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adegenet: adegenet version 2.0.1

Thibaut Jombart; Zhian N. Kamvar; Roman Luštrik; Klaus Schliep; Vladimir Mikryukov; Brian Knaus


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    <dct:description>&lt;a class="anchor" href="#adegenet-version-201"&gt;&lt;span class="octicon octicon-link"&gt;&lt;/span&gt;&lt;/a&gt;Adegenet version 2.0.1 &lt;p&gt;This version contains a few new features, speedups, and bug fixes&lt;/p&gt; &lt;a class="anchor" href="#new-features"&gt;&lt;span class="octicon octicon-link"&gt;&lt;/span&gt;&lt;/a&gt;NEW FEATURES &lt;ul&gt; &lt;li&gt;&lt;p&gt;Hs() is now much faster and will scale better for large number of loci&lt;/p&gt;&lt;/li&gt; &lt;li&gt;&lt;p&gt;Hs.test() allows for testing differences in expected heterozygosity between two groups of individuals&lt;/p&gt;&lt;/li&gt; &lt;li&gt;&lt;p&gt;strata tutorial is now available via adegenetTutorial(which=&amp;quot;strata&amp;quot;)&lt;/p&gt;&lt;/li&gt; &lt;li&gt;&lt;p&gt;repool can now handle objects with no population information, and can return a list of repooled genind (argument 'list' defauling to FALSE)&lt;/p&gt;&lt;/li&gt; &lt;li&gt;&lt;p&gt;read.fstat() can now handle missing data coded by any number of &amp;quot;0&amp;quot;&lt;/p&gt;&lt;/li&gt; &lt;li&gt;&lt;p&gt;scatter.dapc() function can now label individuals using orditorp() function from vegan package, which takes care of overlapping (See issue #100)&lt;/p&gt;&lt;/li&gt; &lt;li&gt;&lt;p&gt;df2genind() is now faster at handling missing data (See issue #114)&lt;/p&gt;&lt;/li&gt; &lt;li&gt;&lt;p&gt;the summary method has better formatting&lt;/p&gt;&lt;/li&gt; &lt;/ul&gt; &lt;a class="anchor" href="#bug-fixes"&gt;&lt;span class="octicon octicon-link"&gt;&lt;/span&gt;&lt;/a&gt;BUG FIXES &lt;ul&gt; &lt;li&gt;&lt;p&gt;Hs() no longer returns NaN if one locus has not been typed; instead, computations are done using all available loci&lt;/p&gt;&lt;/li&gt; &lt;li&gt;&lt;p&gt;adegenetTutorial() now opens up-to-date tutorials&lt;/p&gt;&lt;/li&gt; &lt;li&gt;&lt;p&gt;subsetting genlight objects now treats missing data appropriately when given logical, character, or negative subscripts. (See issue #83)&lt;/p&gt;&lt;/li&gt; &lt;li&gt;&lt;p&gt;fixed occasional spurious warning about duplicated individual labels in df2genind()&lt;/p&gt;&lt;/li&gt; &lt;li&gt;&lt;p&gt;fixed issues with mis-placed missing data in df2genind() when samples were labeled with numbers (See issue #96)&lt;/p&gt;&lt;/li&gt; &lt;li&gt;&lt;p&gt;frequencies can now be obtained from P/A genpop objects (See issue #105)&lt;/p&gt;&lt;/li&gt; &lt;li&gt;&lt;p&gt;Windows no longer throws an error with as.genlight() (See issue #109)&lt;/p&gt;&lt;/li&gt; &lt;li&gt;&lt;p&gt;read.genpop() now returns individual names (See issue #117)&lt;/p&gt;&lt;/li&gt; &lt;/ul&gt;</dct:description>
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