r.li.* manual: cleanup; example added

git-svn-id: https://svn.osgeo.org/grass/grass/trunk@58997 15284696-431f-4ddb-bdfa-cd5b030d7da7

raster/r.li/TODO

@@ -19,11 +19,21 @@ A few remaining things should be done soon:
 - add relevant references
 - use English variable names in C code
 
-Please change the examples to Spearfish wherever possible:
+Please change the examples to North Carolina wherever possible:
+
 
 # Spearfish
 g.region rast=landcover.30m -p
-r.mapcalc "forests=if(landcover.30m >= 41 && landcover.30m <=43,1,null())"
+r.mapcalc "forests = if(landcover.30m >= 41 && landcover.30m <= 43,1,null())"
+d.mon wx0
+d.rast forests
+
+# g.gui.rlisetup:
+# created as described in EXAMPLES, moving window, in gui/wxgui/rlisetup/g.gui.rlisetup.html:
+echo "SAMPLINGFRAME 0|0|1|1
+SAMPLEAREA -1|-1|0.015021459227467811|0.011058451816745656
+MOVINGWINDOW" > $HOME/.grass7/r.li/movwindow7
+
 r.li.patchdensity forests conf=movwindow7 out=forests_p_dens7
 d.rast.leg forests_p_dens7
 
@@ -46,4 +56,8 @@ min=19.841270
 max=19.841270
 # -> all cells are 19.841270 ?!
 
+---------
+
+Add example which results in an ASCII output file
+
 

raster/r.li/r.li.cwed/r.li.cwed.html

@@ -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>
 
 
@@ -25,53 +27,47 @@ 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>~/.grass7/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 input=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 input=my_map conf=my_conf path=my_file output=my_out
+r.li.cwed input=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.
-
-
-<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>
-
+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>
-
+<i>Last changed: $Date$</i></p>

raster/r.li/r.li.daemon/r.li.daemon.html

@@ -32,13 +32,12 @@ To write a new index only two steps are needed:
 	folder, which contains all index declarations. This function must be of this kind:
 	<br><div class="code"><pre>
         int index(int fd, char ** par, area_des ad, double * result)
-	</pre></div>
-	<br>
+	</pre></div><br>
 	where: <ul>
-		    <li><i>fd</i> is the raster map descriptor
-		    <li><i>par</i> is a matrix for special parameter (like argv in main)
-		    <li><i>ad</i> is the area descriptor 
-		    <li><i>result</i> is where to put the index calculation result
+			<li><i>fd</i> is the raster map descriptor
+			<li><i>par</i> is a matrix for special parameter (like argv in main)
+			<li><i>ad</i> is the area descriptor 
+			<li><i>result</i> is where to put the index calculation result
 		</ul>
 	This function has to return 1 on success and 0 otherwise. <br><br>
 	<li>
@@ -58,7 +57,6 @@ To write a new index only two steps are needed:
 </ol>
 Compile it using a changed Makefile based on the file for <em>r.li.patchdensity</em>.
 
-
 <h2>NOTES</h2>
 
 Using GRASS library function to access raster rows can slow down moving windows 
@@ -75,8 +73,7 @@ The documentation is in doxygen files.
 <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>
 
 
@@ -85,13 +82,12 @@ 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>
 
 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.
 

raster/r.li/r.li.dominance/r.li.dominance.html

@@ -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>
@@ -16,32 +17,43 @@ 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>~/.grass7/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 input=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 input=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 input=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>
-</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></p>

raster/r.li/r.li.edgedensity/r.li.edgedensity.html

@@ -1,20 +1,21 @@
-
 <h2>DESCRIPTION</h2>
+
 <em>r.li.edgedensity </em>calculates:<br>
 <br>
 <ul>
-   <li> the density of all the edge of patch i<br>
-	<img src="rliEdgeDensity_formula1.png"><br>
-	or<br><br></li>
-   <li> the density of all the edge in the sampling area if i isn't specified<br>
-	<img src="rliEdgeDensity_formula2.png"><br></li></ul>
+   <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 @@ 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>~/.grass7/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 input=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 input=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 input=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 input=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 @@ Commission from Faunalia Pontedera (PI), Italy (www.faunalia.it)
 
 <p>
 <i>Last changed: $Date$</i>
-

raster/r.li/r.li.html

@@ -105,7 +105,7 @@ in the Spearfish sample dataset, using a 5x5 moving window:
 
   <li> run <em>r.li.patchdensity</em>:
 <div class="code"><pre>
-  r.li.patchdensity map=geology conf=my_conf out=patchdens
+  r.li.patchdensity input=geology conf=my_conf out=patchdens
 </pre></div>
   </ol>
 </ol>

raster/r.li/r.li.mpa/r.li.mpa.html

@@ -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>
@@ -20,37 +18,45 @@ 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>~/.grass7/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 input=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 input=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 input=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>
-</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>

raster/r.li/r.li.mps/r.li.mps.html

@@ -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>
@@ -18,36 +17,43 @@ 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>~/.grass7/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 input=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 input=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 input=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>
-</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>

raster/r.li/r.li.padcv/r.li.padcv.html

@@ -2,14 +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>
-  <img src="rlipadcv_formula2.png"> <br></li>
-  <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>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>
@@ -19,31 +19,38 @@ 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>~/.grass7/r.li/output/</tt> folder.
 <p>
-If input raster is not full of null values r.li.padcv returns a value &gt;=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 &gt;=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 input=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 input=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 input=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>
@@ -51,4 +58,3 @@ Commission from Faunalia Pontedera (PI), Italy (www.faunalia.it)
 
 <p>
 <i>Last changed: $Date$</i>
-

raster/r.li/r.li.padrange/r.li.padrange.html

@@ -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 input=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 @@ 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>~/.grass7/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 input=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 input=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 input=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>
-
+<i>Last changed: $Date$</i></p>

raster/r.li/r.li.padsd/r.li.padsd.html

@@ -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>
@@ -18,32 +18,37 @@ the <tt>~/.grass7/r.li/output/</tt> folder.
 <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 input=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 input=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 input=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)

raster/r.li/r.li.patchdensity/r.li.patchdensity.html

@@ -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 @@ 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>~/.grass7/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 input=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 input=my_map conf=my_conf out=my_out
+r.li.patchdensity input=my_map conf=my_conf output=my_out
 </pre></div>
 
 <p>
@@ -50,15 +45,20 @@ r.mapcalc "forests = if(landcover.30m >= 41 && landcover.30m <= 43, 1, null())"
 r.li.patchdensity forests conf=movwindow7 out=forests_p_dens7
 d.rast.leg forests_p_dens7
 
-r.to.vect forests out=forests type=area
+r.to.vect forests out=forests feature=area
 d.vect forests type=boundary
 </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
+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>
 

raster/r.li/r.li.patchnum/r.li.patchnum.html

@@ -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 @@ 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>~/.grass7/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 input=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 input=my_map conf=my_conf out=my_out
+r.li.patchnum input=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 input=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>

raster/r.li/r.li.pielou/r.li.pielou.html

@@ -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 @@ 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>~/.grass7/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 input=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 input=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. (<a href="http://treesearch.fs.fed.us/pubs/3064">PDF</a>)
+# forest map example:
+g.region rast=landcover.30m -p
+r.mapcalc "forests = if(landcover.30m >= 41 && landcover.30m <= 43,1,null())"
+r.li.pielou input=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>,
+<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>
 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>
-

raster/r.li/r.li.renyi/r.li.renyi.html

@@ -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 @@ 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>~/.grass7/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 input=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 input=my_map conf=my_conf output=my_out alpha=0.6
-</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. (<a href="http://treesearch.fs.fed.us/pubs/3064">PDF</a>)
+# forest map example:
+g.region rast=landcover.30m -p
+r.mapcalc "forests = if(landcover.30m >= 41 && landcover.30m <= 43,1,null())"
+r.li.renyi input=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>,
+<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>
 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 @@ Computer Science University of Pisa (Italy).<br>
 
 <p>
 <i>Last changed: $Date$</i>
-

raster/r.li/r.li.richness/r.li.richness.html

@@ -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 @@ 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>~/.grass7/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 input=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 input=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.richness input=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>
+<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>
-

raster/r.li/r.li.setup/r.li.setup.html

@@ -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, 
@@ -14,25 +14,27 @@ in your choices.
 
 Definition of region for analysis:
 <ul>
-<li> Whole map layer: entire map (current region),
-<li> Keyboard setting: based on keyboard selection for region definition,
-<li> Draw the sampling frame: based on interactive region selection via mouse.
+  <li> Whole map layer: entire map (current region),</li>
+  <li> Keyboard setting: based on keyboard selection for region definition,</li>
+  <li> Draw the sampling frame: based on interactive region selection via mouse.</li>
 </ul>
 
 Definition of creation of sampling area:
 <ul>
-<li> Whole map layer: use entire area selected above,
-<li> Regions: select one to many subareas via mouse,
-<li> Sample units: automated selection of sampling area (for details see below)
-<ul>
-  <li> Random nonoverlapping,
-  <li> Systematic contiguous,
-  <li> Systematic noncontiguous,
-  <li> Stratified random,
-  <li> Centered over sites (vector points).
-</ul>
-<li> Moving window: rectagular or circular with size
-<li> Select areas from the overlaid vector map (for details see below)
+  <li> Whole map layer: use entire area selected above,</li>
+  <li> Regions: select one to many subareas via mouse,</li>
+  <li> Sample units: automated selection of sampling area (for details see below)</li>
+
+  <ul>
+    <li> Random nonoverlapping,</li>
+    <li> Systematic contiguous,</li>
+    <li> Systematic noncontiguous,</li>
+    <li> Stratified random,</li>
+    <li> Centered over sites (vector points).</li>
+  </ul>
+
+  <li> Moving window: rectangular or circular with size</li>
+  <li> Select areas from the overlaid vector map (for details see below)</li>
 </ul>
 
 <img src="sampleAreas.jpg" alt="Sampling area definition">
@@ -41,110 +43,180 @@ Definition of creation of sampling area:
 <h3>Usage details</h3>
 
 The startup window shows your configuration files, you can: 
+
 <ol>
 <li><em><b>Load a file</b></em>: the configuration is printed using 
-rectangles with differents colors (green for the raster map, 
-red for the sample 
-frame and blue for the sample areas), and other notes (disposition of 
-sample areas etc).
-The configuration file is saved in <tt>~/.grass7/r.li/my_conf</tt>
-(the file name can be defined by the user).
-<!-- NOT REALLY CLEAR: -->
-Configuration output files are raster if moving window disposition was
-selected, otherwise they are in <tt>~/.grass7/r.li/output</tt> folder.
-<br> 
-All dimension are percentage of raster rows or columns.
-<li><em><b>Create a new file:</b></em> this create a new configuration 
-file in an interactive way, in three steps
-     <ol> 
-     <li> Choose file name and maps to use for setting:
-          <ul>
+ rectangles with differents colors (green for the raster map, red for 
+ the sample frame and blue for the sample areas), and other notes 
+ (disposition of sample areas etc). The configuration file is saved 
+ in <tt>~/.r.li/history/my_conf</tt> (the file name can be defined by 
+ the user). The output can either be a new raster map (in case of 
+ using a "moving window" analysis) or be an ASCII text file (when not 
+ performing a "moving window" analysis) containing the result which 
+ is then saved to the folder <tt>~/.grass7/r.li/output/</tt>.
+ <br>
+ <!-- TODO: applies to all output or only ASCII output?? -->
+ All dimensions are percentages of raster rows or columns.</li>
+
+ <li><em><b>Create a new file:</b></em> this create a new configuration 
+ file in an interactive way, in three steps:</li>
+
+  <ol> 
+     <li> Choose file name and maps to use for setting:</li>
+	<ul>
 	  <li> <em>Configuration file name </em>(required): the name
-	  of new configuration file
-	  <li> <em>Raster map name</em> (required): the name of raster
-	  map to use for setting
+	  of new configuration file</li>
+	  <li> <em>Raster map name to use to select areas</em> (required): the name of raster
+	  map to use for setting <!-- TODO: ... map to be analysed?? --></li>
 	  <li> <em>Vector areas map to overlay</em> (optional): name of a vector 
-	  map to overlay in setting
+	  map to overlay in setting</li>
 	  <li> <em>Vector points map to overlay</em> (optional): name of vector map 
-	  of points type to overlay in setting
-	  </ul>
+	  of points type to overlay in setting</li>
+	</ul>
+
      <li> Set the sampling frame. The sample frame is a rectangular area 
      which contains all the areas to analyze. It can be defined in three 
-     ways: 
-          <ul>
-	  <li><em>Whole map layer</em>: the sample frame is the whole map
-	  <li><em>Keyboard setting</em>: the user enters the coordinates in
-	  cells of upper left corner of sampling frame and its length in
-	  rows and columns.
-	  <li><em>Draw the sample frame</em>: the user draws the sample frame
-	  on map using mouse.
-	  </ul>
+     ways: </li>
+	<ul>
+	   <li><em>Whole map layer</em>: the sample frame is the whole map</li>
+	   <li><em>Keyboard setting</em>: the user enters the coordinates in
+	   cells of upper left corner of sampling frame and its length in
+	   rows and columns.</li>
+	   <li><em>Draw the sample frame</em>: the user draws the sample frame
+	   on map using mouse.</li>
+	</ul>
+
      <li> Set the sample areas. The sample areas are simply the areas to 
-     analyze. They can be defined in five ways (see the picture below):
-          <ul>
+       analyze. They can be defined in five ways (see the picture below):</li>
+	<ul>
 	  <li><em>Whole map layer</em>: the sample area is the whole sample 
-	  frame
+	  frame</li>
 	  <li><em>Regions</em>: the user enters the number of areas and then 
-	  draws them using mouse. 
+	  draws them using mouse.</li> 
 	  <li><em>Sample units</em>: they are areas of rectangular or circular 
-	  shape. The user can define them using keyboard or mouse.
-	      <ul>
+	  shape. The user can define them using keyboard or mouse.</li>
+
+	   <ul>
 	      <li>keyboard: the user define the shape of sample unists and 
-	      their disposition: 
+	      their disposition:</li>
 	          <ul>
-		  <li><em>Random non overlapping</em>: the user specifies 
+		    <li><em>Random non overlapping</em>: the user specifies 
 		  the number of sample units and they are placed in a 
-		  random way at runtime. It is guaranted that the 
-		  areas do not intersect themselfs.
-		  <li><em>Systematic contiguous</em>: the defined sample
+		  random way at runtime. It is guaranteed that the 
+		  areas do not intersect themselves.</li>
+		    <li><em>Systematic contiguous</em>: the defined sample
 		  is placed covering the sample frame, side by side 
-		  across rows.
-		  <li><em>Systematic non contiguous</em>: the same as above, 
+		  across rows.</li>
+		    <li><em>Systematic non contiguous</em>: the same as above, 
 		  but here ever rectangle is spaced from another by
-		  a specified number of cells
-		  <li><em>Stratified random</em>: the sample frame is
-		  divided in n strats of rows and m strats of columns 
-		  (n and m are given by user), then the specified 
+		  a specified number of cells.</li>
+		    <li><em>Stratified random</em>: the sample frame is
+		  divided in <i>n</i> strats of rows and <i>m</i> strats of columns 
+		  (<i>n</i> and <i>m</i> are given by user), then the specified 
 		  number of sample areas are placed in a random way, 
-		  one for every m*n areas defined by strats.
-		  <li><em>Centered over sites</em>: the sample areas
+		  one for every <i>m*n</i> areas defined by strats.</li>
+		    <li><em>Centered over sites</em>: the sample areas
 		  are placed into sample frame centering them on points 
-		  in site file. 
+		  in site file.</li>
 		  </ul>
 	      <li>mouse: the user chooses the shape and then draws the 
-	      specified number of sample areas on map.
-	      </ul>
-	    </ul>
-	 <li><em>Moving Window:</em> the user defines a rectangular or 
+	      specified number of sample areas on map.</li>
+	   </ul>
+
+	   <li><em>Moving Window:</em> the user defines a rectangular or 
 	 circular area, it is moved over all the raster increasing only
 	 of a cell for every move(in columns if possible, if not in rows). 
-	 It produces a new raster containing the result of all analysis.
-	 <li><em>Select areas from the overlaid vector map</em>: 
+	 It produces a new raster containing the result of all analysis.</li>
+	   <li><em>Select areas from the overlaid vector map</em>: 
 	 the sample areas are defined by the vector map selected above.
 	 For every cat in vector map, the procedure prompts the 
 	 user if he wants to include it as sample area.
 	 The resulting configuration file can be used only with the 
 	 specified raster map, and the procedure can be used only if
-	 whole map layer is selected as sampling frame.
+	 whole map layer is selected as sampling frame.</li>
+	</ul>
    </ol>
-<li><em><b>Remove a file</b></em> the selected file is deleted from the
-available configuration files.
-<li><em><b>Help</b></em>: open this help text.
-<li><em><b>Close</b></em> module window.
+
+  <li><em><b>Remove a file</b></em> the selected file is deleted from the
+   available configuration files.</li>
+  <li><em><b>Help</b></em>: open this help text.</li>
+  <li><em><b>Close</b></em> module window.</li>
 </ol>
 
+<h2>EXAMPLES</h2>
+
+<h3>Moving window analysis on full region</h3>
+
+Example for a 7x7 moving window analysis on full region:
+
+<ul>
+<li> Click on "New"</li>
+ <ul>
+  <li> Configuration file name: "movwindow7"</li>
+  <li> Raster map name to use to select areas: "forests"</li>
+ </ul>
+</ul>
+
+1. Setup sampling frame:
+<ul>
+<li> Define a sampling frame (region for analysis): "Whole map layer", then "OK"</li>
+</ul>
+
+2. Setup sampling frame
+<ul>
+<li> Define sampling areas: "Moving window", then "OK"</li>
+<li> Then click on "Use keyboard to define moving window dimension"</li>
+<ul>
+ <li>Select type of shape</li>
+ <ul>
+  <li> [x] Rectangular</li>
+  <li> Width size (in cells)?: "7"</li>
+  <li> Height size (in cells)?: "7"</li>
+  <li> Then "Save settings"</li>
+ </ul>
+ </ul>
+</ul>
+
+3. Save settings: click on button
+<br>
+(4.) Close
+<p>
+Now an anaysis can be performed using one of the analytical modules, e.g.
+<div class="code"><pre>
+r.li.patchdensity input=forests conf=movwindow7 output=forests_p_dens7
+</pre></div>
+
+The result is a new raster map "forests_p_dens7".
+<br>
+See the respective modules for further examples.
+
+<!-- TODO: add configuration example which results in ASCII output rather than raster map -->
+
 <h2>NOTES</h2>
+
 Configuration files are raster map independent because areas are saved using 
 relative coordinates.
 
+
 <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.daemon.html">r.li.daemon</a></em>,
-<em><a href="r.li.patchdensity.html">r.li.patchdensity</a></em>
+
+<em>
+<a href="r.li.html">r.li</a> - package overview<br>
+<a href="r.li.daemon.html">r.li.daemon</a>
+</em>
+<p>
+<em>
+<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>
-Claudio Porta and Lucio Davide Spano, students of Computer Science 
+
+Claudio Porta and Lucio Davide Spano, students of Computer Science<br>
 University of Pisa (Italy).<br>
 Commission from Faunalia Pontedera (PI)<br>
 Rebuild of <em>r.le.setup</em> from William L. Baker

raster/r.li/r.li.shannon/r.li.shannon.html

@@ -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 @@ Do not use absolute path names for the <b>output</b> map/file.
 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>~/.grass7/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 input=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 input=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 input=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>
@@ -50,4 +58,3 @@ Commission from Faunalia Pontedera (PI), Italy (www.faunalia.it)
 
 <p>
 <i>Last changed: $Date$</i>
-

raster/r.li/r.li.shape/r.li.shape.html

@@ -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 @@ 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>~/.grass7/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 input=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 input=my_map conf=my_conf out=my_out
+r.li.shape input=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 input=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

raster/r.li/r.li.simpson/r.li.simpson.html

@@ -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 @@ 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>~/.grass7/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 input=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 input=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 input=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)