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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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       © 2003-2019 GRASS Development Team, GRASS GIS 7.8.2 Reference Manual