r.li manual: describe where config files are stored; minor cleanup

git-svn-id: https://svn.osgeo.org/grass/grass/trunk@61665 15284696-431f-4ddb-bdfa-cd5b030d7da7

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

@@ -22,10 +22,13 @@ consider in the calculation. Each row must be saved using this syntax:<br>
 
 <h2>NOTES</h2>
 
-Do not use absolute path names for the <b>output</b> map/file.
+Do not use absolute path names for the <b>config</b> and <b>output</b>
+file/map parameters.
+
 If the "moving window" method was selected in <b>g.gui.rlisetup</b>, then the
 output will be a raster map, otherwise an ASCII file will be generated in
-the <tt>$HOME/.grass7/r.li/output/</tt> folder.
+the folder <tt>C:\Users\normal\AppData\Roaming\GRASS7\r.li\output\</tt>
+(MS-Windows) or <tt>$HOME/.grass7/r.li/output/</tt> (GNU/Linux).
 <p>
 <!-- TODO: verify next: -->
 If the sample area contains only NULL values it is considered to

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

@@ -12,10 +12,13 @@ patch type <i>i</i> </li>
 
 <h2>NOTES</h2>
 
-Do not use absolute path names for the <b>output</b> map/file.
+Do not use absolute path names for the <b>config</b> and <b>output</b>
+file/map parameters.
+
 If the "moving window" method was selected in <b>g.gui.rlisetup</b>, then the
 output will be a raster map, otherwise an ASCII file will be generated in
-the <tt>$HOME/.grass7/r.li/output/</tt> folder.
+the folder <tt>C:\Users\normal\AppData\Roaming\GRASS7\r.li\output\</tt>
+(MS-Windows) or <tt>$HOME/.grass7/r.li/output/</tt> (GNU/Linux).
 <p>
 <!-- TODO: verify next: -->
 If the input raster map contains only NULL values then 

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

@@ -24,10 +24,13 @@ The unit is meters per hectare.
 
 <h2>NOTES</h2>
 
-Do not use absolute path names for the <b>output</b> map/file.
+Do not use absolute path names for the <b>config</b> and <b>output</b>
+file/map parameters.
+
 If the "moving window" method was selected in <b>g.gui.rlisetup</b>, then the
 output will be a raster map, otherwise an ASCII file will be generated in
-the <tt>$HOME/.grass7/r.li/output/</tt> folder.
+the folder <tt>C:\Users\normal\AppData\Roaming\GRASS7\r.li\output\</tt>
+(MS-Windows) or <tt>$HOME/.grass7/r.li/output/</tt> (GNU/Linux).
 <p>
 <!-- TODO: verify next: -->
 If the input raster map contains only NULL values then <em>r.li.edgedensity</em>

raster/r.li/r.li.html

@@ -2,10 +2,12 @@
 <h2>DESCRIPTION</h2>
 
 The <em>r.li</em> suite is a toolset for multiscale analysis of landscape structure.
-<!-- rephrase reference to r.le which is long time ago ...-->
+<!-- rephrase reference to r.le which is long time ago ...
 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).
+multiprocess implementation.
+-->
+It aims at implementing metrics as found in external software for quantitative
+measures of landscape structure like 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
@@ -27,30 +29,28 @@ 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>
+<h2>NOTES</h2>
+
 The general procedure to calculate an index from a raster map is two-fold:
 
 <ol>
-<li>run <em>g.gui.rlisetup</em>: create a configuration file selecting the parts of
-    raster to analyze.
+<li>run <em>g.gui.rlisetup</em>: create a configuration file selecting
+    the parts of raster map to be analyzed. This file allows to re-run
+    an analysis easily. It is stored on Windows in the directory <tt>C:\Users\normal\AppData\Roaming\GRASS7\r.li\</tt>, on GNU/Linux in
+    <tt>$HOME/.grass7/r.li/</tt>. <!-- TODO: and Mac OSX? -->
 
 <li>run one or more of the <em>r.li.<b>[index]</b></em> modules (e.g.,
     <em>r.li.<b>patchdensity</b></em>) to calculate the selected index
     using on the areas selected on configuration file.
 </ol>
 
-
-<h2>NOTE</h2>
-
-The <em>r.li.daemon</em> module also has a "main" function front-end
-which can be run, but it is only a template for development of new
-indices so not built by default.
 <!-- mhh ??: 
-The function itself has no meaning, it is only useful as an example and 
-for debugging.
+The <em>r.li.daemon</em> source code has a "main" function front-end
+which can be run, but it is only a template for development of new
+indices.
 -->
 
-<h2>EXAMPLE</h2>
+<h2>EXAMPLES</h2>
 
 Calculate a patch density index on the entire 'geology' raster map
 in the Spearfish sample dataset, using a 5x5 moving window:
@@ -116,7 +116,7 @@ configuration file on a 200x200 raster map, then the sample area is
 
 <b>Core modules</b>:
 <ul>
-  <li> <a href="r.li.daemon.html">r.li.daemon</a>: job launch daemon</li>
+  <li> <a href="r.li.daemon.html">r.li.daemon</a>: job launch daemon (not visible to the user)</li>
   <li> <a href="g.gui.rlisetup.html">g.gui.rlisetup</a>: Configuration editor for r.li.'index'</li>
 </ul>
 

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

@@ -13,10 +13,13 @@ with:<br>
 
 <h2>NOTES</h2>
 
-Do not use absolute path names for the <b>output</b> map/file.
+Do not use absolute path names for the <b>config</b> and <b>output</b>
+file/map parameters.
+
 If the "moving window" method was selected in <b>g.gui.rlisetup</b>, then the
 output will be a raster map, otherwise an ASCII file will be generated in
-the <tt>$HOME/.grass7/r.li/output/</tt> folder.
+the folder <tt>C:\Users\normal\AppData\Roaming\GRASS7\r.li\output\</tt>
+(MS-Windows) or <tt>$HOME/.grass7/r.li/output/</tt> (GNU/Linux).
 <p>
 <!-- TODO: verify next: -->
 If the input raster map contains only NULL values then <em>r.li.mpa</em> considers to

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

@@ -23,10 +23,13 @@ are ignored when tracing a patch.
 
 <h2>NOTES</h2>
 
-Do not use absolute path names for the <b>output</b> map/file.
+Do not use absolute path names for the <b>config</b> and <b>output</b>
+file/map parameters.
+
 If the "moving window" method was selected in <b>g.gui.rlisetup</b>, then the
 output will be a raster map, otherwise an ASCII file will be generated in
-the <tt>$HOME/.grass7/r.li/output/</tt> folder.
+the folder <tt>C:\Users\normal\AppData\Roaming\GRASS7\r.li\output\</tt>
+(MS-Windows) or <tt>$HOME/.grass7/r.li/output/</tt> (GNU/Linux).
 <p>
 If the sample area contains only NULL value cells, <em>r.li.mps</em>
 returns 0 (zero). <br>

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

@@ -14,10 +14,13 @@ with:<br>
 
 <h2>NOTES</h2>
 
-Do not use absolute path names for the <b>output</b> map/file.
+Do not use absolute path names for the <b>config</b> and <b>output</b>
+file/map parameters.
+
 If the "moving window" method was selected in <b>g.gui.rlisetup</b>, then the
 output will be a raster map, otherwise an ASCII file will be generated in
-the <tt>$HOME/.grass7/r.li/output/</tt> folder.
+the folder <tt>C:\Users\normal\AppData\Roaming\GRASS7\r.li\output\</tt>
+(MS-Windows) or <tt>$HOME/.grass7/r.li/output/</tt> (GNU/Linux).
 <p>
 The result is NULL if the sample area contains only NULL values.
 

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

@@ -15,10 +15,13 @@ are ignored when tracing a patch.
 
 <h2>NOTES</h2>
 
-Do not use absolute path names for the <b>output</b> map/file.
+Do not use absolute path names for the <b>config</b> and <b>output</b>
+file/map parameters.
+
 If the "moving window" method was selected in <b>g.gui.rlisetup</b>, then the
 output will be a raster map, otherwise an ASCII file will be generated in
-the <tt>$HOME/.grass7/r.li/output/</tt> folder.
+the folder <tt>C:\Users\normal\AppData\Roaming\GRASS7\r.li\output\</tt>
+(MS-Windows) or <tt>$HOME/.grass7/r.li/output/</tt> (GNU/Linux).
 <p>
 If the sample area contains only NULL values then <em>r.li.padrange</em>
 returns NULL.<br>

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

@@ -16,10 +16,13 @@ are ignored when tracing a patch.
 
 <h2>NOTES</h2>
 
-Do not use absolute path names for the <b>output</b> map/file.
+Do not use absolute path names for the <b>config</b> and <b>output</b>
+file/map parameters.
+
 If the "moving window" method was selected in <b>g.gui.rlisetup</b>, then the
 output will be a raster map, otherwise an ASCII file will be generated in
-the <tt>$HOME/.grass7/r.li/output/</tt> folder.
+the folder <tt>C:\Users\normal\AppData\Roaming\GRASS7\r.li\output\</tt>
+(MS-Windows) or <tt>$HOME/.grass7/r.li/output/</tt> (GNU/Linux).
 <p>
 The result is NULL if the sample area contains only NULL values.
 

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

@@ -18,10 +18,13 @@ are ignored when tracing a patch.
 
 <h2>NOTES</h2>
 
-Do not use absolute path names for the <b>output</b> map/file.
+Do not use absolute path names for the <b>config</b> and <b>output</b>
+file/map parameters.
+
 If the "moving window" method was selected in <b>g.gui.rlisetup</b>, then the
 output will be a raster map, otherwise an ASCII file will be generated in
-the <tt>$HOME/.grass7/r.li/output/</tt> folder.
+the folder <tt>C:\Users\normal\AppData\Roaming\GRASS7\r.li\output\</tt>
+(MS-Windows) or <tt>$HOME/.grass7/r.li/output/</tt> (GNU/Linux).
 <p>
 A sample area of only NULL values is considered to have zero patches, 
 that is, the result is always &ge; 0.

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

@@ -9,10 +9,13 @@ are ignored when tracing a patch.
 
 <h2>NOTES</h2>
 
-Do not use absolute path names for the <b>output</b> map/file.
+Do not use absolute path names for the <b>config</b> and <b>output</b>
+file/map parameters.
+
 If the "moving window" method was selected in <b>g.gui.rlisetup</b>, then the
 output will be a raster map, otherwise an ASCII file will be generated in
-the <tt>$HOME/.grass7/r.li/output/</tt> folder.
+the folder <tt>C:\Users\normal\AppData\Roaming\GRASS7\r.li\output\</tt>
+(MS-Windows) or <tt>$HOME/.grass7/r.li/output/</tt> (GNU/Linux).
 <p>
 If the sample area contains only NULL values then it is considered to 
 have zero patches. <br>

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

@@ -11,10 +11,13 @@ with:
 
 <h2>NOTES</h2>
 
-Do not use absolute path names for the <b>output</b> map/file.
+Do not use absolute path names for the <b>config</b> and <b>output</b>
+file/map parameters.
+
 If the "moving window" method was selected in <b>g.gui.rlisetup</b>, then the
 output will be a raster map, otherwise an ASCII file will be generated in
-the <tt>$HOME/.grass7/r.li/output/</tt> folder.
+the folder <tt>C:\Users\normal\AppData\Roaming\GRASS7\r.li\output\</tt>
+(MS-Windows) or <tt>$HOME/.grass7/r.li/output/</tt> (GNU/Linux).
 <p>
 <!-- TODO: verify next: -->
 If the input raster contains NULL value cells, <em>r.li.pielou</em>

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

@@ -14,10 +14,13 @@ patch type <i>i</i> </li>
 
 <h2>NOTES</h2>
 
-Do not use absolute path names for the <b>output</b> map/file.
+Do not use absolute path names for the <b>config</b> and <b>output</b>
+file/map parameters.
+
 If the "moving window" method was selected in <b>g.gui.rlisetup</b>, then the
 output will be a raster map, otherwise an ASCII file will be generated in
-the <tt>$HOME/.grass7/r.li/output/</tt> folder.
+the folder <tt>C:\Users\normal\AppData\Roaming\GRASS7\r.li\output\</tt>
+(MS-Windows) or <tt>$HOME/.grass7/r.li/output/</tt> (GNU/Linux).
 <p>
 <!-- TODO: verify next: -->
 If the input raster map contains only NULL values then <em>r.li.renyi</em>

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

@@ -12,10 +12,13 @@ with:
 
 <h2>NOTES</h2>
 
-Do not use absolute path names for the <b>output</b> map/file.
+Do not use absolute path names for the <b>config</b> and <b>output</b>
+file/map parameters.
+
 If the "moving window" method was selected in <b>g.gui.rlisetup</b>, then the
 output will be a raster map, otherwise an ASCII file will be generated in
-the <tt>$HOME/.grass7/r.li/output/</tt> folder.
+the folder <tt>C:\Users\normal\AppData\Roaming\GRASS7\r.li\output\</tt>
+(MS-Windows) or <tt>$HOME/.grass7/r.li/output/</tt> (GNU/Linux).
 <p>
 <!-- TODO: verify next: -->
 If the input raster map contains only NULL values then <em>r.li.richness</em>

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

@@ -1,6 +1,9 @@
 <h2>DESCRIPTION</h2>
 
-<em>g.gui.rlisetup</em>  creates and shows configuration files for the 
+<b>DEPRECATED: merge into gui/wxpython/rlisetup/g.gui.rlisetup.html</b>
+
+<p></p>
+<em>r.li.setup/</em>  creates and shows configuration files for the 
 other analytical <em>r.li</em> modules. For a general introduction, see 
 <a href="r.li.html">r.li</a>.
 <br>

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

@@ -12,10 +12,13 @@ patch type <i>i</i> </li>
 
 <h2>NOTES</h2>
 
-Do not use absolute path names for the <b>output</b> map/file.
+Do not use absolute path names for the <b>config</b> and <b>output</b>
+file/map parameters.
+
 If the "moving window" method was selected in <b>g.gui.rlisetup</b>, then the
 output will be a raster map, otherwise an ASCII file will be generated in
-the <tt>$HOME/.grass7/r.li/output/</tt> folder.
+the folder <tt>C:\Users\normal\AppData\Roaming\GRASS7\r.li\output\</tt>
+(MS-Windows) or <tt>$HOME/.grass7/r.li/output/</tt> (GNU/Linux).
 <p>
 <!-- TODO: verify next: -->
 If the input raster map contains only NULL values then <em>r.li.shannon</em>

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

@@ -13,10 +13,13 @@ with:
 
 <h2>NOTES</h2>
 
-Do not use absolute path names for the <b>output</b> map/file.
+Do not use absolute path names for the <b>config</b> and <b>output</b>
+file/map parameters.
+
 If the "moving window" method was selected in <b>g.gui.rlisetup</b>, then the
 output will be a raster map, otherwise an ASCII file will be generated in
-the <tt>$HOME/.grass7/r.li/output/</tt> folder.
+the folder <tt>C:\Users\normal\AppData\Roaming\GRASS7\r.li\output\</tt>
+(MS-Windows) or <tt>$HOME/.grass7/r.li/output/</tt> (GNU/Linux).
 <p>
 <!-- TODO: verify next: -->
 If the input raster map contains only NULL values then <em>r.li.shape</em>

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

@@ -12,10 +12,12 @@ patch type <i>i</i> </li>
 
 <h2>NOTES</h2>
 
-Do not use absolute path names for the <b>output</b> map/file.
+Do not use absolute path names for the <b>config</b> and <b>output</b>
+file/map parameters.
 If the "moving window" method was selected in <b>g.gui.rlisetup</b>, then the
 output will be a raster map, otherwise an ASCII file will be generated in
-the <tt>$HOME/.grass7/r.li/output/</tt> folder.
+the folder <tt>C:\Users\normal\AppData\Roaming\GRASS7\r.li\output\</tt>
+(MS-Windows) or <tt>$HOME/.grass7/r.li/output/</tt> (GNU/Linux).
 <p>
 <!-- TODO: verify next: -->
 If the input raster map contains only NULL values then <em>r.li.simpson</em>