[GRASS-SVN] r58996 - in grass/branches/develbranch_6/raster/r.li: . r.li.cwed r.li.daemon r.li.dominance r.li.edgedensity r.li.mpa r.li.mps r.li.padcv r.li.padrange r.li.padsd r.li.patchdensity r.li.patchnum r.li.pielou r.li.renyi r.li.richness r.li.setup r.li.shannon r.li.shape r.li.simpson
svn_grass at osgeo.org
svn_grass at osgeo.org
Tue Feb 11 06:05:36 PST 2014
Author: neteler
Date: 2014-02-11 06:05:36 -0800 (Tue, 11 Feb 2014)
New Revision: 58996
Modified:
grass/branches/develbranch_6/raster/r.li/TODO
grass/branches/develbranch_6/raster/r.li/r.li.cwed/description.html
grass/branches/develbranch_6/raster/r.li/r.li.daemon/description.html
grass/branches/develbranch_6/raster/r.li/r.li.dominance/description.html
grass/branches/develbranch_6/raster/r.li/r.li.edgedensity/description.html
grass/branches/develbranch_6/raster/r.li/r.li.mpa/description.html
grass/branches/develbranch_6/raster/r.li/r.li.mps/description.html
grass/branches/develbranch_6/raster/r.li/r.li.padcv/description.html
grass/branches/develbranch_6/raster/r.li/r.li.padrange/description.html
grass/branches/develbranch_6/raster/r.li/r.li.padsd/description.html
grass/branches/develbranch_6/raster/r.li/r.li.patchdensity/description.html
grass/branches/develbranch_6/raster/r.li/r.li.patchnum/description.html
grass/branches/develbranch_6/raster/r.li/r.li.pielou/description.html
grass/branches/develbranch_6/raster/r.li/r.li.renyi/description.html
grass/branches/develbranch_6/raster/r.li/r.li.richness/description.html
grass/branches/develbranch_6/raster/r.li/r.li.setup/description.html
grass/branches/develbranch_6/raster/r.li/r.li.shannon/description.html
grass/branches/develbranch_6/raster/r.li/r.li.shape/description.html
grass/branches/develbranch_6/raster/r.li/r.li.simpson/description.html
Log:
r.li.* manual: cleanup; example added
Modified: grass/branches/develbranch_6/raster/r.li/TODO
===================================================================
--- grass/branches/develbranch_6/raster/r.li/TODO 2014-02-11 14:04:30 UTC (rev 58995)
+++ grass/branches/develbranch_6/raster/r.li/TODO 2014-02-11 14:05:36 UTC (rev 58996)
@@ -12,6 +12,13 @@
r.mapcalc "forests = if(landcover.30m >= 41 && landcover.30m <= 43,1,null())"
d.mon x0
d.rast forests
+
+# r.li.setup:
+# created as described in EXAMPLES, moving window, in r.li.setup/description.html:
+echo "SAMPLINGFRAME 0|0|1|1
+SAMPLEAREA -1|-1|0.015021459227467811|0.011058451816745656
+MOVINGWINDOW" > $HOME/.r.li/history/movwindow7
+
r.li.patchdensity forests conf=movwindow7 out=forests_p_dens7
d.rast.leg forests_p_dens7
Modified: grass/branches/develbranch_6/raster/r.li/r.li.cwed/description.html
===================================================================
--- grass/branches/develbranch_6/raster/r.li/r.li.cwed/description.html 2014-02-11 14:04:30 UTC (rev 58995)
+++ grass/branches/develbranch_6/raster/r.li/r.li.cwed/description.html 2014-02-11 14:05:36 UTC (rev 58996)
@@ -1,20 +1,22 @@
<h2>DESCRIPTION</h2>
-<em>r.li.cwed</em> (contrast weighted edge density) calculates the edge density
-between patch types specified:
-<p><img src="rlicwed_formula.png">
+<em>r.li.cwed</em> (contrast weighted edge density) calculates the
+edge density between patch types specified: <!-- TODO fix grammar -->
+<p><img src="rlicwed_formula.png" alt="rlicwed formula">
<p>with:
<ul>
-<li> <b>k</b>: attribute<br>
-<li> <b>m</b>: number of non-null attributes in the sampling area<br>
-<li> <b>e<small><small>ik</small></small></b>: total length of edge in landscape between patch types i and k<br>
-<li><b> d<small><small>ik</small></small></b>: dissimilarity (edge contrast weight) between patch types i and k<br>
+<li> <b>k</b>: attribute</li>
+<li> <b>m</b>: number of non-null attributes in the sampling area</li>
+<li> <b>e<small><small>ik</small></small></b>: total length of edge in
+ landscape between patch types i and k</li>
+<li><b> d<small><small>ik</small></small></b>: dissimilarity (edge contrast
+ weight) between patch types i and k</li>
<li> <b>Area</b>: total landscape area<br>
</ul><br>
-The input file have a row for each couple of patch type that we want to
-consider in the calculation. Each row must to have this syntax:<br>
+The input file contains a row for each couple of patch type that we want to
+consider in the calculation. Each row must be saved using this syntax:<br>
<small>patchType1,patchType2,dissimilarityBetweenPatchType1andPatchType2</small><br>
@@ -25,47 +27,47 @@
output will be a raster map, otherwise an ASCII file will be generated in
the <tt>~/.r.li/output/</tt> folder.
<p>
-<br>
-If the raster is full of null value it is considered to have 0 patch and CWED=0.
-If Area is 0 r.li.cwed returns -1. This is possible
-only if the map is masked.<br>
-If you want to have null values instead run <br>
+<!-- TODO: verify next: -->
+If the input raster map contains only NULL values it is considered to
+have 0 patch and CWED=0. If Area is 0 <em>r.li.cwed</em> returns -1.
+This is only possible if the map is masked.<br>
+If you want to change these -1 values to NULL, run subsequently on the resulting map:
<div class="code"><pre>
r.null setnull=-1 map=my_map
</pre></div>
-after index calculation.<br>
-<br>
+after index calculation.
-
<h2>EXAMPLES</h2>
-To calculate mean pixel attribute index on map my_map, using
-my_conf configuration file and saving results in
-my_out file run:<br>
+To calculate the contrast weighted edge density index on map <em>my_map</em>, using
+<em>my_conf</em> configuration file (previously defined with
+<em>r.li.setup</em>) and saving results in <em>my_out</em>, run:
<div class="code"><pre>
-r.li.cwed map=my_map conf=my_conf path=my_file output=my_out
+r.li.cwed map=my_map conf=my_conf path=my_file output=my_out \
+ path=/path/to/weights.csv
</pre></div>
-<br>Example of input file:<br>
-12,16,0.65<br>
-44,123,0.32<br>
-56,12,0.54<br>
-23,66,0.99<br>
+<br>Example for input "weights.csv" file:
+<pre>
+12,16,0.65
+44,123,0.32
+56,12,0.54
+23,66,0.99
+</pre>
+<h2>SEE ALSO</h2>
+<em>
+<a href="r.li.html">r.li</a> - package overview<br>
+<a href="r.li.setup.html">r.li.setup</a>
+</em>
+
<h2>REFERENCES</h2>
McGarigal, K., and B. J. Marks. 1995. FRAGSTATS: spatial pattern
analysis program for quantifying landscape structure. USDA For. Serv.
-Gen. Tech. Rep. PNW-351.
+Gen. Tech. Rep. PNW-351. (<a href="http://treesearch.fs.fed.us/pubs/3064">PDF</a>)
-<h2>SEE ALSO</h2>
-
-<em><a href="r.li.html">r.li</a></em> package overview <br>
-<em><a href="r.li.daemon.html">r.li.daemon</a></em><br>
-<em><a href="r.li.setup.html">r.li.setup</a></em>
-
<h2>AUTHORS</h2>
Serena Pallecchi student of Computer Science University of Pisa (Italy).<br>
Commission from Faunalia Pontedera (PI), Italy (www.faunalia.it)
<p>
<i>Last changed: $Date$</i></p>
-
Modified: grass/branches/develbranch_6/raster/r.li/r.li.daemon/description.html
===================================================================
--- grass/branches/develbranch_6/raster/r.li/r.li.daemon/description.html 2014-02-11 14:04:30 UTC (rev 58995)
+++ grass/branches/develbranch_6/raster/r.li/r.li.daemon/description.html 2014-02-11 14:05:36 UTC (rev 58996)
@@ -76,8 +76,7 @@
<h2>SEE ALSO</h2>
<em><a href="http://grass.osgeo.org/gdp/landscape/r_le_manual5.pdf">old r.le manual</a></em><br>
-<em><a href="r.li.html">r.li</a></em> package overview <br>
-<em><a href="r.li.patchdensity.html">r.li.patchdensity</a></em>,
+<em><a href="r.li.html">r.li</a></em> - package overview <br>
<em><a href="r.li.setup.html">r.li.setup</a></em>
@@ -91,7 +90,7 @@
Claudio Porta and Lucio Davide Spano, students of Computer Science
University of Pisa (Italy).<br>
Commission from Faunalia Pontedera (PI)<br>
-Rebuild of r.le.setup from William L. Baker
+Rewritten from "r.le.setup" by William L. Baker
This program is free software under the GPL (>=v2)
Read the COPYING file that comes with GRASS for details.
Modified: grass/branches/develbranch_6/raster/r.li/r.li.dominance/description.html
===================================================================
--- grass/branches/develbranch_6/raster/r.li/r.li.dominance/description.html 2014-02-11 14:04:30 UTC (rev 58995)
+++ grass/branches/develbranch_6/raster/r.li/r.li.dominance/description.html 2014-02-11 14:05:36 UTC (rev 58996)
@@ -1,12 +1,13 @@
<h2>DESCRIPTION</h2>
-<em>r.li.dominance</em>
-calculates the "dominance's diversity index" as:<br>
-<img src="rliDominance_formula.png"> <br>
-with: <br>
+
+<em>r.li.dominance</em> calculates the "dominance diversity index" as:<br>
+<img src="rliDominance_formula.png" alt="rliDominance formula"> <br>
+with:
<ul>
- <li><b>m</b>: number of different patch type<br> </li>
- <li><b>i</b>: patch type<br></li>
- <li><b>p<small><small>i</small></small></b>: proportion of the landscape occupied by patch type i<br></li>
+<li><b>i</b>: patch type</li>
+<li><b>m</b>: number of different patch types</li>
+<li><b>p<small><small>i</small></small></b>: proportion of the landscape
+ occupied by patch type <i>i</i> </li>
</ul>
<h2>NOTES</h2>
@@ -16,31 +17,40 @@
output will be a raster map, otherwise an ASCII file will be generated in
the <tt>~/.r.li/output/</tt> folder.
<p>
-If input raster is full of null values r.li.dominance returns -1.<br>
-If you want to have null values instead run <br>
+<!-- TODO: verify next: -->
+If the input raster map contains only NULL values then <em>r.li.dominance</em>
+returns -1.<br>
+If you want to change these -1 values to NULL, run subsequently on the resulting map:
<div class="code"><pre>
r.null setnull=-1 map=my_map
</pre></div>
after index calculation.
<h2>EXAMPLES</h2>
-To calculate dominance's diversity index on map my_map, using
-my_conf configuration file and saving results in my_out file run:<br>
+To calculate the dominance diversity index on map <em>my_map</em>, using
+<em>my_conf</em> configuration file (previously defined with
+<em>r.li.setup</em>) and saving results in <em>my_out</em>, run:
<div class="code"><pre>
r.li.dominance map=my_map conf=my_conf output=my_out
+
+# forest map example:
+g.region rast=landcover.30m -p
+r.mapcalc "forests = if(landcover.30m >= 41 && landcover.30m <= 43,1,null())"
+r.li.dominance map=forests conf=movwindow7 out=forests_dominance_mov7
+r.univar forests_dominance_mov7
</pre></div>
+<h2>SEE ALSO</h2>
+<em>
+<a href="r.li.html">r.li</a> - package overview<br>
+<a href="r.li.setup.html">r.li.setup</a>
+</em>
+
<h2>REFERENCES</h2>
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://treesearch.fs.fed.us/pubs/3064">PDF</a>)
-<h2>SEE ALSO</h2>
-<em>
-<a href="r.li.html">r.li</a>,
-<a href="r.le.html">r.le</a>
-</em>
-
<h2>AUTHORS</h2>
Serena Pallecchi student of Computer Science University of Pisa (Italy).<br>
Commission from Faunalia Pontedera (PI), Italy (www.faunalia.it)
Modified: grass/branches/develbranch_6/raster/r.li/r.li.edgedensity/description.html
===================================================================
--- grass/branches/develbranch_6/raster/r.li/r.li.edgedensity/description.html 2014-02-11 14:04:30 UTC (rev 58995)
+++ grass/branches/develbranch_6/raster/r.li/r.li.edgedensity/description.html 2014-02-11 14:05:36 UTC (rev 58996)
@@ -1,20 +1,21 @@
+<h2>DESCRIPTION</h2>
-<h2>DESCRIPTION</h2>
<em>r.li.edgedensity </em>calculates:<br>
<br>
<ul>
- <li> the density of all the edge of patch i<br></li>
- <img alt="" src="rliEdgeDensity_formula1.png"><br>
- or<br><br>
- <li> the density of all the edge in the sampling area if i isn't specified<br></li>
- <img alt="" src="rliEdgeDensity_formula2.png"><br></ul>
-<p>with:</p>
+ <li> the density of all the edge of patch i
+ <img alt="rliEdgeDensity formula1" src="rliEdgeDensity_formula1.png">
+ , or
+ <li> the density of all the edge in the sampling area if i isn't specified,
+ <img alt="rliEdgeDensity formula2" src="rliEdgeDensity_formula2.png">
+</ul>
+<p>with:
<ul>
- <li><b>k</b>: patch type<br></li>
- <li><b>m</b>: number of patch type<br> </li>
- <li><b>n</b>: number of edge segment of patch type k</li>
- <li><b>e<small><small>ik </small></small></b>:total length of edge in landscape involving patch type k</li>
- <li> <b>Area</b>: total landscape area<br>
+<li><b>k</b>: patch type</li>
+<li><b>m</b>: number of patch types</li>
+<li><b>n</b>: number of edge segments of patch type k</li>
+<li><b>e<small><small>ik </small></small></b>:total length of edge in landscape involving patch type k</li>
+<li> <b>Area</b>: total landscape area</li>
</ul>
<h2>NOTES</h2>
@@ -24,40 +25,48 @@
output will be a raster map, otherwise an ASCII file will be generated in
the <tt>~/.r.li/output/</tt> folder.
<p>
-If input raster is full of null values <em>r.li.edgedensity</em> consider to have 0
-patch.<br>
-If area is 0 <em>r.li.edgedensity</em> returns -1; this is possible only if input
+<!-- TODO: verify next: -->
+If the input raster map contains only NULL values then <em>r.li.edgedensity</em>
+consider to have 0 patches.<br>
+If area is 0 <em>r.li.edgedensity</em> returns -1; this is only possible if input
raster is masked.
-If you want to have null values instead run <br>
+If you want to change these -1 values to NULL, run subsequently on the resulting map:
<div class="code"><pre>
r.null setnull=-1 map=my_map
</pre></div>
after index calculation.
<h2>EXAMPLES</h2>
-To calculate edge density index on map my_map, using
-my_conf configuration file and saving results in
-my_out file run:<br>
+To calculate the edge density index on map <em>my_map</em>, using
+<em>my_conf</em> configuration file (previously defined with
+<em>r.li.setup</em>) and saving results in <em>my_out</em>, run:
<div class="code"><pre>
r.li.edgedensity map=my_map conf=my_conf output=my_out
</pre></div>
To calculate edge density index of patch_type 34, using
-my_conf configuration file and on map my_map, saving results in my_out
+"my_conf" configuration file and on map "my_map", saving results in "my_out"
file run:<br>
<div class="code"><pre>
r.li.edgedensity map=my_map conf=my_conf output=my_out patch_type=34
+
+# forest map example:
+g.region rast=landcover.30m -p
+r.mapcalc "forests = if(landcover.30m >= 41 && landcover.30m <= 43,1,null())"
+r.li.edgedensity map=forests conf=movwindow7 out=forests_edgedens_mov7
+r.univar forests_edgedens_mov7
</pre></div>
<h2>SEE ALSO</h2>
<em>
-<a href="r.li.html">r.li</a>
+<a href="r.li.html">r.li</a> - package overview<br>
+<a href="r.li.setup.html">r.li.setup</a>
</em>
<h2>REFERENCES</h2>
McGarigal, K., and B. J. Marks. 1995. FRAGSTATS: spatial pattern
analysis program for quantifying landscape structure. USDA For. Serv.
-Gen. Tech. Rep. PNW-351.
+Gen. Tech. Rep. PNW-351. (<a href="http://treesearch.fs.fed.us/pubs/3064">PDF</a>)
<h2>AUTHORS</h2>
Serena Pallecchi student of Computer Science University of Pisa (Italy).<br>
@@ -65,4 +74,3 @@
<p>
<i>Last changed: $Date$</i>
-
Modified: grass/branches/develbranch_6/raster/r.li/r.li.mpa/description.html
===================================================================
--- grass/branches/develbranch_6/raster/r.li/r.li.mpa/description.html 2014-02-11 14:04:30 UTC (rev 58995)
+++ grass/branches/develbranch_6/raster/r.li/r.li.mpa/description.html 2014-02-11 14:05:36 UTC (rev 58996)
@@ -1,16 +1,14 @@
<h2>DESCRIPTION</h2>
-<em>r.li.mpa</em>
-(mean pixel attribute) calculates the average value of the attribute of all the non-null
-cells in the sampling area as:<br>
-<img src="rlimpa_formula.png"> <br>
+<em>r.li.mpa</em> (mean pixel attribute) calculates the average value of the
+attribute of all the non-null cells in the sampling area as:<br>
+<img src="rlimpa_formula.png" alt="rlimpa formula"> <br>
with:<br>
<ul>
- <li><b>i</b>: attribute<br></li>
+ <li><b>i</b>: attribute</li>
<li><b>m</b>: number of non-null attributes in the sampling area </li>
<li><b>w<small><small>i</small></small></b>: number of cells of attribute i</li>
- <li><b>size</b>: size of sampling area (in cells)<br>
- </li>
+ <li><b>size</b>: size of sampling area (in cells)</li>
</ul>
<h2>NOTES</h2>
@@ -20,39 +18,45 @@
output will be a raster map, otherwise an ASCII file will be generated in
the <tt>~/.r.li/output/</tt> folder.
<p>
-If input raster is full of null values r.li.mpa consider to
-have 0 patch.<br>
-If area is 0 r.li.mpa returns -1; it is possible only if the
+<!-- TODO: verify next: -->
+If the input raster map contains only NULL values then <em>r.li.mpa</em> considers to
+have 0 patches.<br>
+If area is 0 <em>r.li.mpa</em> returns -1; it is possible only if the
raster is masked <br>
-If you want to have null values instead run <br>
+If you want to change these -1 values to NULL, run subsequently on the resulting map:
<div class="code"><pre>
r.null setnull=-1 map=my_map
</pre></div>
after index calculation.
<h2>EXAMPLES</h2>
-To calculate mean pixel attribute index on map my_map, using
-my_conf configuration file and saving results in
-my_out file run:<br>
+To calculate the mean pixel attribute index on map <em>my_map</em>, using
+<em>my_conf</em> configuration file (previously defined with
+<em>r.li.setup</em>) and saving results in <em>my_out</em>, run:
<div class="code"><pre>
r.li.mpa map=my_map conf=my_conf output=my_out
+
+# forest map example:
+g.region rast=landcover.30m -p
+r.mapcalc "forests = if(landcover.30m >= 41 && landcover.30m <= 43,1,null())"
+r.li.mpa map=forests conf=movwindow7 out=forests_mpa_mov7
+r.univar forests_mpa_mov7
</pre></div>
+<h2>SEE ALSO</h2>
+<em>
+<a href="r.li.html">r.li</a> - package overview<br>
+<a href="r.li.setup.html">r.li.setup</a>
+</em>
+
<h2>REFERENCES</h2>
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://treesearch.fs.fed.us/pubs/3064">PDF</a>)
-<h2>SEE ALSO</h2>
-<em>
-<a href="r.li.html">r.li</a>,
-<a href="r.le.html">r.le</a>
-</em>
-
<h2>AUTHORS</h2>
Serena Pallecchi student of Computer Science University of Pisa (Italy).<br>
Commission from Faunalia Pontedera (PI), Italy (www.faunalia.it)
<p>
<i>Last changed: $Date$</i>
-
Modified: grass/branches/develbranch_6/raster/r.li/r.li.mps/description.html
===================================================================
--- grass/branches/develbranch_6/raster/r.li/r.li.mps/description.html 2014-02-11 14:04:30 UTC (rev 58995)
+++ grass/branches/develbranch_6/raster/r.li/r.li.mps/description.html 2014-02-11 14:05:36 UTC (rev 58996)
@@ -1,14 +1,13 @@
<h2>DESCRIPTION</h2>
-<em>r.li.mps</em>
-(mean patch size) calculates the mean size of the patches in the sampling area as:<br>
-<img src="rlimps_formula.png"><br>
+<em>r.li.mps</em> (mean patch size) calculates the mean size of the patches
+in the sampling area as:<br>
+<img src="rlimps_formula.png" alt="rliMps formula"><br>
with:
<ul>
<li><b>A</b>:sampling area size without null cells</li>
- <li><b>Npatch</b>: number of patches<br>
- </li>
+ <li><b>Npatch</b>: number of patches</li>
</ul>
<h2>NOTES</h2>
@@ -18,38 +17,43 @@
output will be a raster map, otherwise an ASCII file will be generated in
the <tt>~/.r.li/output/</tt> folder.
<p>
+<!-- TODO: verify next: -->
If the input raster contains NULL value cells, <em>r.li.mps</em>
returns 0 for these cells. <br>
-If you want to keep NULL values instead, run subsequently on the resulting map:
+If you want to change these 0 values to NULL, run subsequently on the resulting map:
<div class="code"><pre>
r.null setnull=0 map=my_map
</pre></div>
-
after index calculation.
<h2>EXAMPLES</h2>
-To calculate mean path size index on map my_map, using
-my_conf configuration file and saving results in
-my_out file run:<br>
+To calculate mean path size index on map <em>my_map</em>, using
+<em>my_conf</em> configuration file (previously defined with
+<em>r.li.setup</em>) and saving results in <em>my_out</em>, run:
<div class="code"><pre>
r.li.mps map=my_map conf=my_conf output=my_out
+
+# forest map example:
+g.region rast=landcover.30m -p
+r.mapcalc "forests = if(landcover.30m >= 41 && landcover.30m <= 43,1,null())"
+r.li.mps map=forests conf=movwindow7 out=forests_mps_mov7
+r.univar forests_mps_mov7
</pre></div>
+<h2>SEE ALSO</h2>
+<em>
+<a href="r.li.html">r.li</a> - package overview<br>
+<a href="r.li.setup.html">r.li.setup</a>
+</em>
+
<h2>REFERENCES</h2>
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://treesearch.fs.fed.us/pubs/3064">PDF</a>)
-<h2>SEE ALSO</h2>
-<em>
-<a href="r.li.html">r.li</a>,
-<a href="r.le.html">r.le</a>
-</em>
-
<h2>AUTHORS</h2>
Serena Pallecchi student of Computer Science University of Pisa (Italy).<br>
Commission from Faunalia Pontedera (PI), Italy (www.faunalia.it)
<p>
<i>Last changed: $Date$</i>
-
Modified: grass/branches/develbranch_6/raster/r.li/r.li.padcv/description.html
===================================================================
--- grass/branches/develbranch_6/raster/r.li/r.li.padcv/description.html 2014-02-11 14:04:30 UTC (rev 58995)
+++ grass/branches/develbranch_6/raster/r.li/r.li.padcv/description.html 2014-02-11 14:05:36 UTC (rev 58996)
@@ -2,15 +2,14 @@
<em>r.li.padcv</em> (patch area distribution coefficient of variation) calculates
as:<br>
-<img src="rlipadcv_formula1.png"> <br>
+<img src="rlipadcv_formula1.png" alt="rlipadcv formula"> <br>
with:<br>
<ul>
- <li><b>SD</b>: standard deviation of patch area size <br></li>
- <img src="rlipadcv_formula2.png"> <br>
- <li><b>MPS</b>: mean patch area size<br></li>
- <li><b>a<small><small>i</small></small></b>: area of patch i<br></li>
- <li><b>N<small>patch</small></b>: number of patch<br></li>
- </li>
+ <li><b>SD</b>: standard deviation of patch area size
+ <img src="rlipadcv_formula2.png"> </li>
+ <li><b>MPS</b>: mean patch area size </li>
+ <li><b>a<small><small>i</small></small></b>: area of patch i</li>
+ <li><b>N<small>patch</small></b>: number of patch</li>
</ul>
<h2>NOTES</h2>
@@ -20,31 +19,38 @@
output will be a raster map, otherwise an ASCII file will be generated in
the <tt>~/.r.li/output/</tt> folder.
<p>
-If input raster is not full of null values r.li.padcv returns a value >=0 that is PADcv. <br>
-If input raster is full of null values r.li.padcv returns -1. <br>
-If you want to have null values instead run <br>
+If input raster is not full of null values <em>r.li.padcv</em> returns a value >=0 that is PADcv. <br>
+If the input raster map contains only NULL values then <em>r.li.padcv</em> returns -1. <br>
+If you want to change these -1 values to NULL, run subsequently on the resulting map:
<div class="code"><pre>
r.null setnull=-1 map=my_map
</pre></div>
after index calculation.
<h2>EXAMPLES</h2>
-To calculate mean pixel attribute index on map my_map, using
-my_conf configuration file and saving results in
-my_out file run:<br>
+To calculate patch area distribution coefficient of variation index on map <em>my_map</em>, using
+<em>my_conf</em> configuration file (previously defined with
+<em>r.li.setup</em>) and saving results in <em>my_out</em>, run:
<div class="code"><pre>
r.li.padcv map=my_map conf=my_conf output=my_out
+
+# forest map example:
+g.region rast=landcover.30m -p
+r.mapcalc "forests = if(landcover.30m >= 41 && landcover.30m <= 43,1,null())"
+r.li.padcv map=forests conf=movwindow7 out=forests_padcv_mov7
+r.univar forests_padcv_mov7
</pre></div>
<h2>SEE ALSO</h2>
<em>
-<a href="r.li.html">r.li</a>
+<a href="r.li.html">r.li</a> - package overview<br>
+<a href="r.li.setup.html">r.li.setup</a>
</em>
<h2>REFERENCES</h2>
McGarigal, K., and B. J. Marks. 1995. FRAGSTATS: spatial pattern
analysis program for quantifying landscape structure. USDA For. Serv.
-Gen. Tech. Rep. PNW-351.
+Gen. Tech. Rep. PNW-351. (<a href="http://treesearch.fs.fed.us/pubs/3064">PDF</a>)
<h2>AUTHORS</h2>
Serena Pallecchi student of Computer Science University of Pisa (Italy).<br>
@@ -52,4 +58,3 @@
<p>
<i>Last changed: $Date$</i>
-
Modified: grass/branches/develbranch_6/raster/r.li/r.li.padrange/description.html
===================================================================
--- grass/branches/develbranch_6/raster/r.li/r.li.padrange/description.html 2014-02-11 14:04:30 UTC (rev 58995)
+++ grass/branches/develbranch_6/raster/r.li/r.li.padrange/description.html 2014-02-11 14:05:36 UTC (rev 58996)
@@ -1,23 +1,14 @@
<h2>DESCRIPTION</h2>
-<em>r.li.padrange</em>
- (patch area distribution range) calculates
+<em>r.li.padrange</em> (patch area distribution range) calculates
as:<br>
-<img src="rlipadrange_formula.png"> <br>
+<img src="rlipadrange_formula.png" alt="rlipadrange formula"> <br>
with:<br>
<ul>
- <li><b>a<small><small>max</small></small></b>: max patch area size<br></li>
- <li><b>a<small><small>min</small></small></b>: min patch area size<br></li>
+ <li><b>a<small><small>max</small></small></b>: max patch area size</li>
+ <li><b>a<small><small>min</small></small></b>: min patch area size</li>
</ul>
-<h2>EXAMPLES</h2>
-To calculate range of patch area size, using
-my_conf configuration file and saving results in
-my_out file run:<br>
-<div class="code"><pre>
-r.li.padrange map=my_map conf=my_conf output=my_out
-</pre></div>
-
<h2>NOTES</h2>
Do not use absolute path names for the <b>output</b> map/file.
@@ -25,30 +16,43 @@
output will be a raster map, otherwise an ASCII file will be generated in
the <tt>~/.r.li/output/</tt> folder.
<p>
-If the input raster contains NULL value cells, <em>r.li.padrange</em>
-returns -1 for these cells. <br>
-If you want to keep NULL values instead, run subsequently on the resulting map:
-
+<!-- TODO: verify next: -->
+If the input raster map contains only NULL values then <em>r.li.padrange</em>
+returns -1.<br>
+If you want to change these -1 values to NULL, run subsequently on the resulting map:
<div class="code"><pre>
r.null setnull=-1 map=my_map
</pre></div>
-
after index calculation.
-<h2>REFERENCES</h2>
-McGarigal, K., and B. J. Marks. 1995. FRAGSTATS: spatial pattern
-analysis program for quantifying landscape structure. USDA For. Serv.
-Gen. Tech. Rep. PNW-351.
+<h2>EXAMPLES</h2>
+To calculate range of patch area size index on map <em>my_map</em>, using
+<em>my_conf</em> configuration file (previously defined with
+<em>r.li.setup</em>) and saving results in <em>my_out</em>, run:
+<div class="code"><pre>
+r.li.padrange map=my_map conf=my_conf output=my_out
+# forest map example:
+g.region rast=landcover.30m -p
+r.mapcalc "forests = if(landcover.30m >= 41 && landcover.30m <= 43,1,null())"
+r.li.padrange map=forests conf=movwindow7 out=forests_padrange_mov7
+r.univar forests_padrange_mov7
+</pre></div>
+
<h2>SEE ALSO</h2>
<em>
-<a href="r.li.html">r.li</a>
+<a href="r.li.html">r.li</a> - package overview<br>
+<a href="r.li.setup.html">r.li.setup</a>
</em>
+<h2>REFERENCES</h2>
+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://treesearch.fs.fed.us/pubs/3064">PDF</a>)
+
<h2>AUTHORS</h2>
Serena Pallecchi student of Computer Science University of Pisa (Italy).<br>
Commission from Faunalia Pontedera (PI), Italy (www.faunalia.it)
<p>
<i>Last changed: $Date$</i></p>
-
Modified: grass/branches/develbranch_6/raster/r.li/r.li.padsd/description.html
===================================================================
--- grass/branches/develbranch_6/raster/r.li/r.li.padsd/description.html 2014-02-11 14:04:30 UTC (rev 58995)
+++ grass/branches/develbranch_6/raster/r.li/r.li.padsd/description.html 2014-02-11 14:05:36 UTC (rev 58996)
@@ -1,12 +1,12 @@
<h2>DESCRIPTION</h2>
<em>r.li.padsd</em> (patch area distribution standard deviation) calculates as:<br>
-<img src="rlipadsd_formula.png"> <br>
+<img src="rlipadsd_formula.png" alt="rlipadsd formula"> <br>
with:<br>
<ul>
- <li><b>MPS</b>: mean patch area size<br></li>
- <li><b>a<small><small>i</small></small></b>: area of patch i<br></li>
- <li><b>N<small>patch</small></b>: number of patch<br></li>
+ <li><b>MPS</b>: mean patch area size</li>
+ <li><b>a<small><small>i</small></small></b>: area of patch i</li>
+ <li><b>N<small>patch</small></b>: number of patch</li>
</ul>
<h2>NOTES</h2>
@@ -18,35 +18,40 @@
<p>
If input raster is not full of null values <em>r.li.padsd</em> returns a
value >=0 that is PADsd. <br>
-If input raster is full of null values <em>r.li.padsd</em> returns -1. <br>
-If you want to have null values instead run <br>
+If the input raster map contains only NULL values then <em>r.li.padsd</em> returns -1. <br>
+If you want to change these -1 values to NULL, run subsequently on the resulting map:
<div class="code"><pre>
r.null setnull=-1 map=my_map
</pre></div>
-
after index calculation.
<h2>EXAMPLES</h2>
-To calculate mean pixel attribute index on map my_map, using
-my_conf configuration file and saving results in
-my_out file run:<br>
+To calculate patch area distribution standard deviation index on map <em>my_map</em>, using
+<em>my_conf</em> configuration file (previously defined with
+<em>r.li.setup</em>) and saving results in <em>my_out</em>, run:
<div class="code"><pre>
r.li.padsd map=my_map conf=my_conf output=my_out
-</pre></div>
-<h2>REFERENCES</h2>
-McGarigal, K., and B. J. Marks. 1995. FRAGSTATS: spatial pattern
-analysis program for quantifying landscape structure. USDA For. Serv.
-Gen. Tech. Rep. PNW-351.
+# forest map example:
+g.region rast=landcover.30m -p
+r.mapcalc "forests = if(landcover.30m >= 41 && landcover.30m <= 43,1,null())"
+r.li.padsd map=forests conf=movwindow7 out=forests_padsd_mov7
+r.univar forests_padsd_mov7</pre></div>
<h2>SEE ALSO</h2>
<em>
-<a href="r.li.html">r.li</a>
+<a href="r.li.html">r.li</a> - package overview<br>
+<a href="r.li.setup.html">r.li.setup</a>
</em>
+<h2>REFERENCES</h2>
+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://treesearch.fs.fed.us/pubs/3064">PDF</a>)
+
<h2>AUTHORS</h2>
Serena Pallecchi student of Computer Science University of Pisa (Italy).<br>
Commission from Faunalia Pontedera (PI), Italy (www.faunalia.it)
<p>
-<i>Last changed: $Date$</i></p>
+<i>Last changed: $Date$</i>
Modified: grass/branches/develbranch_6/raster/r.li/r.li.patchdensity/description.html
===================================================================
--- grass/branches/develbranch_6/raster/r.li/r.li.patchdensity/description.html 2014-02-11 14:04:30 UTC (rev 58995)
+++ grass/branches/develbranch_6/raster/r.li/r.li.patchdensity/description.html 2014-02-11 14:05:36 UTC (rev 58996)
@@ -1,8 +1,6 @@
<h2>DESCRIPTION</h2>
-<em>r.li.patchdensity</em> is a patch index for <em>r.li</em> suite.
-It calculates the function:
-
+<em>r.li.patchdensity</em> calculates the "patch density index" as:
<div class="code"><pre>
f(sample_area) = (Patch_Number/Area) * 1000000
</pre></div>
@@ -17,25 +15,22 @@
output will be a raster map, otherwise an ASCII file will be generated in
the <tt>~/.r.li/output/</tt> folder.
<p>
+<!-- TODO: verify next: -->
A map of NULL values is considered to have zero patches. <br>
-If you want to have null values instead run <br>
+If raster area is 0, <em>r.li.patchdensity</em> returns -1. This is only
+possible if the raster is masked.<br>
+If you want to change these -1 values to NULL, run subsequently on the resulting map:
<div class="code"><pre>
-r.null setnull=0 map=my_out
+r.null setnull=-1 map=my_out
</pre></div>
-after index calculation.<br>
-<!-- next ??????: -->
-If raster area is 0, <em>r.li.patchdensity</em> returns -1. This is only
-possible if the raster is masked.
+after index calculation.
<h2>EXAMPLES</h2>
-
To calculate patch density index on map <em>my_map</em>, using
<em>my_conf</em> configuration file (previously defined with
-<em>r.li.setup</em>) and saving results in the raster map
-<em>my_out</em>, run:
-
+<em>r.li.setup</em>) and saving results in <em>my_out</em>, run:
<div class="code"><pre>
-r.li.patchdensity map=my_map conf=my_conf out=my_out
+r.li.patchdensity map=my_map conf=my_conf output=my_out
</pre></div>
<p>
@@ -55,10 +50,15 @@
</pre></div>
<h2>SEE ALSO</h2>
+<em>
+<a href="r.li.html">r.li</a> - package overview<br>
+<a href="r.li.setup.html">r.li.setup</a>
+</em>
-<em><a href="r.li.html">r.li</a></em> package overview <br>
-<em><a href="r.li.daemon.html">r.li.daemon</a></em><br>
-<em><a href="r.li.setup.html">r.li.setup</a></em>
+<h2>REFERENCES</h2>
+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://treesearch.fs.fed.us/pubs/3064">PDF</a>)
<h2>AUTHORS</h2>
Modified: grass/branches/develbranch_6/raster/r.li/r.li.patchnum/description.html
===================================================================
--- grass/branches/develbranch_6/raster/r.li/r.li.patchnum/description.html 2014-02-11 14:04:30 UTC (rev 58995)
+++ grass/branches/develbranch_6/raster/r.li/r.li.patchnum/description.html 2014-02-11 14:05:36 UTC (rev 58996)
@@ -1,7 +1,6 @@
<h2>DESCRIPTION</h2>
-<em>r.li.patchnum</em> is a patch index for r.li program.<br>
-It calculates the function <br>
+<em>r.li.patchnum</em> calculates the "patch number index" as:<br>
<I> f(sample_area)= Patch_Number </I><br>
This index is calculated using a 4 neighbour algorithm<br>
@@ -12,31 +11,39 @@
output will be a raster map, otherwise an ASCII file will be generated in
the <tt>~/.r.li/output/</tt> folder.
<p>
-An that is full of null values is considered to have zero patch. <br>
-If you want to have null values instead run <br>
+<!-- TODO verify: -->
+If the input raster map contains only NULL values then it is considered to have zero patch. <br>
+If you want to keep NULL values, run subsequently on the resulting map:
<div class="code"><pre>
r.null setnull=0 map=my_map
</pre></div>
-after index calculation.<br>
+after index calculation.
<h2>EXAMPLES</h2>
-To calculate patch number index on map my_map, using
-<em>my_conf</em> configuration file and saving results in
-my_out file run:
+To calculate patch number index on map <em>my_map</em>, using
+<em>my_conf</em> configuration file (previously defined with
+<em>r.li.setup</em>) and saving results in <em>my_out</em>, run:
<div class="code"><pre>
-r.li.patchnumber map=my_map conf=my_conf out=my_out
+r.li.patchnum map=my_map conf=my_conf out=my_out
+
+# forest map example:
+g.region rast=landcover.30m -p
+r.mapcalc "forests = if(landcover.30m >= 41 && landcover.30m <= 43,1,null())"
+r.li.patchnum map=forests conf=movwindow7 out=forests_patchnum_mov7
+r.univar forests_patchnum_mov7
</pre></div>
+<h2>SEE ALSO</h2>
+<em>
+<a href="r.li.html">r.li</a> - package overview<br>
+<a href="r.li.setup.html">r.li.setup</a>
+</em>
+
<h2>REFERENCES</h2>
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://treesearch.fs.fed.us/pubs/3064">PDF</a>)
-<h2>SEE ALSO</h2>
-<em><a href="r.li.html">r.li</a></em> package overview <br>
-<em><a href="r.li.daemon.html">r.li.daemon</a></em><br>
-<em><a href="r.li.setup.html">r.li.setup</a></em>
-
<h2>AUTHORS</h2>
Claudio Porta and Lucio Davide Spano, students of Computer Science
University of Pisa (Italy).<br>
Modified: grass/branches/develbranch_6/raster/r.li/r.li.pielou/description.html
===================================================================
--- grass/branches/develbranch_6/raster/r.li/r.li.pielou/description.html 2014-02-11 14:04:30 UTC (rev 58995)
+++ grass/branches/develbranch_6/raster/r.li/r.li.pielou/description.html 2014-02-11 14:05:36 UTC (rev 58996)
@@ -1,6 +1,6 @@
<h2>DESCRIPTION</h2>
-<em>r.li.pielou</em> calculates the "pielou's diversity index" as: <br>
+<em>r.li.pielou</em> calculates the "Pielou's diversity index" as: <br>
<img src="r_li_pielou.png"><br>
with:
<ul>
@@ -16,38 +16,42 @@
output will be a raster map, otherwise an ASCII file will be generated in
the <tt>~/.r.li/output/</tt> folder.
<p>
-
If the input raster contains NULL value cells, <em>r.li.pielou</em>
returns -1 for these cells. <br>
-If you want to keep NULL values instead, run subsequently on the resulting map:
-<br>
+If you want to change these -1 values to NULL, run subsequently on the resulting map:
<div class="code"><pre>
r.null setnull=-1 map=my_map
</pre></div>
+after index calculation.
<h2>EXAMPLES</h2>
-To calculate Pielou's diversity index on the map "my_map", using the
-previously created "my_conf" configuration file (<em>r.li.setup</em>)
-and saving results in "my_out" raster map, run:<br>
+To calculate Pielou's diversity index on map <em>my_map</em>, using
+<em>my_conf</em> configuration file (previously defined with
+<em>r.li.setup</em>) and saving results in <em>my_out</em>, run:
<div class="code"><pre>
r.li.pielou map=my_map conf=my_conf output=my_out
+
+# forest map example:
+g.region rast=landcover.30m -p
+r.mapcalc "forests = if(landcover.30m >= 41 && landcover.30m <= 43,1,null())"
+r.li.pielou map=forests conf=movwindow7 out=forests_pielou_mov7
+r.univar forests_pielou_mov7
</pre></div>
+<h2>SEE ALSO</h2>
+<em>
+<a href="r.li.html">r.li</a> - package overview<br>
+<a href="r.li.setup.html">r.li.setup</a>
+</em>
+
<h2>REFERENCES</h2>
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://treesearch.fs.fed.us/pubs/3064">PDF</a>)
-<h2>SEE ALSO</h2>
-<em>
-<a href="r.li.html">r.li</a>,
-<a href="r.li.setup.html">r.li.setup</a>
-</em>
-
<h2>AUTHORS</h2>
Luca Delucchi and Duccio Rocchini, Fondazione E. Mach (Italy), based on the <em>r.li.shannon</em> code
developed by Serena Pallecchi student of Computer Science University of Pisa (Italy).<br>
<p>
<i>Last changed: $Date$</i>
-
Modified: grass/branches/develbranch_6/raster/r.li/r.li.renyi/description.html
===================================================================
--- grass/branches/develbranch_6/raster/r.li/r.li.renyi/description.html 2014-02-11 14:04:30 UTC (rev 58995)
+++ grass/branches/develbranch_6/raster/r.li/r.li.renyi/description.html 2014-02-11 14:05:36 UTC (rev 58996)
@@ -1,9 +1,8 @@
<h2>DESCRIPTION</h2>
-<em>r.li.renyi</em>
-calculates the "renyi's diversity index" as:<br>
+<em>r.li.renyi</em> calculates the "Renyi's diversity index" as:<br>
<img src="r_li_renyi.png"> <br>
-with: <br>
+with:
<ul>
<li><b>H</b>: Renyi entropy</li>
<li><b>alpha</b>: order of the generalized entropy</li>
@@ -19,34 +18,40 @@
output will be a raster map, otherwise an ASCII file will be generated in
the <tt>~/.r.li/output/</tt> folder.
<p>
-
-If input raster contain NULL values <em>r.li.renyi</em> returns -1.<br>
-If you want to keep NULL values instead, run subsequently on the resulting map:
+<!-- TODO: verify next: -->
+If the input raster map contains only NULL values then <em>r.li.renyi</em>
+returns -1.<br>
+If you want to change these -1 values to NULL, run subsequently on the resulting map:
<div class="code"><pre>
r.null setnull=-1 map=my_map
</pre></div>
after index calculation.
<h2>EXAMPLES</h2>
-
-To calculate Renyi's diversity index on map "my_map", using the
-previously created "my_conf" configuration file (<em>r.li.setup</em>)
-and saving results in "my_out" raster map, run:<br>
+To calculate Renyi's diversity index on map <em>my_map</em>, using
+<em>my_conf</em> configuration file (previously defined with
+<em>r.li.setup</em>) and saving results in <em>my_out</em>, run:
<div class="code"><pre>
r.li.renyi map=my_map conf=my_conf output=my_out alpha=0.6
+
+# forest map example:
+g.region rast=landcover.30m -p
+r.mapcalc "forests = if(landcover.30m >= 41 && landcover.30m <= 43,1,null())"
+r.li.renyi map=forests conf=movwindow7 out=forests_renyi_mov7_a06 alpha=0.6
+r.univar forests_renyi_mov7_a06
</pre></div>
+<h2>SEE ALSO</h2>
+<em>
+<a href="r.li.html">r.li</a> - package overview<br>
+<a href="r.li.setup.html">r.li.setup</a>
+</em>
+
<h2>REFERENCES</h2>
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://treesearch.fs.fed.us/pubs/3064">PDF</a>)
-<h2>SEE ALSO</h2>
-<em>
-<a href="r.li.html">r.li</a>,
-<a href="r.li.setup.html">r.li.setup</a>
-</em>
-
<h2>AUTHORS</h2>
Luca Delucchi and Duccio Rocchini, Fondazione E. Mach (Italy), based on
the <em>r.li.shannon</em> code developed by Serena Pallecchi student of
@@ -54,4 +59,3 @@
<p>
<i>Last changed: $Date$</i>
-
Modified: grass/branches/develbranch_6/raster/r.li/r.li.richness/description.html
===================================================================
--- grass/branches/develbranch_6/raster/r.li/r.li.richness/description.html 2014-02-11 14:04:30 UTC (rev 58995)
+++ grass/branches/develbranch_6/raster/r.li/r.li.richness/description.html 2014-02-11 14:05:36 UTC (rev 58996)
@@ -1,9 +1,10 @@
<h2>DESCRIPTION</h2>
-<em>r.li.richness</em> calculates the "richness's diversity index" as:<br>
-<img src="rliRichness_formula.png"> <br>
-with: <br>
+
+<em>r.li.richness</em> calculates the "richness diversity index" as:<br>
+<img src="rliRichness_formula.png alt="rliRichness formula"> <br>
+with:
<ul>
- <li><b>m</b>: number of different patch type</li>
+ <li><b>m</b>: number of different patch types</li>
</ul>
<h2>NOTES</h2>
@@ -13,33 +14,43 @@
output will be a raster map, otherwise an ASCII file will be generated in
the <tt>~/.r.li/output/</tt> folder.
<p>
-
-If input raster is full of null values r.li.richness returns -1.<br>
-If you want to have null values instead run <br>
+<!-- TODO: verify next: -->
+If the input raster map contains only NULL values then <em>r.li.richness</em>
+returns -1.<br>
+If you want to change these -1 values to NULL, run subsequently on the resulting map:
+<div class="code"><pre>
+r.null setnull=-1 map=my_map
+</pre></div>
after index calculation.
<h2>EXAMPLES</h2>
-
-To calculate richness's diversity index on map my_map, using
-my_conf configuration file and saving results in my_out file run:<br>
+To calculate the richness diversity index on map <em>my_map</em>, using
+<em>my_conf</em> configuration file (previously defined with
+<em>r.li.setup</em>) and saving results in <em>my_out</em>, run:
<div class="code"><pre>
r.li.richness map=my_map conf=my_conf output=my_out
+
+# forest map example:
+g.region rast=landcover.30m -p
+r.mapcalc "forests = if(landcover.30m >= 41 && landcover.30m <= 43,1,null())"
+r.li.richness map=forests conf=movwindow7 out=forests_richness_mov7
+r.univar forests_richness_mov7
</pre></div>
+<h2>SEE ALSO</h2>
+<em>
+<a href="r.li.html">r.li</a> - package overview<br>
+<a href="r.li.setup.html">r.li.setup</a>
+</em>
+
<h2>REFERENCES</h2>
McGarigal, K., and B. J. Marks. 1995. FRAGSTATS: spatial pattern
analysis program for quantifying landscape structure. USDA For. Serv.
-Gen. Tech. Rep. PNW-351.
+Gen. Tech. Rep. PNW-351. (<a href="http://treesearch.fs.fed.us/pubs/3064">PDF</a>)
-<h2>SEE ALSO</h2>
-<em>
-<a href="r.li.html">r.li</a>
-</em>
-
<h2>AUTHORS</h2>
Serena Pallecchi student of Computer Science University of Pisa (Italy).<br>
Commission from Faunalia Pontedera (PI), Italy (www.faunalia.it)
<p>
-<i>Last changed: $Date$</i></p>
-
+<i>Last changed: $Date$</i>
Modified: grass/branches/develbranch_6/raster/r.li/r.li.setup/description.html
===================================================================
--- grass/branches/develbranch_6/raster/r.li/r.li.setup/description.html 2014-02-11 14:04:30 UTC (rev 58995)
+++ grass/branches/develbranch_6/raster/r.li/r.li.setup/description.html 2014-02-11 14:05:36 UTC (rev 58996)
@@ -1,7 +1,7 @@
<h2>DESCRIPTION</h2>
<em>r.li.setup</em> creates and shows configuration files for the
-others r.li programs. For a general introduction, see
+others <em>r.li</em> modules. For a general introduction, see
<a href="r.li.html">r.li</a>.
<br>
The configurations are raster map independent,
@@ -209,6 +209,10 @@
<a href="http://grass.osgeo.org/gdp/landscape/r_le_manual5.pdf">Old r.le suite manual</a>
</em>
+<h2>REFERENCES</h2>
+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://treesearch.fs.fed.us/pubs/3064">PDF</a>)
<h2>AUTHORS</h2>
Modified: grass/branches/develbranch_6/raster/r.li/r.li.shannon/description.html
===================================================================
--- grass/branches/develbranch_6/raster/r.li/r.li.shannon/description.html 2014-02-11 14:04:30 UTC (rev 58995)
+++ grass/branches/develbranch_6/raster/r.li/r.li.shannon/description.html 2014-02-11 14:05:36 UTC (rev 58996)
@@ -1,13 +1,13 @@
<h2>DESCRIPTION</h2>
-<em>r.li.shannon</em>
-calculates the "shannon's diversity index" as: <br>
-<img src="rliShannon_formula.png"><br>
-with:<br>
+
+<em>r.li.shannon</em> calculates the "Shannon's diversity index" as:<br>
+<img src="rliShannon_formula.png" alt="rliShannon formula"> <br>
+with:
<ul>
- <li><b>i</b>: patch type<br></li>
- <li><b>m</b>: number of patch type<br></li>
- <li><b>p<small><small>i</small></small></b>: proportion of the landscape
- occupied by patch type i<br></li>
+<li><b>i</b>: patch type</li>
+<li><b>m</b>: number of patch types</li>
+<li><b>p<small><small>i</small></small></b>: proportion of the landscape
+ occupied by patch type <i>i</i> </li>
</ul>
<h2>NOTES</h2>
@@ -16,33 +16,41 @@
If the "moving window" method was selected in <b>r.li.setup</b>, then the
output will be a raster map, otherwise an ASCII file will be generated in
the <tt>~/.r.li/output/</tt> folder.
-
<p>
-If input raster is full of null values r.li.shannon returns -1. <br>
+<!-- TODO: verify next: -->
+If the input raster map contains only NULL values then <em>r.li.shannon</em>
+returns -1.<br>
<!-- does that mean the program exit code or raster values?? -->
-If you want to have null values instead run <br>
+If you want to change these -1 values to NULL, run subsequently on the resulting map:
<div class="code"><pre>
r.null setnull=-1 map=my_map
</pre></div>
after index calculation.
-
<h2>EXAMPLES</h2>
-To calculate shannon's diversity index on map my_map, using
-my_conf configuration file and saving results in my_out file run:<br>
+To calculate Shannon's diversity index on map <em>my_map</em>, using
+<em>my_conf</em> configuration file (previously defined with
+<em>r.li.setup</em>) and saving results in <em>my_out</em>, run:
<div class="code"><pre>
r.li.shannon map=my_map conf=my_conf output=my_out
+
+# forest map 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
</pre></div>
<h2>SEE ALSO</h2>
<em>
-<a href="r.li.html">r.li</a>
+<a href="r.li.html">r.li</a> - package overview<br>
+<a href="r.li.setup.html">r.li.setup</a>
</em>
<h2>REFERENCES</h2>
McGarigal, K., and B. J. Marks. 1995. FRAGSTATS: spatial pattern
analysis program for quantifying landscape structure. USDA For. Serv.
-Gen. Tech. Rep. PNW-351.
+Gen. Tech. Rep. PNW-351. (<a href="http://treesearch.fs.fed.us/pubs/3064">PDF</a>)
<h2>AUTHORS</h2>
Serena Pallecchi student of Computer Science University of Pisa (Italy).<br>
Modified: grass/branches/develbranch_6/raster/r.li/r.li.shape/description.html
===================================================================
--- grass/branches/develbranch_6/raster/r.li/r.li.shape/description.html 2014-02-11 14:04:30 UTC (rev 58995)
+++ grass/branches/develbranch_6/raster/r.li/r.li.shape/description.html 2014-02-11 14:05:36 UTC (rev 58996)
@@ -1,6 +1,6 @@
<h2>DESCRIPTION</h2>
-<em>r.li.shape</em> is a patch index for r.li program.<br>
-It calculates the function <br>
+
+<em>r.li.shape</em> calculates the "shape index" as:<br>
<I> f(sample_area)= Area </I><br>
<h2>NOTES</h2>
@@ -10,27 +10,35 @@
output will be a raster map, otherwise an ASCII file will be generated in
the <tt>~/.r.li/output/</tt> folder.
<p>
-
-If the input raster contains NULL value cells, <em>r.li.shape</em>
-returns -1 for these cells. <br>
-If you want to keep NULL values instead, run subsequently on the resulting map:
-<br>
+<!-- TODO: verify next: -->
+If the input raster map contains only NULL values then <em>r.li.shape</em>
+returns -1.<br>
+<!-- does that mean the program exit code or raster values?? -->
+If you want to change these -1 values to NULL, run subsequently on the resulting map:
<div class="code"><pre>
r.null setnull=-1 map=my_map
</pre></div>
+after index calculation.
<h2>EXAMPLES</h2>
-To calculate area index on map my_map, using
-<em>my_conf</em> configuration file and saving results in
-my_out file run:
+To calculate the shape index on map <em>my_map</em>, using
+<em>my_conf</em> configuration file (previously defined with
+<em>r.li.setup</em>) and saving results in <em>my_out</em>, run:
<div class="code"><pre>
-r.li.shape map=my_map conf=my_conf out=my_out
+r.li.shape map=my_map conf=my_conf output=my_out
+
+# forest map example:
+g.region rast=landcover.30m -p
+r.mapcalc "forests = if(landcover.30m >= 41 && landcover.30m <= 43,1,null())"
+r.li.shape map=forests conf=movwindow7 out=forests_shape_mov7
+r.univar forests_shape_mov7
</pre></div>
<h2>SEE ALSO</h2>
-<em><a href="r.li.html">r.li</a></em> package overview <br>
-<em><a href="r.li.daemon.html">r.li.daemon</a></em><br>
-<em><a href="r.li.setup.html">r.li.setup</a></em>
+<em>
+<a href="r.li.html">r.li</a> - package overview<br>
+<a href="r.li.setup.html">r.li.setup</a>
+</em>
<h2>REFERENCES</h2>
McGarigal, K., and B. J. Marks. 1995. FRAGSTATS: spatial pattern
Modified: grass/branches/develbranch_6/raster/r.li/r.li.simpson/description.html
===================================================================
--- grass/branches/develbranch_6/raster/r.li/r.li.simpson/description.html 2014-02-11 14:04:30 UTC (rev 58995)
+++ grass/branches/develbranch_6/raster/r.li/r.li.simpson/description.html 2014-02-11 14:05:36 UTC (rev 58996)
@@ -1,13 +1,13 @@
<h2>DESCRIPTION</h2>
-<em>r.li.simpson</em>
-calculates the "simpson's diversity index" as:<br>
-<img src="rliSimpson_formula.png"> <br>
-with: <br>
+
+<em>r.li.simpson</em> calculates the "Simpson's diversity index" as:<br>
+<img src="rliSimpson_formula.png" alt="rliSimpson formula"> <br>
+with:
<ul>
- <li><b>i</b>: patch type<br> </li>
- <li><b>m</b>: number of patch type<br> </li>
- <li><b>p<small><small>i</small></small></b>: proportion of the landscape
- occupied by patch type i<br> </li>
+<li><b>i</b>: patch type</li>
+<li><b>m</b>: number of patch types</li>
+<li><b>p<small><small>i</small></small></b>: proportion of the landscape
+ occupied by patch type <i>i</i> </li>
</ul>
<h2>NOTES</h2>
@@ -17,31 +17,40 @@
output will be a raster map, otherwise an ASCII file will be generated in
the <tt>~/.r.li/output/</tt> folder.
<p>
-
-If input raster is full of null values <em>r.li.simpson</em> returns -1.<br>
-If you want to have null values instead run <br>
+<!-- TODO: verify next: -->
+If the input raster map contains only NULL values then <em>r.li.simpson</em>
+returns -1.<br>
+If you want to change these -1 values to NULL, run subsequently on the resulting map:
<div class="code"><pre>
r.null setnull=-1 map=my_map
</pre></div>
after index calculation.
<h2>EXAMPLES</h2>
-To calculate simpson's diversity index on map my_map, using
-my_conf configuration file and saving results in my_out file run:<br>
+To calculate Simpson's diversity index on map <em>my_map</em>, using
+<em>my_conf</em> configuration file (previously defined with
+<em>r.li.setup</em>) and saving results in <em>my_out</em>, run:
<div class="code"><pre>
r.li.simpson map=my_map conf=my_conf output=my_out
+
+# forest map example:
+g.region rast=landcover.30m -p
+r.mapcalc "forests = if(landcover.30m >= 41 && landcover.30m <= 43,1,null())"
+r.li.simpson map=forests conf=movwindow7 out=forests_simpson_mov7
+r.univar forests_simpson_mov7
</pre></div>
+<h2>SEE ALSO</h2>
+<em>
+<a href="r.li.html">r.li</a> - package overview<br>
+<a href="r.li.setup.html">r.li.setup</a>
+</em>
+
<h2>REFERENCES</h2>
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://treesearch.fs.fed.us/pubs/3064">PDF</a>)
-<h2>SEE ALSO</h2>
-<em>
-<a href="r.li.html">r.li</a>
-</em>
-
<h2>AUTHORS</h2>
Serena Pallecchi student of Computer Science University of Pisa (Italy).<br>
Commission from Faunalia Pontedera (PI), Italy (www.faunalia.it)
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