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- <!-- meta page description: Landscape structure analysis package overview -->
- <h2>DESCRIPTION</h2>
- The <em>r.li</em> 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).
- <p>
- The <em>r.li</em> 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 <em>g.gui.rlisetup</em> 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.
- <p>
- The <em>r.li</em> 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.
- <p>
- All modules require configuration file which can be created by the
- <em>g.gui.rlisetup</em> 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.
- <h2>NOTES</h2>
- The general procedure to calculate an index from a raster map is two-fold:
- <ol>
- <li>run <em>g.gui.rlisetup</em>: 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 <tt>C:\Users\userxy\AppData\Roaming\GRASS7\r.li\</tt>, on GNU/Linux in
- <tt>$HOME/.grass7/r.li/</tt>. <!-- TODO: and Mac OSX? -->
- <li>run one or more of the <em>r.li.<b>[index]</b></em> modules (e.g.,
- <em>r.li.<b>patchdensity</b></em>) to calculate the selected index
- using on the areas selected on configuration file.
- </ol>
- <!-- mhh ??:
- The <em>r.li.daemon</em> source code has a "main" function front-end
- which can be run, but it is only a template for development of new
- indices.
- -->
- <h2>EXAMPLES</h2>
- Calculate a patch density index on the entire 'geology' raster map
- in the Spearfish sample dataset, using a 5x5 moving window:
- <!-- TODO: update to new wxGUI: -->
- <ol>
- <li> CREATE A NEW CONFIGURATION FILE
- <ol>
- <li> run
- <div class="code"><pre>
- g.gui.rlisetup
- </pre></div>
- <li> The main <em>g.gui.rlisetup</em> window is displayed, click on "New"
- <li> 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.
- <li> Click on "Setup sampling frame", select "Whole map layer" and click "OK"
- <li> Click on "Setup sampling areas", select "Moving window" and click "OK"
- <li> Click on "Use keyboard to enter moving window dimension"
- <li> Select "Rectangle" and enter 5 in the "height" and "width" fields
- <li> Click on "Save settings"
- <li> Close the <em>g.gui.rlisetup</em> window
- </ol>
- <li> CALCULATE PATCHDENSITY INDEX
- <ol>
- <li> set the region settings to the "<tt>geology</tt>" raster map:
- <div class="code"><pre>
- g.region raster=geology -p
- </pre></div>
- <li> run <em>r.li.patchdensity</em>:
- <div class="code"><pre>
- r.li.patchdensity input=geology conf=my_conf out=patchdens
- </pre></div>
- </ol>
- </ol>
- The resulting patch density is stored in "<tt>patchdens</tt>" raster map.
- You can verify the result for example with contour lines:
- <div class="code"><pre>
- r.contour in=patchdens out=patchdens step=5
- d.rast patchdens
- d.vect -c patchdens
- </pre></div>
- 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.
- <h2>SEE ALSO</h2>
- <b>GUI tools</b>:
- <ul>
- <li> <a href="g.gui.rlisetup.html">g.gui.rlisetup</a>: Configuration editor for the <tt>r.li.*</tt> module where <tt>*</tt> is name of the index</li>
- </ul>
- <b>Patch indices</b>:
- <ul>
- <li>Indices based on patch number:
- <ul>
- <li> <a href="r.li.patchdensity.html">r.li.patchdensity</a>: Calculates patch density index on a raster map, using a 4 neighbour algorithm</li>
- <li> <a href="r.li.patchnum.html">r.li.patchnum</a>: Calculates patch number index on a raster map, using a 4 neighbour algorithm</li>
- </ul>
- <li>Indices based on patch dimension:
- <ul>
- <li> <a href="r.li.mps.html">r.li.mps</a>: Calculates mean patch size index on a raster map, using a 4 neighbour algorithm</li>
- <li> <a href="r.li.padcv.html">r.li.padcv</a>: Calculates coefficient of variation of patch area on a raster map</li>
- <li> <a href="r.li.padrange.html">r.li.padrange</a>: Calculates range of patch area size on a raster map</li>
- <li> <a href="r.li.padsd.html">r.li.padsd</a>: Calculates standard deviation of patch area a raster map</li>
- </ul>
- <li>Indices based on patch shape:
- <ul>
- <li> <a href="r.li.shape.html">r.li.shape</a>: Calculates shape index on a raster map</li>
- </ul>
- <li>Indices based on patch edge: <!-- border? -->
- <ul>
- <li> <a href="r.li.edgedensity.html">r.li.edgedensity</a>: Calculates edge density index on a raster map, using a 4 neighbour algorithm</li>
- </ul>
- <li>Indices based on patch attributes:
- <ul>
- <li> <a href="r.li.cwed.html">r.li.cwed</a>: Calculates contrast Weighted Edge Density index on a raster map</li>
- <li> <a href="r.li.mpa.html">r.li.mpa</a>: Calculates mean pixel attribute index on a raster map</li>
- </ul>
- </ul>
- <b>Diversity indices</b>:
- <ul>
- <li> <a href="r.li.dominance.html">r.li.dominance</a>: Calculates dominance diversity index on a raster map</li>
- <li> <a href="r.li.pielou.html">r.li.pielou</a>: Calculates Pielou eveness index on a raster map</li>
- <li> <a href="r.li.renyi.html">r.li.renyi</a>: Calculates Renyi entropy on a raster map</li>
- <li> <a href="r.li.richness.html">r.li.richness</a>: Calculates richness diversity index on a raster map</li>
- <li> <a href="r.li.shannon.html">r.li.shannon</a>: Calculates Shannon diversity index on a raster map</li>
- <li> <a href="r.li.simpson.html">r.li.simpson</a>: Calculates Simpson diversity index on a raster map</li>
- </ul>
- <b>Core library</b>:
- <ul>
- <li> <a href="r.li.daemon.html">r.li.daemon</a>: library with common functionality (not visible to the user)</li>
- </ul>
- <h2>ADDING NEW INDICES</h2>
- 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 <a href="r.li.daemon.html">r.li.daemon</a>
- for more information about development.
- <h2>REFERENCES</h2>
- <ul>
- <li>
- McGarigal, K., and B. J. Marks. 1995. FRAGSTATS: spatial pattern
- analysis program for quantifying landscape structure. USDA For. Serv.
- Gen. Tech. Rep. PNW-351
- (<a href="http://www.fs.fed.us/pnw/pubs/gtr_351.pdf">PDF</a>).
- <li>
- 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.
- </ul>
- <h2>AUTHORS</h2>
- Claudio Porta and Lucio Davide Spano, students of Computer Science,
- University of Pisa (Italy).<br>
- Commission from Faunalia Pontedera (PI)
- <p>
- Partially rewritten by Markus Metz
- <p>
- <i>Last changed: $Date$</i>
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