r.li.* manuals: content standardization, HTML cosmetics

git-svn-id: https://svn.osgeo.org/grass/grass/trunk@58863 15284696-431f-4ddb-bdfa-cd5b030d7da7

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

@@ -17,6 +17,26 @@ 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>
 <small>patchType1,patchType2,dissimilarityBetweenPatchType1andPatchType2</small><br>
 
+
+<h2>NOTES</h2>
+
+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>~/.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>
+<div class="code"><pre>
+r.null setnull=-1 input=my_map
+</pre></div>
+after index calculation.<br>
+<br>
+
+
 <h2>EXAMPLES</h2>
 To calculate mean pixel attribute index on map my_map, using
 my_conf configuration file and saving results in
@@ -31,21 +51,6 @@ r.li.cwed input=my_map conf=my_conf path=my_file output=my_out
 56,12,0.54<br>
 23,66,0.99<br>
 
-<h2>NOTES</h2>
-Do not use absolute path names for output files. They are raster if
-moving window disposition was selected, otherwise they are in
-~/.r.li/output folder.
-<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>
-<div class="code"><pre>
-r.null setnull=-1 map=my_map
-</pre></div>
-after index calculation.<br>
-<br>
-
 <h2>REFERENCES</h2>
 McGarigal, K., and B. J. Marks. 1995. FRAGSTATS: spatial pattern
 analysis program for quantifying landscape structure. USDA For. Serv.
@@ -53,13 +58,14 @@ 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>
+<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>
+<i>Last changed: $Date$</i>
 

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

@@ -10,6 +10,7 @@
 <img src="grass_logo.png" alt="GRASS logo"><hr align=center size=6 noshade>
 
 <h2>NAME</h2>
+
 <em><b>libgrass_rli</b></em> - r.li landscape index support library
 
 <h2>DESCRIPTION</h2>
@@ -57,6 +58,7 @@ To write a new index only two steps are needed:
 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 
 execution. It is recommended to use 
 <br><div class="code"><pre>
@@ -69,12 +71,19 @@ 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.setup.html">r.li.setup</A></em>
+<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.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>
+
 Claudio Porta and Lucio Davide Spano, students of Computer Science 
 University of Pisa (Italy).<br>
 Commission from Faunalia Pontedera (PI)<br>

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

@@ -9,25 +9,32 @@ with: <br>
  <li><b>p<small><small>i</small></small></b>: proportion of the landscape occupied by patch type i<br></li>
 </ul>
 
-<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>
-<div class="code"><pre>
-r.li.dominance input=my_map conf=my_conf output=my_out
-</pre></div>
-
 <h2>NOTES</h2>
-Do not use absolute path names for output files. They are raster if
-moving window disposition was selected, otherwise they are in
-~/.r.li/output folder. <br>
 
+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>~/.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>
 <div class="code"><pre>
-r.null setnull=-1 map=my_map
+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>
+<div class="code"><pre>
+r.li.dominance 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>)
+
 <h2>SEE ALSO</h2>
 <em>
 <a href="r.li.html">r.li</a>

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

@@ -17,10 +17,22 @@
   <li> <b>Area</b>: total landscape area<br>
 </ul>
 
-<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>NOTES</h2>
+
+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>~/.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
+raster is masked.
+If you want to have null values instead run <br>
+<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
@@ -37,29 +49,20 @@ file run:<br>
 r.li.edgedensity input=my_map conf=my_conf output=my_out patch_type=34
 </pre></div>
 
-<h2>NOTES</h2>
-Do not use absolute path names for output files. They are raster if
-moving window disposition was selected, otherwise they are in
-~/.r.li/output folder.
-<br>
-If input raster is full of null values r.li.edgedensity consider to have 0
-patch.<br>
-If area is 0 r.li.edgedensity returns -1; this is possible only if input
-raster is masked.
-If you want to have null values instead run <br>
-<div class="code"><pre>
-r.null setnull=-1 map=my_map
-</pre></div>
-after index calculation.
-
 <h2>SEE ALSO</h2>
 <em>
 <a href="r.li.html">r.li</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>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.html

@@ -9,64 +9,59 @@
 
 <img src="grass_logo.png" alt="GRASS logo"><hr align=center size=6 noshade>
 
-
 <h2>NAME</h2>
 
 <em><b>r.li</b></em> - Landscape structure analysis package overview.
 
-
 <h2>KEYWORDS</h2>
-raster, landscape structure analysis, landscape metrics, landscape pattern, landscape analysis
+
+raster, landscape structure analysis, overview, landscape metrics, landscape pattern, landscape analysis
 
 
 <h2>DESCRIPTION</h2>
 
-The <em>r.li</em> suite is a toolset for multiscale analysis of landscape
-structure. It aims at replacing the <em>r.le</em> suite of modules
-through a client-server, multiprocess implementation. External software
-for quantitative measures of landscape structure is for example FRAGSTATS
-(McGarigal and Marks 1995).
+The <em>r.li</em> suite is a toolset for multiscale analysis of landscape structure.
+It aims at replacing the <em>r.le</em> suite of modules through a client-server,
+multiprocess implementation. External software for quantitative measures of landscape
+structure is for example FRAGSTATS (McGarigal and Marks 1995).
 <p>
-The <em>r.li</em> suite offers a set of patch and diversity indices. It
-supports analysis of landscapes composed of a mosaic of patches, but,
-more generally, the modules work with any two-dimensional raster map
-whose cell values are integer (e.g., 1, 2) or floating point (e.g., 1.1,
-3.2) values. The <em>r.li.setup</em> module has options for controlling
-the shape, size, number, and distribution of sampling areas used to
-collect information about the landscape structure. Sampling area shapes
-can be the entire map or a moving window of square, rectangular or with
-circular shape. The size of sampling areas can be changed, so that the
-landscape can be analyzed at a variety of spatial scales simultaneously.
-Sampling areas may be distributed across the landscape in a random,
-systematic, or stratified-random manner, or as a moving window.
+The <em>r.li</em> suite offers a set of patch and diversity indices.
+It supports analysis of landscapes composed of a mosaic of
+patches, but, more generally, the modules work with any two-dimensional
+raster map whose cell values are integer (e.g., 1, 2) or floating point
+(e.g., 1.1, 3.2) values. The <em>r.li.setup</em> module has options for
+controlling the shape, size, number, and distribution of sampling
+areas used to collect information about the landscape structure.
+Sampling area shapes can be the entire map or a moving
+window of square, rectangular or with circular shape. The size of
+sampling areas can be changed, so that the landscape can be analyzed
+at a variety of spatial scales simultaneously. Sampling areas may be
+distributed across the landscape in a random, systematic, or
+stratified-random manner, or as a moving window.
 <p>
 The <em>r.li</em> modules can calculate a number of measures that produce
-single values as output (e.g. mean patch size in the sampling area), as
-well as measures that produce a distribution of values as output (e.g.
-frequency distribution of patch sizes in the sampling area). The results
-are stored as raster maps.
+single values as output (e.g. mean patch size in the sampling area),
+as well as measures that produce a distribution of values as output
+(e.g. frequency distribution of patch sizes in the sampling area). The
+results are stored as raster maps.
 
 <p>
-The general procedure to calculate an index from a raster map is
-two-fold:
+The general procedure to calculate an index from a raster map is two-fold:
 
 <ol>
-<li>run <em>r.li.setup</em>: create a configuration file selecting the
-    parts of raster to analyze.
+<li>run <em>r.li.setup</em>: create a configuration file selecting the parts of
+    raster to analyze.
 
-<li>run <em>r.li.'index'</em> (e.g., <em>r.li.patchdensity</em>) for
-    calculate the selected index using on the areas selected on
-    configuration file.
+<li>run <em>r.li.'index'</em> (e.g., <em>r.li.patchdensity</em>) for calculate the selected
+    index using on the areas selected on configuration file.
 </ol>
 
+<h2>NOTE</h2>
 
-<h2>NOTES</h2>
-
-Also the <em>r.li.daemon</em> has a main function and it can be run, but
-it is only a template for development of new indices.
+Also the <em>r.li.daemon</em> has a main function and it can be run, but it is only a
+template for development of new indices.
 <!-- mhh ??: -->
-The function itself has no meaning, it can only be used for debugging.
-
+The function itself has no meaning, it can be used only for debug.
 
 <h2>EXAMPLE</h2>
 
@@ -81,10 +76,10 @@ Spearfish region, using a 5x5 moving window, follow this procedure:
   r.li.setup
 </pre></div>
   <li> The main <em>r.li.setup</em> window is displayed, click on "New"
-  <li> Now it is displayed the new configuration window, enter the
-	configuration file name (e.g., "my_conf", do not use absolute
-	paths)  and the name of raster map (e.g., "geology"). The other
-	fields are not needed for this configuration.
+  <li> Now it is displayed the new configuration window,
+	enter the configuration file name (e.g., "my_conf", do not use absolute paths) 
+	and the name of raster map (e.g., "geology").
+	The other fields are not needed for this configuration.
   <li> Click on "Setup sampling frame", select "Whole maplayer" and click "OK"
   <li> Click on "Setup sampling areas", select "Moving window" and click "OK"
   <li> Click on "Use keyboard to enter moving window dimension"
@@ -125,7 +120,6 @@ program rescale it automatically. For instance if you have selected a
 configuration file on a 200x200 raster map, then the sample area is
 10x10.
 
-
 <h2>SEE ALSO</h2>
 
 <b>Core modules</b>:

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

@@ -13,28 +13,36 @@ with:<br>
   </li>
 </ul>
 
-<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>
-<div class="code"><pre>
-r.li.mpa input=my_map conf=my_conf output=my_out
-</pre></div>
-
 <h2>NOTES</h2>
-Do not use absolute path names for output files. They are raster if
-moving window disposition was selected, otherwise they are in
-~/.r.li/output folder.<br>
+
+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>~/.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
 raster is masked <br>
 If you want to have null values instead run <br>
 <div class="code"><pre>
-r.null setnull=-1 map=my_map
+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>
+<div class="code"><pre>
+r.li.mpa 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>)
+
 <h2>SEE ALSO</h2>
 <em>
 <a href="r.li.html">r.li</a>

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

@@ -1,4 +1,5 @@
 <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>
@@ -10,6 +11,22 @@ with:
   </li>
 </ul>
 
+<h2>NOTES</h2>
+
+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>~/.r.li/output/</tt> folder.
+<p>
+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:
+<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
@@ -18,18 +35,10 @@ my_out file run:<br>
 r.li.mps input=my_map conf=my_conf output=my_out
 </pre></div>
 
-<h2>NOTES</h2>
-Do not use absolute path names for output files. They are raster if
-moving window disposition was selected, otherwise they are in
-~/.r.li/output folder.
-<br>
-If input raster is full of null values r.li.mps returns 0.<br>
-If you want to have null values instead run <br>
-<div class="code"><pre>
-r.null setnull=0 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. (<a href="http://treesearch.fs.fed.us/pubs/3064">PDF</a>)
 
 <h2>SEE ALSO</h2>
 <em>

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

@@ -12,34 +12,43 @@ with:<br>
   <li><b>N<small>patch</small></b>: number of patch<br></li>
 </ul>
 
-<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>
-<div class="code"><pre>
-r.li.padcv input=my_map conf=my_conf output=my_out
-</pre></div>
-
 <h2>NOTES</h2>
-Do not use absolute path names for output files. They are raster if
-moving window disposition was selected, otherwise they are in
-~/.r.li/output folder.<br>
+
+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>~/.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>
 <div class="code"><pre>
-r.null setnull=-1 map=my_map
+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>
+<div class="code"><pre>
+r.li.padcv input=my_map conf=my_conf output=my_out
+</pre></div>
+
 <h2>SEE ALSO</h2>
 <em>
 <a href="r.li.html">r.li</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>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.padrange/r.li.padrange.html

@@ -1,4 +1,5 @@
 <h2>DESCRIPTION</h2>
+
 <em>r.li.padrange</em>
  (patch area distribution range) calculates
 as:<br>
@@ -17,18 +18,19 @@ my_out file run:<br>
 r.li.padrange input=my_map conf=my_conf output=my_out
 </pre></div>
 
-
 <h2>NOTES</h2>
-Do not use absolute path names for output files. They are raster if
-moving window disposition was selected, otherwise they are in
-~/.r.li/output folder.<br>
-If input raster is not full of null values r.li.padrange returns a
-value &gt;=0 that is PADcv. <br>
-If input raster is full of null values r.li.padrange returns -1. <br>
-If you want to have null values instead run <br>
+
+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>~/.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:
 
 <div class="code"><pre>
-r.null setnull=-1 map=my_map
+r.null setnull=-1 input=my_map
 </pre></div>
 
 after index calculation.
@@ -47,5 +49,6 @@ Gen. Tech. Rep. PNW-351.
 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.padsd/r.li.padsd.html

@@ -1,4 +1,5 @@
 <h2>DESCRIPTION</h2>
+
 <em>r.li.padsd</em> (patch area distribution standard deviation) calculates as:<br>
 <img src="rlipadsd_formula.png"> <br>
 with:<br>
@@ -8,6 +9,23 @@ with:<br>
   <li><b>N<small>patch</small></b>: number of patch<br></li>
 </ul>
 
+<h2>NOTES</h2>
+
+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>~/.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>
+<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
@@ -16,19 +34,6 @@ my_out file run:<br>
 r.li.padsd input=my_map conf=my_conf output=my_out
 </pre></div>
 
-<h2>NOTES</h2>
-Do not use absolute path names for output files. They are raster if
-moving window disposition was selected, otherwise they are in
-~/.r.li/output folder.<br>
-If input raster is not full of null values r.li.padsd returns a value &gt;=0 that is PADsd. <br>
-If input raster is full of null values r.li.padsd returns -1. <br>
-If you want to have null values instead run <br>
-<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.
@@ -43,4 +48,5 @@ Gen. Tech. Rep. PNW-351.
 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.patchdensity/r.li.patchdensity.html

@@ -10,6 +10,23 @@ f(sample_area) = (Patch_Number/Area) * 1000000
 that is 1000000 by number of patch for area unit.
 This index is calculated using a 4 neighbour algorithm.
 
+<h2>NOTES</h2>
+
+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>~/.r.li/output/</tt> folder.
+<p>
+A map of NULL values is considered to have zero patches. <br>
+If you want to have null values instead run <br>
+<div class="code"><pre>
+r.null setnull=0 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.
+
 <h2>EXAMPLES</h2>
 
 To calculate patch density index on map <em>my_map</em>, using
@@ -37,26 +54,11 @@ r.to.vect forests out=forests type=area
 d.vect forests type=boundary
 </pre></div>
 
-
-<h2>NOTES</h2>
-
-A map of NULL values is considered to have zero patches. <br>
-If you want to have null values instead run <br>
-<div class="code"><pre>
-r.null setnull=0 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.
-
-
 <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></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>
 

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

@@ -1,9 +1,24 @@
 <h2>DESCRIPTION</h2>
+
 <em>r.li.patchnum</em> is a patch index for r.li program.<br>
 It calculates the function <br>
 <I> f(sample_area)= Patch_Number </I><br>
 This index is calculated using a 4 neighbour algorithm<br>
 
+<h2>NOTES</h2>
+
+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>~/.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>
+<div class="code"><pre>
+r.null setnull=0 input=my_map
+</pre></div>
+after index calculation.<br>
+
 <h2>EXAMPLES</h2>
 To calculate patch number index on map my_map, using 
 <em>my_conf</em> configuration file and saving results in
@@ -12,23 +27,20 @@ my_out file run:
 r.li.patchnumber input=my_map conf=my_conf out=my_out
 </pre></div>
 
-<h2>NOTES</h2>
-
-An that is full of null values is considered to have zero patch. <br>
-If you want to have null values instead run <br>
-<div class="code"><pre>
-r.null setnull=0 map=my_map
-</pre></div>
-after index calculation.<br>
+<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>
+<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>
 Commission from Faunalia Pontedera (PI) (www.faunalia.it)<br>
 
-<p><i>Last changed: $Date$</i>
+<p>
+<i>Last changed: $Date$</i>

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

@@ -10,16 +10,19 @@ with:
 </ul>
 
 <h2>NOTES</h2>
-Do not use absolute path names for output files. They are raster if
-moving window disposition was selected, otherwise they are in
-<tt>~/.r.li/output/</tt> folder.
-<br>
+
+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>~/.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>
 <div class="code"><pre>
-r.null setnull=-1 map=my_map
+r.null setnull=-1 input=my_map
 </pre></div>
 
 <h2>EXAMPLES</h2>
@@ -27,7 +30,7 @@ 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>
 <div class="code"><pre>
-r.li.pielou map=my_map conf=my_conf output=my_out
+r.li.pielou input=my_map conf=my_conf output=my_out
 </pre></div>
 
 <h2>REFERENCES</h2>
@@ -45,5 +48,6 @@ Gen. Tech. Rep. PNW-351. (<a href="http://treesearch.fs.fed.us/pubs/3064">PDF</a
 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>
+<p>
+<i>Last changed: $Date$</i>
 

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

@@ -1,4 +1,5 @@
 <h2>DESCRIPTION</h2>
+
 <em>r.li.renyi</em> 
 calculates the "renyi's diversity index" as:<br>
 <img src="r_li_renyi.png"> <br>
@@ -12,38 +13,29 @@ with: <br>
 </ul>
 
 <h2>NOTES</h2>
-Do not use absolute path names for output files. They are raster if
-moving window disposition was selected, otherwise they are in
-<tt>~/.r.li/output/</tt> folder.
-<br>
-If the input raster contains NULL value cells, <em>r.li.renyi</em>
-returns -1 for these cells. <br>
+
+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>~/.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:
-<br>
 <div class="code"><pre>
-r.null setnull=-1 map=my_map
+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>
 <div class="code"><pre>
-r.li.renyi map=my_map conf=my_conf output=my_out alpha=0.6
+r.li.renyi input=my_map conf=my_conf output=my_out alpha=0.6
 </pre></div>
 
-<h2>NOTES</h2>
-Do not use absolute path names for output files. They are raster if
-moving window disposition was selected, otherwise they are in
-~/.r.li/output folder. <br>
-
-If input raster is full of null values <em>r.li.renyi</em> returns -1.<br>
-If you want to have null values instead run <br>
-<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.
@@ -56,8 +48,10 @@ Gen. Tech. Rep. PNW-351. (<a href="http://treesearch.fs.fed.us/pubs/3064">PDF</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>
+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>
+<p>
+<i>Last changed: $Date$</i>
 

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

@@ -6,22 +6,26 @@ with: <br>
   <li><b>m</b>: number of different patch type</li>
 </ul>
 
+<h2>NOTES</h2>
+
+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>~/.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>
+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>
 <div class="code"><pre>
 r.li.richness input=my_map conf=my_conf output=my_out
 </pre></div>
 
-<h2>NOTES</h2>
-Do not use absolute path names for output files. They are raster if
-moving window disposition was selected, otherwise they are in
-~/.r.li/output folder. <br>
-
-If input raster is full of null values r.li.richness returns -1.<br>
-If you want to have null values instead run <br>
-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.
@@ -36,5 +40,6 @@ Gen. Tech. Rep. PNW-351.
 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.setup/r.li.setup.html

@@ -74,7 +74,7 @@ file in an interactive way, in three steps
 	  <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
+	  rows and columns.
 	  <li><em>Draw the sample frame</em>: the user draws the sample frame
 	  on map using mouse.
 	  </ul>
@@ -137,17 +137,16 @@ 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="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>
 
 <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
+Rebuild of <em>r.le.setup</em> from William L. Baker
 
 <p>
 <i>Last changed: $Date$</i>

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

@@ -6,38 +6,43 @@ with:<br>
 <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>p<small><small>i</small></small></b>: proportion of the landscape
+  occupied by patch type i<br></li>
 </ul>
 
-<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 shannon's diversity index on map my_map, using
-my_conf configuration file and saving results in my_out file run:<br>
-<div class="code"><pre>
-r.li.shannon input=my_map conf=my_conf output=my_out
-</pre></div>
-
 <h2>NOTES</h2>
-Do not use absolute path names for output files. They are raster if
-moving window disposition was selected, otherwise they are in
-~/.r.li/output folder. <br>
+
+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>~/.r.li/output/</tt> folder.
+<p>
 If input raster is full of null values r.li.shannon returns -1. <br>
 <!-- does that mean the program exit code or raster values?? -->
 If you want to have null values instead run <br>
 <div class="code"><pre>
-r.null setnull=-1 map=my_map
+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>
+<div class="code"><pre>
+r.li.shannon input=my_map conf=my_conf output=my_out
+</pre></div>
+
 <h2>SEE ALSO</h2>
 <em>
 <a href="r.li.html">r.li</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>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.shape/r.li.shape.html

@@ -3,6 +3,22 @@
 It calculates the function <br>
 <I> f(sample_area)= Area </I><br>
 
+<h2>NOTES</h2>
+
+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>~/.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>
+<div class="code"><pre>
+r.null setnull=-1 input=my_map
+</pre></div>
+
 <h2>EXAMPLES</h2>
 To calculate area index on map my_map, using 
 <em>my_conf</em> configuration file and saving results in
@@ -12,13 +28,19 @@ r.li.shape input=my_map conf=my_conf out=my_out
 </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></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>
 Claudio Porta and Lucio Davide Spano, students of Computer Science 
 University of Pisa (Italy).<br>
 Commission from Faunalia Pontedera (PI) (www.faunalia.it)<br>
 
-<p><i>Last changed: $Date$</i>
+<p>
+<i>Last changed: $Date$</i>

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

@@ -10,6 +10,21 @@ with: <br>
   occupied by patch type i<br> </li>
 </ul>
 
+<h2>NOTES</h2>
+
+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>~/.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>
+<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>
@@ -17,17 +32,10 @@ my_conf configuration file and saving results in my_out file run:<br>
 r.li.simpson input=my_map conf=my_conf output=my_out
 </pre></div>
 
-<h2>NOTES</h2>
-Do not use absolute path names for output files. They are raster if
-moving window disposition was selected, otherwise they are in
-~/.r.li/output folder. <br>
-
-If input raster is full of null values r.li.simpson returns -1.<br>
-If you want to have null values instead run <br>
-<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. (<a href="http://treesearch.fs.fed.us/pubs/3064">PDF</a>)
 
 <h2>SEE ALSO</h2>
 <em>
@@ -38,5 +46,5 @@ after index calculation.
 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>