[GRASS-SVN] r66675 - grass-addons/grass7/raster/r.biodiversity
svn_grass at osgeo.org
svn_grass at osgeo.org
Fri Oct 30 07:27:56 PDT 2015
Author: neteler
Date: 2015-10-30 07:27:56 -0700 (Fri, 30 Oct 2015)
New Revision: 66675
Modified:
grass-addons/grass7/raster/r.biodiversity/r.biodiversity.html
Log:
r.biodiversity manual: fix HTML
Modified: grass-addons/grass7/raster/r.biodiversity/r.biodiversity.html
===================================================================
--- grass-addons/grass7/raster/r.biodiversity/r.biodiversity.html 2015-10-30 13:14:31 UTC (rev 66674)
+++ grass-addons/grass7/raster/r.biodiversity/r.biodiversity.html 2015-10-30 14:27:56 UTC (rev 66675)
@@ -1,6 +1,6 @@
<h2>DESCRIPTION</h2>
-<p><em>r.biodiversity</em> computes one or more biodiversity indici
+<em>r.biodiversity</em> computes one or more biodiversity indices
based on 2 or more input layers. Each layer should represents a
species (or other categories being used), and its raster values the
category count/value. The name of the output layers will consist of
@@ -12,7 +12,7 @@
<h4>The Renyi enthropy</h4>
-<p>This index uantify the diversity, uncertainty, or randomness of a
+This index quantify the diversity, uncertainty, or randomness of a
system. The user can define the order of diversity by setting the
order (<i>alpha</i>) value. The order of a diversity indicates its
sensitivity to common and rare species. The diversity of order zero
@@ -24,7 +24,7 @@
<h4>Species richness</h4>
-<p>The species richness is simply the count of the number of layers.
+The species richness is simply the count of the number of layers.
It is a special case of the Reny enthropy: <i>S = exp(R0)</i>,
whereby <i>S</i> is the species richness <i>R0</i> the renyi index
for <i>alpha=0</i>. The name of the output layer is composed of the
@@ -32,7 +32,7 @@
<h4>Shannon index</h4>
-<p>The Shannon (also called the Shannon-Weaver or Shannon-Wiener)
+The Shannon (also called the Shannon-Weaver or Shannon-Wiener)
index is defined as <i>H' = -sum(p_i x log(p_i))</i>, where <i>p_i
</i> is the proportional abundance of species <i>i</i>. The function
uses the natural logarithm (one can also use other bases for the
@@ -43,7 +43,7 @@
<h4>Effective number of species (ENS)</h4>
-<p>This option gives the Shannon index, converted to into equivalent
+This option gives the Shannon index, converted to into equivalent
or effective numbers of species (also known as Hill numbers) (Lou
Jost, 2006). The Shannon index, and other indice, can be converted
so they represent the number of equally abundant species necessary
@@ -52,16 +52,15 @@
is a more intuitive behavious, e.g., if two communities with equally
abundant but totally distinct species are combined, the ENS of the
combined community is twice that of the original communities. See
-for an explanation and examples this <a href=
-"http://www.loujost.com/Statistics%20and%20Physics/Diversity%20and%20S
-imilarity/EffectiveNumberOfSpecies.htm">blog post</a> or <a href=
-"http://jonlefcheck.net/2012/10/23/diversity-as-effective-numbers">
-this one</a>. The name of the output layer is composed of the
+for an explanation and examples this
+<a href="http://www.loujost.com/Statistics%20and%20Physics/Diversity%20and%20Similarity/EffectiveNumberOfSpecies.htm">blog post</a>
+or <a href="http://jonlefcheck.net/2012/10/23/diversity-as-effective-numbers">this one</a>.
+The name of the output layer is composed of the
basename + ens.
<h4>Pielou's eveness (equitability) index</h4>
-<p>Species evenness refers to how close in numbers each species in
+Species evenness refers to how close in numbers each species in
an environment are. The evenness of a community can be represented
by Pielou's evenness index, which is defined as <i>H' / Hmax</i>. H'
is the Shannon diversity index and Hmax the maximum value of H',
@@ -73,7 +72,7 @@
<h4>Inverse Simpson index (Simpson's Reciprocal Index)</h4>
-<p>The Simpson's index is defined as <i>D = sum p_i^2</i>. This is
+The Simpson's index is defined as <i>D = sum p_i^2</i>. This is
equivalent to <i>-1 * 1 / exp(R2)</i>, with <i>R2</i> the renyi
index for <i>alpha=2</i>. With this index, 0 represents infinite
diversity and 1, no diversity. This is counterintuitive behavior for
@@ -86,7 +85,7 @@
<h4>Gini-Simpson index</h4>
-<p>An alternative way to overcome the problem of the
+An alternative way to overcome the problem of the
counter-intuitive nature of Simpson's Index is to use <i>1 - D)</i>.
The lowest value of this index is 1 and represent a community
containing only one species. The higher the value, the greater the
@@ -96,16 +95,16 @@
<h2>NOTES</h2>
-<p>Note that if you are interested in the landscape diversity, you
-should have a look at the <a href=
-"https://grass.osgeo.org/grass70/manuals/addons/r.diversity.html">
-r.diversity</a> addon or the various related r.li.* addons (see
+Note that if you are interested in the landscape diversity, you
+should have a look at the
+<a href="https://grass.osgeo.org/grass70/manuals/addons/r.diversity.html">r.diversity</a>
+addon or the various related r.li.* addons (see
below). These functions requires one input layer and compute the
diversity using a moving window.
<h2>EXAMPLES</h2>
-<p>Suppose we have five layers, each representing number of
+Suppose we have five layers, each representing number of
individuals of a different species. To keep it simple, let's assume
individuals of all five species are homogeneous distributed, with
respectively 60, 10, 25, 1 and 4 individuals / raster cell densities.
@@ -126,10 +125,11 @@
</pre></div>
<p>You can also compute the species richness, shannon, simpson,
-inverse simpson and gini-simpson indici
+inverse simpson and gini-simpson indices
-<div class="code"><pre> r.biodiversity -s -h -d -p -g
-in=spec1,spec2,spec3,spec4,spec5 out=biodiversity </pre></div>
+<div class="code"><pre>
+r.biodiversity -s -h -d -p -g in=spec1,spec2,spec3,spec4,spec5 out=biodiversity
+</pre></div>
<p>The species richness you get should of course be 5. The shannon
index is the same as the renyi index with alpha=1 (1.06). The
@@ -138,11 +138,13 @@
<h2>SEE ALSO</h2>
-<a href="r.li.html">r.li</a>, <a href="r.li.pielou.html">r.li.pielou
-</a>, <a href="r.li.renyi.html">r.li.renyi</a>, <a href=
-"r.li.shannon.html">r.li.shannon</a>, <a href="r.li.simpson.html">
-r.li.simpson</a> are all add-ons that compute landscape diversity
-indici.
+<em>
+<a href="r.li.html">r.li</a>,
+<a href="r.li.pielou.html">r.li.pielou</a>,
+<a href="r.li.renyi.html">r.li.renyi</a>,
+<a href="r.li.shannon.html">r.li.shannon</a>,
+<a href="r.li.simpson.html">r.li.simpson</a>
+</em>
<h2>REFERENCES</h2>
<ul>
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