r.li(1grass) GRASS GIS User's Manual r.li(1grass)
NAME
r.li - Toolset for multiscale analysis of landscape structure
KEYWORDS
raster, landscape structure analysis, diversity index, patch index
DESCRIPTION
The r.li suite is a toolset for multiscale analysis of landscape struc-
ture. It aims at implementing metrics as found in external software for
quantitative measures of landscape structure like FRAGSTATS (McGarigal
and Marks 1995).
The r.li suite offers a set of patch and diversity indices. It sup-
ports analysis of landscapes composed of a mosaic of patches, but, more
generally, the modules work with any two-dimensional raster map whose
cell values are integer (e.g., 1, 2) or floating point (e.g., 1.1, 3.2)
values. The g.gui.rlisetup module has options for controlling the
shape, size, number, and distribution of sampling areas used to collect
information about the landscape structure. Sampling area shapes can be
the entire map or a moving window of square, rectangular or circular
shape. The size of sampling areas can be changed, so that the landscape
can be analyzed at a variety of spatial scales simultaneously. Sampling
areas may be distributed across the landscape in a random, systematic,
or stratified-random manner, or as a moving window.
The r.li modules can calculate a number of measures that produce single
values as output (e.g. mean patch size in the sampling area), as well
as measures that produce a distribution of values as output (e.g. fre-
quency distribution of patch sizes in the sampling area). The results
are stored as raster maps.
All modules require configuration file which can be created by the
g.gui.rlisetup module which is a GUI tool providing a convenient way to
set all necessary parameters. This file can be used repetitively saving
user from the need to specify all parameters over and over again.
NOTES
The general procedure to calculate an index from a raster map is
two-fold:
1 run g.gui.rlisetup: create a configuration file selecting the
parts of raster map to be analyzed. This file allows re-running
an analysis easily. It is stored on Windows in the directory
C:\Users\userxy\AppData\Roaming\GRASS7\r.li\, on GNU/Linux in
$HOME/.grass7/r.li/.
2 run one or more of the r.li.[index] modules (e.g., r.li.patch-
density) to calculate the selected index using on the areas se-
lected on configuration file.
EXAMPLES
Calculate a patch density index on the entire ’geology’ raster map in
the Spearfish sample dataset, using a 5x5 moving window:
1 CREATE A NEW CONFIGURATION FILE
1.1 run
g.gui.rlisetup
1.2 The main g.gui.rlisetup window is displayed, click on "New"
1.3 The new configuration window is now displayed, enter the config-
uration file name (e.g., "my_conf", do not use absolute paths)
Now the new configuration window is displayed. Enter the con-
figuration file name (e.g., "my_conf", do not use absolute
paths) and the name of raster map (e.g., "geology"). The other
fields are not needed for this configuration.
1.4 Click on "Setup sampling frame", select "Whole map layer" and
click "OK"
1.5 Click on "Setup sampling areas", select "Moving window" and
click "OK"
1.6 Click on "Use keyboard to enter moving window dimension"
1.7 Select "Rectangle" and enter 5 in the "height" and "width"
fields
1.8 Click on "Save settings"
1.9 Close the g.gui.rlisetup window
2 CALCULATE PATCHDENSITY INDEX
2.1 set the region settings to the "geology" raster map:
g.region raster=geology -p
2.2 run r.li.patchdensity:
r.li.patchdensity input=geology conf=my_conf out=patchdens
The resulting patch density is stored in "patchdens" raster map. You
can verify the result for example with contour lines:
r.contour in=patchdens out=patchdens step=5
d.rast patchdens
d.vect -c patchdens
Note that if you want to run another index with the same area configu-
ration, you don’t have to create another configuration file. You can
also use the same area configuration file on another map. The program
rescale it automatically. For instance if you have selected a 5x5 sam-
ple area on 100x100 raster map, and you use the same configuration file
on a 200x200 raster map, then the sample area is 10x10.
SEE ALSO
GUI tools:
• g.gui.rlisetup: Configuration editor for the r.li.* module
where * is name of the index
Patch indices:
• Indices based on patch number:
• r.li.patchdensity: Calculates patch density index on a
raster map, using a 4 neighbour algorithm
• r.li.patchnum: Calculates patch number index on a raster
map, using a 4 neighbour algorithm
• Indices based on patch dimension:
• r.li.mps: Calculates mean patch size index on a raster map,
using a 4 neighbour algorithm
• r.li.padcv: Calculates coefficient of variation of patch
area on a raster map
• r.li.padrange: Calculates range of patch area size on a
raster map
• r.li.padsd: Calculates standard deviation of patch area a
raster map
• Indices based on patch shape:
• r.li.shape: Calculates shape index on a raster map
• Indices based on patch edge:
• r.li.edgedensity: Calculates edge density index on a raster
map, using a 4 neighbour algorithm
• Indices based on patch attributes:
• r.li.cwed: Calculates contrast Weighted Edge Density index
on a raster map
• r.li.mpa: Calculates mean pixel attribute index on a raster
map
Diversity indices:
• r.li.dominance: Calculates dominance diversity index on a
raster map
• r.li.pielou: Calculates Pielou eveness index on a raster map
• r.li.renyi: Calculates Renyi entropy on a raster map
• r.li.richness: Calculates richness diversity index on a raster
map
• r.li.shannon: Calculates Shannon diversity index on a raster
map
• r.li.simpson: Calculates Simpson diversity index on a raster
map
Core library:
• r.li.daemon: library with common functionality (not visible to
the user)
ADDING NEW INDICES
New indices can be defined and implemented by any C programmer, without
having to deal with all basic functions (IO etc.). The computing archi-
tecture and the functions are clearly separated, thus allowing an easy
expandability. Every index is defined separately, placed in a directory
along with its Makefile for compiling it and a file <module_name>.html
which describes the index including a simple example of use. See
r.li.daemon for more information about development.
REFERENCES
• McGarigal, K., and B. J. Marks. 1995. FRAGSTATS: spatial pat-
tern analysis program for quantifying landscape structure. USDA
For. Serv. Gen. Tech. Rep. PNW-351 (PDF).
• Baker, W.L. and Y. Cai. 1992. The r.le programs for multiscale
analysis of landscape structure using the GRASS geographical
information system. Landscape Ecology 7(4):291-302.
AUTHORS
Claudio Porta and Lucio Davide Spano, students of Computer Science,
University of Pisa (Italy).
Commission from Faunalia Pontedera (PI)
Partially rewritten by Markus Metz
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