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mulTree: v1.2

Thomas Guillerme; Kevin Healy


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&lt;li&gt;2016/01/22  - &lt;strong&gt;v1.2&lt;/strong&gt;

&lt;ul&gt;
&lt;li&gt;complete new architectural structure!&lt;/li&gt;
&lt;li&gt;all the functions are now unit tested!&lt;/li&gt;
&lt;li&gt;all manuals are now written in Roxygen2 format!&lt;/li&gt;
&lt;li&gt;many functions arguments names have been modified, please check individual functions manual.&lt;/li&gt;
&lt;li&gt;
rTreeBind is renamed to tree.bind.&lt;/li&gt;
&lt;li&gt;In as.mulTree, the argument species is now taxa.&lt;/li&gt;
&lt;li&gt;
mulTree output: when output chain name already exists in current directory, the function now asks if user wants to overwrite the existing files.&lt;/li&gt;
&lt;li&gt;In read.mulTree, the argument mulTree.mcmc is now mulTree.chain.&lt;/li&gt;
&lt;li&gt;In summary.mulTree, the argument mulTree.mcmc is now mulTree.results and the argument CI is now prob.&lt;/li&gt;
&lt;li&gt;
summary.mulTree now outputs a c(&amp;quot;matrix&amp;quot;, &amp;quot;mulTree&amp;quot;) class object.&lt;/li&gt;
&lt;li&gt;In plot.mulTree, the argument mulTree.mcmc must now be an object returned from summary.mulTree.&lt;/li&gt;
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