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NAME

r.li.shannon - Calculates Shannon's diversity index on a raster map

KEYWORDS

raster, landscape structure analysis, diversity index

SYNOPSIS

r.li.shannon
r.li.shannon help
r.li.shannon map=name conf=name output=name [--overwrite] [--verbose] [--quiet]

Flags:

--overwrite
Allow output files to overwrite existing files
--verbose
Verbose module output
--quiet
Quiet module output

Parameters:

map=name
Name of input raster map
conf=name
Configuration file
output=name
Name for output raster map

DESCRIPTION

r.li.shannon calculates the "Shannon's diversity index" as:
r.li.shannon formula
with:

NOTES

Do not use absolute path names for the config and output file/map parameters. If the "moving window" method was selected in r.li.setup, then the output will be a raster map, otherwise an ASCII file will be generated in the folder C:\Users\userxy\.r.li\output\ (MS-Windows) or $HOME/.r.li/output/ (GNU/Linux).

If the input raster map contains only NULL values then r.li.shannon returns -1.
If you want to change these -1 values to NULL, run subsequently on the resulting map:

r.null setnull=-1 map=my_map
after index calculation.

EXAMPLES

To calculate Shannon's diversity index on map my_map, using my_conf configuration file (previously defined with r.li.setup) and saving results in my_out, run:
r.li.shannon map=my_map conf=my_conf output=my_out

Forest map (Spearfish sample dataset) example:

g.region rast=landcover.30m -p
r.mapcalc "forests = if(landcover.30m >= 41 && landcover.30m <= 43,1,null())"
r.li.shannon map=forests conf=movwindow7 out=forests_shannon_mov7
r.univar forests_shannon_mov7

Forest map (North Carolina sample dataset) example:

g.region rast=landclass96 -p
r.mapcalc "forests = if(landclass96 == 5, 1, null() )"
r.li.shannon map=forests conf=movwindow7 out=forests_shannon_mov7

# verify
r.univar forests_shannon_mov7
r.to.vect input=forests output=forests feature=area
d.mon x0
d.rast forests_shannon_mov7
d.vect forests type=boundary

SEE ALSO

r.li - package overview
r.li.setup

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)

AUTHORS

Serena Pallecchi student of Computer Science University of Pisa (Italy).
Commission from Faunalia Pontedera (PI), Italy (www.faunalia.it)

Last changed: $Date: 2014-10-19 14:32:22 -0700 (Sun, 19 Oct 2014) $


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