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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 structure. 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 supports 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. frequency 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.patchdensity) to calculate
the selected index using on the areas selected 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 configuration file name
(e.g., "my_conf", do not use absolute paths) Now the new configuration window is
displayed. Enter the configuration 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 configuration, 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 sample 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 architecture 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 pattern 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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