[GRASS-SVN] r66154 - grass-addons/grass7/raster/r.biodiversity
svn_grass at osgeo.org
svn_grass at osgeo.org
Wed Sep 9 09:30:02 PDT 2015
Author: pvanbosgeo
Date: 2015-09-09 09:30:02 -0700 (Wed, 09 Sep 2015)
New Revision: 66154
Added:
grass-addons/grass7/raster/r.biodiversity/r.biodiversity.html
Removed:
grass-addons/grass7/raster/r.biodiversity/r_biodiversity.html
Log:
Sorry, typo in name html file
Copied: grass-addons/grass7/raster/r.biodiversity/r.biodiversity.html (from rev 66153, grass-addons/grass7/raster/r.biodiversity/r_biodiversity.html)
===================================================================
--- grass-addons/grass7/raster/r.biodiversity/r.biodiversity.html (rev 0)
+++ grass-addons/grass7/raster/r.biodiversity/r.biodiversity.html 2015-09-09 16:30:02 UTC (rev 66154)
@@ -0,0 +1,140 @@
+<h2>DESCRIPTION</h2>
+
+<p><em>r.biodiversity</em> computes one or more biodiversity indici
+based on 2 or more input layers. Each layer should represents a
+species (or other categories being used), and its raster values the
+species count. The name of the output layers will consist of the
+base name provided by the user.
+
+<p>Currently implemented are the Rényi entropy index and three
+specialized cases of the Renyi enthropy, viz.the species richness, the
+Shannon index and the Simpson index (Legendre & Legendre, 1998).
+
+<h4>The Renyi enthropy</h4>
+
+This index uantify 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
+( <i>alpha</i> = 0) is completely insensitive to species
+frequencies and is better known as species richness. Increasing the
+order diminishes the relative weights of rare species in the
+resulting index (Jost 2006, Legendre & Legendre 1998). The name of
+the output layer is composed of the basename + renyi + alpha.
+
+<h4>Species richness</h4>
+
+<p>The species richness is simply the count of the number of layers.
+It is a special case of the Reny enthropy: <pre>s = exp(R0)</pre>,
+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 basename +
+richness.
+
+<h4>Shannon index</h4>
+
+<p>The Shannon (also called the Shannon–Weaver or Shannon–Wiener)
+index is defined as <pre>H = -sum(p_i x log(p_i))</pre>, where <i>p_i
+</i> is the proportional abundance of species <i>i</i>. The
+r.biodiversity uses the natural logarithm (one can also use other
+bases for the log, but that is currently not implemented, and
+doesn't make a real difference). Note the Shannon index is a special
+case of the Renyi enthropy for <i>alpha = 2<i>. The name of the output
+layer is composed of the basename + shannon.
+
+<h4>Simpson (concentration) index</h4>
+
+<p>The Simpson's index is defined as <pre>D = sum p_i^2</pre>. This
+is equivalent to <pre>-1 * 1 / exp(R2)</pre>, with <i>R2</i> the renyi
+index for <i>alpha=2</i>. With this index, 0 represents infinite
+diversity and 1, no diversity. The name of the output
+layer is composed of the basename + simpson.
+
+<h4>Inverse Simpson index (Simpson's Reciprocal Index)</h4>
+
+<p>D obtains small values in datasets of high diversity and large
+values in datasets of low diversity. This is counterintuitive
+behavior for a diversity index. An alternative is the inverse
+Simpson index, which is <pre>ID = 1 / D)</pre>. The index represents
+the probability that two individuals randomly selected from a sample
+will belong to different species. The value ranges between 0 and 1,
+but now, the greater the value, the greater the sample diversity.
+The name of the output layer is composed of the basename + invsimpson.
+
+<h4>Gini–Simpson index</h4>
+
+<p>An alternative way to overcome the problem of the
+counter-intuitive nature of Simpson's Index is to use <pre>1 - D)</pre>. The lowest value of
+this index is 1 and represent a community containing only one
+species. The higher the value, the greater the diversity. The
+maximum value is the number of species in the sample. The name of the output
+layer is composed of the basename + ginisimpson.
+
+<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
+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
+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.
+
+<div class="code"><pre>
+r.mapcalc "spec1 = 60"
+r.mapcalc "spec2 = 10"
+r.mapcalc "spec3 = 25"
+r.mapcalc "spec4 = 1"
+r.mapcalc "spec5 = 4"
+</pre></div>
+
+Now we can calculate the renyi index for alpha is 0, 1 and 2 (this
+will give you 1.61, 1.06 and 0.83 respectively)
+
+<div class="code"><pre>
+r.biodiversity in=spec1,spec2,spec3,spec4,spec5 out=renyi alpha=0,1,2
+</pre></div>
+
+You can also compute the species richness, shannon, simpson, inverse
+simpson and gini-simpson indici
+
+<div class="code"><pre>
+r.biodiversity -s -h -d -p -g in=spec1,spec2,spec3,spec4,spec5 out=biodiversity
+</pre></div>
+
+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
+simpson should be 0.43, and inverse simpson and gini-simpson will be
+2.3 and 0.57 respectively.
+
+<h2>SEE ALSO</h2>
+1<em>
+<a href="r.li.html">r.li</a>,
+60 <a href="r.li.pielou.html">r.li.pielou</a>,
+61 <a href="r.li.renyi.html">r.li.renyi</a>,
+62 <a href="r.li.shannon.html">r.li.shannon</a>,
+63 <a href="r.li.simpson.html">r.li.simpson</a>
+</em>
+153
+
+<h2>CITATION</h2> <p>Suggested citation: <p>van Breugel P,
+r.biodiversity, a grass addon to compute biodiversity indici based
+on 2 or more input layers. Available from
+https://grass.osgeo.org/grass70/manuals/addons/r.biodiversity.html
+
+<h2>REFERENCES</h2>
+<ul>
+<li>Jost L. 2006. Entropy and diversity. Oikos 113:363–75</li>
+<li>Legendre P, Legendre L. 1998. Numerical Ecology. Second English edition. Elsevier, Amsterdam</li>
+</ul>
+
+
+<h2>AUTHOR</h2>
+Paulo van Breugel, paulo at ecodiv.org
+
+<p><i>Last changed: $Date$</i>
Deleted: grass-addons/grass7/raster/r.biodiversity/r_biodiversity.html
===================================================================
--- grass-addons/grass7/raster/r.biodiversity/r_biodiversity.html 2015-09-09 16:29:19 UTC (rev 66153)
+++ grass-addons/grass7/raster/r.biodiversity/r_biodiversity.html 2015-09-09 16:30:02 UTC (rev 66154)
@@ -1,140 +0,0 @@
-<h2>DESCRIPTION</h2>
-
-<p><em>r.biodiversity</em> computes one or more biodiversity indici
-based on 2 or more input layers. Each layer should represents a
-species (or other categories being used), and its raster values the
-species count. The name of the output layers will consist of the
-base name provided by the user.
-
-<p>Currently implemented are the Rényi entropy index and three
-specialized cases of the Renyi enthropy, viz.the species richness, the
-Shannon index and the Simpson index (Legendre & Legendre, 1998).
-
-<h4>The Renyi enthropy</h4>
-
-This index uantify 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
-( <i>alpha</i> = 0) is completely insensitive to species
-frequencies and is better known as species richness. Increasing the
-order diminishes the relative weights of rare species in the
-resulting index (Jost 2006, Legendre & Legendre 1998). The name of
-the output layer is composed of the basename + renyi + alpha.
-
-<h4>Species richness</h4>
-
-<p>The species richness is simply the count of the number of layers.
-It is a special case of the Reny enthropy: <pre>s = exp(R0)</pre>,
-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 basename +
-richness.
-
-<h4>Shannon index</h4>
-
-<p>The Shannon (also called the Shannon–Weaver or Shannon–Wiener)
-index is defined as <pre>H = -sum(p_i x log(p_i))</pre>, where <i>p_i
-</i> is the proportional abundance of species <i>i</i>. The
-r.biodiversity uses the natural logarithm (one can also use other
-bases for the log, but that is currently not implemented, and
-doesn't make a real difference). Note the Shannon index is a special
-case of the Renyi enthropy for <i>alpha = 2<i>. The name of the output
-layer is composed of the basename + shannon.
-
-<h4>Simpson (concentration) index</h4>
-
-<p>The Simpson's index is defined as <pre>D = sum p_i^2</pre>. This
-is equivalent to <pre>-1 * 1 / exp(R2)</pre>, with <i>R2</i> the renyi
-index for <i>alpha=2</i>. With this index, 0 represents infinite
-diversity and 1, no diversity. The name of the output
-layer is composed of the basename + simpson.
-
-<h4>Inverse Simpson index (Simpson's Reciprocal Index)</h4>
-
-<p>D obtains small values in datasets of high diversity and large
-values in datasets of low diversity. This is counterintuitive
-behavior for a diversity index. An alternative is the inverse
-Simpson index, which is <pre>ID = 1 / D)</pre>. The index represents
-the probability that two individuals randomly selected from a sample
-will belong to different species. The value ranges between 0 and 1,
-but now, the greater the value, the greater the sample diversity.
-The name of the output layer is composed of the basename + invsimpson.
-
-<h4>Gini–Simpson index</h4>
-
-<p>An alternative way to overcome the problem of the
-counter-intuitive nature of Simpson's Index is to use <pre>1 - D)</pre>. The lowest value of
-this index is 1 and represent a community containing only one
-species. The higher the value, the greater the diversity. The
-maximum value is the number of species in the sample. The name of the output
-layer is composed of the basename + ginisimpson.
-
-<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
-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
-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.
-
-<div class="code"><pre>
-r.mapcalc "spec1 = 60"
-r.mapcalc "spec2 = 10"
-r.mapcalc "spec3 = 25"
-r.mapcalc "spec4 = 1"
-r.mapcalc "spec5 = 4"
-</pre></div>
-
-Now we can calculate the renyi index for alpha is 0, 1 and 2 (this
-will give you 1.61, 1.06 and 0.83 respectively)
-
-<div class="code"><pre>
-r.biodiversity in=spec1,spec2,spec3,spec4,spec5 out=renyi alpha=0,1,2
-</pre></div>
-
-You can also compute the species richness, shannon, simpson, inverse
-simpson and gini-simpson indici
-
-<div class="code"><pre>
-r.biodiversity -s -h -d -p -g in=spec1,spec2,spec3,spec4,spec5 out=biodiversity
-</pre></div>
-
-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
-simpson should be 0.43, and inverse simpson and gini-simpson will be
-2.3 and 0.57 respectively.
-
-<h2>SEE ALSO</h2>
-1<em>
-<a href="r.li.html">r.li</a>,
-60 <a href="r.li.pielou.html">r.li.pielou</a>,
-61 <a href="r.li.renyi.html">r.li.renyi</a>,
-62 <a href="r.li.shannon.html">r.li.shannon</a>,
-63 <a href="r.li.simpson.html">r.li.simpson</a>
-</em>
-153
-
-<h2>CITATION</h2> <p>Suggested citation: <p>van Breugel P,
-r.biodiversity, a grass addon to compute biodiversity indici based
-on 2 or more input layers. Available from
-https://grass.osgeo.org/grass70/manuals/addons/r.biodiversity.html
-
-<h2>REFERENCES</h2>
-<ul>
-<li>Jost L. 2006. Entropy and diversity. Oikos 113:363–75</li>
-<li>Legendre P, Legendre L. 1998. Numerical Ecology. Second English edition. Elsevier, Amsterdam</li>
-</ul>
-
-
-<h2>AUTHOR</h2>
-Paulo van Breugel, paulo at ecodiv.org
-
-<p><i>Last changed: $Date$</i>
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