Properties window for grids.

4


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