1r.li(1) Grass User's Manual r.li(1)
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6 r.li - Toolset for multiscale analysis of landscape structure
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9 raster, landscape structure analysis, diversity index, patch index
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12 The r.li suite is a toolset for multiscale analysis of landscape struc‐
13 ture. It aims at implementing metrics as found in external software for
14 quantitative measures of landscape structure like FRAGSTATS (McGarigal
15 and Marks 1995).
16 The r.li suite offers a set of patch and diversity indices. It sup‐
18 ports analysis of landscapes composed of a mosaic of patches, but, more
19 generally, the modules work with any two-dimensional raster map whose
20 cell values are integer (e.g., 1, 2) or floating point (e.g., 1.1, 3.2)
21 values. The g.gui.rlisetup module has options for controlling the
22 shape, size, number, and distribution of sampling areas used to collect
23 information about the landscape structure. Sampling area shapes can be
24 the entire map or a moving window of square, rectangular or circular
25 shape. The size of sampling areas can be changed, so that the landscape
26 can be analyzed at a variety of spatial scales simultaneously. Sampling
27 areas may be distributed across the landscape in a random, systematic,
28 or stratified-random manner, or as a moving window.
29 The r.li modules can calculate a number of measures that produce single
31 values as output (e.g. mean patch size in the sampling area), as well
32 as measures that produce a distribution of values as output (e.g. fre‐
33 quency distribution of patch sizes in the sampling area). The results
34 are stored as raster maps.
35 All modules require configuration file which can be created by the
37 g.gui.rlisetup module which is a GUI tool providing a convenient way to
38 set all necessary parameters. This file can be used repetitively saving
39 user from the need to specify all parameters over and over again.
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42 The general procedure to calculate an index from a raster map is
43 two-fold:
44 1 run g.gui.rlisetup: create a configuration file selecting the
46 parts of raster map to be analyzed. This file allows re-running
47 an analysis easily. It is stored on Windows in the directory
48 C:\Users\userxy\AppData\Roaming\GRASS7\r.li\, on GNU/Linux in
49 $HOME/.grass7/r.li/.
50 2 run one or more of the r.li.[index] modules (e.g., r.li.patch‐
52 density) to calculate the selected index using on the areas
53 selected on configuration file.
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56 Calculate a patch density index on the entire ’geology’ raster map in
57 the Spearfish sample dataset, using a 5x5 moving window:
58 1 CREATE A NEW CONFIGURATION FILE
60 1.1 run
62 g.gui.rlisetup
63 1.2 The main g.gui.rlisetup window is displayed, click on "New"
65 1.3 The new configuration window is now displayed, enter the config‐
67 uration file name (e.g., "my_conf", do not use absolute paths)
68 Now the new configuration window is displayed. Enter the con‐
69 figuration file name (e.g., "my_conf", do not use absolute
70 paths) and the name of raster map (e.g., "geology"). The other
71 fields are not needed for this configuration.
72 1.4 Click on "Setup sampling frame", select "Whole map layer" and
74 click "OK"
75 1.5 Click on "Setup sampling areas", select "Moving window" and
77 click "OK"
78 1.6 Click on "Use keyboard to enter moving window dimension"
80 1.7 Select "Rectangle" and enter 5 in the "height" and "width"
82 fields
83 1.8 Click on "Save settings"
85 1.9 Close the g.gui.rlisetup window
87 2 CALCULATE PATCHDENSITY INDEX
89 2.1 set the region settings to the "geology" raster map:
91 g.region raster=geology -p
92 2.2 run r.li.patchdensity:
94 r.li.patchdensity input=geology conf=my_conf out=patchdens
95 The resulting patch density is stored in "patchdens" raster map. You
97 can verify the result for example with contour lines:
98 r.contour in=patchdens out=patchdens step=5
99 d.rast patchdens
100 d.vect -c patchdens
101 Note that if you want to run another index with the same area configu‐
102 ration, you don’t have to create another configuration file. You can
103 also use the same area configuration file on another map. The program
104 rescale it automatically. For instance if you have selected a 5x5 sam‐
105 ple area on 100x100 raster map, and you use the same configuration file
106 on a 200x200 raster map, then the sample area is 10x10.
107
109 GUI tools:
110 · g.gui.rlisetup: Configuration editor for the r.li.* module
112 where * is name of the index
113 Patch indices:
114 · Indices based on patch number:
116 · r.li.patchdensity: Calculates patch density index on a
118 raster map, using a 4 neighbour algorithm
119 · r.li.patchnum: Calculates patch number index on a raster
121 map, using a 4 neighbour algorithm
122 · Indices based on patch dimension:
124 · r.li.mps: Calculates mean patch size index on a raster map,
126 using a 4 neighbour algorithm
127 · r.li.padcv: Calculates coefficient of variation of patch
129 area on a raster map
130 · r.li.padrange: Calculates range of patch area size on a
132 raster map
133 · r.li.padsd: Calculates standard deviation of patch area a
135 raster map
136 · Indices based on patch shape:
138 · r.li.shape: Calculates shape index on a raster map
140 · Indices based on patch edge:
142 · r.li.edgedensity: Calculates edge density index on a raster
144 map, using a 4 neighbour algorithm
145 · Indices based on patch attributes:
147 · r.li.cwed: Calculates contrast Weighted Edge Density index
149 on a raster map
150 · r.li.mpa: Calculates mean pixel attribute index on a raster
152 map
153 Diversity indices:
154 · r.li.dominance: Calculates dominance diversity index on a
156 raster map
157 · r.li.pielou: Calculates Pielou eveness index on a raster map
159 · r.li.renyi: Calculates Renyi entropy on a raster map
161 · r.li.richness: Calculates richness diversity index on a raster
163 map
164 · r.li.shannon: Calculates Shannon diversity index on a raster
166 map
167 · r.li.simpson: Calculates Simpson diversity index on a raster
169 map
170 Core library:
171 · r.li.daemon: library with common functionality (not visible to
173 the user)
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176 New indices can be defined and implemented by any C programmer, without
177 having to deal with all basic functions (IO etc.). The computing archi‐
178 tecture and the functions are clearly separated, thus allowing an easy
179 expandability. Every index is defined separately, placed in a directory
180 along with its Makefile for compiling it and a file <module_name>.html
181 which describes the index including a simple example of use. See
182 r.li.daemon for more information about development.
183
185 · McGarigal, K., and B. J. Marks. 1995. FRAGSTATS: spatial pat‐
186 tern analysis program for quantifying landscape structure. USDA
187 For. Serv. Gen. Tech. Rep. PNW-351 (PDF).
188 · Baker, W.L. and Y. Cai. 1992. The r.le programs for multiscale
190 analysis of landscape structure using the GRASS geographical
191 information system. Landscape Ecology 7(4):291-302.
192
194 Claudio Porta and Lucio Davide Spano, students of Computer Science,
195 University of Pisa (Italy).
196 Commission from Faunalia Pontedera (PI)
197 Partially rewritten by Markus Metz
199 Main index | Topics index | Keywords index | Graphical index | Full
201 index
202 © 2003-2019 GRASS Development Team, GRASS GIS 7.8.2 Reference Manual
204GRASS 7.8.2 r.li(1)