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<!DOCTYPE html>
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<head>
<meta charset="utf-8">
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<title>EcoSimR</title>
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<a class="navbar-brand" href="index.html">EcoSimR 0.1.0</a>
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<li><a href="index.html"><i class="icon-home icon-white"></i><span class="glyphicon glyphicon-home"> </span> Home</a></li>
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<div id="header">
<h1 class="title">EcoSimR</h1>
</div>
<p><strong>A software package to fit ecological null models</strong></p>
<div id="overview" class="section level3">
<h3>Overview</h3>
<p>EcoSimR is an open source R version of the <a href="">EcoSim software project</a>, details about the package can be found in the <a href="http://docs.ecosimr.org">full documentation</a></p>
</div>
<div id="quickstart" class="section level3">
<h3>Quickstart</h3>
<pre class="r"><code>## Install development version
install.packages("devtools")
library(devtools)
install_github("gotellilab/EcoSimR")</code></pre>
<p><em>Co-Occurrence null model</em></p>
<p>Data for co-occurrence null models should be a species by site matrix of incidence data.</p>
<table>
<caption>West Indian Finch Data</caption>
<thead>
<tr class="header">
<th align="left">Species</th>
<th align="right">Cuba</th>
<th align="right">Hispaniola</th>
<th align="right">Jamaica</th>
<th align="right">Puerto_Rico</th>
<th align="right">Guadeloupe</th>
<th align="right">Martinique</th>
<th align="right">Dominica</th>
<th align="right">St_Lucia</th>
<th align="right">Barbados</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td align="left">Carduelis_dominicensis</td>
<td align="right">0</td>
<td align="right">1</td>
<td align="right">0</td>
<td align="right">0</td>
<td align="right">0</td>
<td align="right">0</td>
<td align="right">0</td>
<td align="right">0</td>
<td align="right">0</td>
</tr>
<tr class="even">
<td align="left">Loxia_leucoptera</td>
<td align="right">0</td>
<td align="right">1</td>
<td align="right">0</td>
<td align="right">0</td>
<td align="right">0</td>
<td align="right">0</td>
<td align="right">0</td>
<td align="right">0</td>
<td align="right">0</td>
</tr>
<tr class="odd">
<td align="left">Volatinia_jacarina</td>
<td align="right">0</td>
<td align="right">0</td>
<td align="right">0</td>
<td align="right">0</td>
<td align="right">0</td>
<td align="right">0</td>
<td align="right">0</td>
<td align="right">0</td>
<td align="right">0</td>
</tr>
<tr class="even">
<td align="left">Sporophila_nigricollis</td>
<td align="right">0</td>
<td align="right">0</td>
<td align="right">0</td>
<td align="right">0</td>
<td align="right">0</td>
<td align="right">0</td>
<td align="right">0</td>
<td align="right">0</td>
<td align="right">0</td>
</tr>
<tr class="odd">
<td align="left">Melopyrrha_nigra</td>
<td align="right">1</td>
<td align="right">0</td>
<td align="right">0</td>
<td align="right">0</td>
<td align="right">0</td>
<td align="right">0</td>
<td align="right">0</td>
<td align="right">0</td>
<td align="right">0</td>
</tr>
</tbody>
</table>
<p><code>EcoSimR</code> provides an easy way to plot and summarize output. We’ll use the <em>SIM9</em> algorithm (See table 2 Gotelli 2000) and the C-Score metric (Stone and Roberts 1990).</p>
<pre class="r"><code>finchMod <- cooc_null_model(dataWiFinches, algo="sim9",nReps=10000,burn_in = 500)</code></pre>
<pre class="r"><code>## Summary and plot info
summary(finchMod)</code></pre>
<pre><code>## Time Stamp: Mon Mar 23 22:30:11 2015
## Reproducible:
## Number of Replications:
## Elapsed Time: 1.7 secs
## Metric: c_score
## Algorithm: sim9
## Observed Index: 3.7941
## Mean Of Simulated Index: 2.756
## Variance Of Simulated Index: 0.027207
## Lower 95% (1-tail): 2.5294
## Upper 95% (1-tail): 3.0662
## Lower 95% (2-tail): 2.4926
## Upper 95% (2-tail): 3.1471
## Lower-tail P > 0.9999
## Upper-tail P < 1e-04
## Observed metric > 10000 simulated metrics
## Observed metric < 0 simulated metrics
## Observed metric = 0 simulated metrics
## Standardized Effect Size (SES): 6.2937</code></pre>
<pre class="r"><code>plot(finchMod,type="hist")</code></pre>
<p><img src="index_files/figure-html/coocnull-1.png" title="" alt="" width="480" style="display: block; margin: auto;" /></p>
<p>See a plot of the actual matrix compared to a single simulated matrix</p>
<pre class="r"><code>plot(finchMod,type="cooc")</code></pre>
<p><img src="index_files/figure-html/unnamed-chunk-5-1.png" title="" alt="" width="576" style="display: block; margin: auto;" /></p>
</div>
<div id="references" class="section level3">
<h3>References</h3>
<p>Gotelli, N.J. 2000. Null model analysis of species co-occurrence patterns. <strong>Ecology</strong> 81: 2606-2621 <a href = "https://www.uvm.edu/~ngotelli/manuscriptpdfs/Ecology81p2606.pdf",target = _new><i class="fa fa-file-pdf-o"></i></a></p>
<p>Stone, Lewis and Roberts, Alan 1990. The checkerboard score and species distributions. <strong>Oecologia</strong> 85 (1): 74–79. <a href = "http://life.tau.ac.il/departments/zoology/members/stone/documents/checkerboardscoreandspecies.pdf", targe=_new><i class="fa fa-file-pdf-o"></i></a></p>
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