1r.li(1)                     GRASS GIS User's Manual                    r.li(1)
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NAME

6       r.li  - Toolset for multiscale analysis of landscape structure
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KEYWORDS

9       raster, landscape structure analysis, diversity index, patch index
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DESCRIPTION

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).
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17       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.
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30       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.
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36       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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NOTES

42       The general procedure to calculate  an  index  from  a  raster  map  is
43       two-fold:
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45       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/.
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51       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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EXAMPLES

56       Calculate  a  patch density index on the entire ’geology’ raster map in
57       the Spearfish sample dataset, using a 5x5 moving window:
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59       1      CREATE A NEW CONFIGURATION FILE
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61       1.1    run
62                g.gui.rlisetup
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64       1.2    The main g.gui.rlisetup window is displayed, click on "New"
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66       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.
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73       1.4    Click  on  "Setup  sampling frame", select "Whole map layer" and
74              click "OK"
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76       1.5    Click on "Setup sampling  areas",  select  "Moving  window"  and
77              click "OK"
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79       1.6    Click on "Use keyboard to enter moving window dimension"
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81       1.7    Select  "Rectangle"  and  enter  5  in  the "height" and "width"
82              fields
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84       1.8    Click on "Save settings"
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86       1.9    Close the g.gui.rlisetup window
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88       2      CALCULATE PATCHDENSITY INDEX
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90       2.1    set the region settings to the "geology" raster map:
91                g.region raster=geology -p
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93       2.2    run r.li.patchdensity:
94                r.li.patchdensity input=geology conf=my_conf out=patchdens
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96       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.
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SEE ALSO

109       GUI tools:
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111           ·   g.gui.rlisetup: Configuration  editor  for  the  r.li.*  module
112               where * is name of the index
113       Patch indices:
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115           ·   Indices based on patch number:
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117               ·   r.li.patchdensity:  Calculates  patch  density  index  on a
118                   raster map, using a 4 neighbour algorithm
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120               ·   r.li.patchnum: Calculates patch number index  on  a  raster
121                   map, using a 4 neighbour algorithm
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123           ·   Indices based on patch dimension:
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125               ·   r.li.mps: Calculates mean patch size index on a raster map,
126                   using a 4 neighbour algorithm
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128               ·   r.li.padcv: Calculates coefficient of  variation  of  patch
129                   area on a raster map
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131               ·   r.li.padrange:  Calculates  range  of  patch area size on a
132                   raster map
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134               ·   r.li.padsd: Calculates standard deviation of patch  area  a
135                   raster map
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137           ·   Indices based on patch shape:
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139               ·   r.li.shape: Calculates shape index on a raster map
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141           ·   Indices based on patch edge:
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143               ·   r.li.edgedensity: Calculates edge density index on a raster
144                   map, using a 4 neighbour algorithm
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146           ·   Indices based on patch attributes:
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148               ·   r.li.cwed: Calculates contrast Weighted Edge Density  index
149                   on a raster map
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151               ·   r.li.mpa: Calculates mean pixel attribute index on a raster
152                   map
153       Diversity indices:
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155           ·   r.li.dominance:  Calculates  dominance  diversity  index  on  a
156               raster map
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158           ·   r.li.pielou: Calculates Pielou eveness index on a raster map
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160           ·   r.li.renyi: Calculates Renyi entropy on a raster map
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162           ·   r.li.richness:  Calculates richness diversity index on a raster
163               map
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165           ·   r.li.shannon: Calculates Shannon diversity index  on  a  raster
166               map
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168           ·   r.li.simpson:  Calculates  Simpson  diversity index on a raster
169               map
170       Core library:
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172           ·   r.li.daemon: library with common functionality (not visible  to
173               the user)
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ADDING NEW INDICES

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.
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REFERENCES

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).
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189           ·   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.
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AUTHORS

194       Claudio  Porta  and  Lucio  Davide Spano, students of Computer Science,
195       University of Pisa (Italy).
196       Commission from Faunalia Pontedera (PI)
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198       Partially rewritten by Markus Metz
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200       Main index | Topics index | Keywords index |  Graphical  index  |  Full
201       index
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203       © 2003-2020 GRASS Development Team, GRASS GIS 7.8.5 Reference Manual
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207GRASS 7.8.5                                                            r.li(1)
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