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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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  <identifier identifierType="DOI">10.5281/zenodo.46188</identifier>
  <creators>
    <creator>
      <creatorName>Thibaut Jombart</creatorName>
      <affiliation>Imperial College London</affiliation>
    </creator>
    <creator>
      <creatorName>Zhian N. Kamvar</creatorName>
      <affiliation>Oregon State University</affiliation>
    </creator>
    <creator>
      <creatorName>Roman Luštrik</creatorName>
      <affiliation>PhD student</affiliation>
    </creator>
    <creator>
      <creatorName>Klaus Schliep</creatorName>
    </creator>
    <creator>
      <creatorName>Vladimir Mikryukov</creatorName>
      <affiliation>IPAE</affiliation>
    </creator>
    <creator>
      <creatorName>Brian Knaus</creatorName>
      <affiliation>USDA-Agricultural Research Service</affiliation>
    </creator>
  </creators>
  <titles>
    <title>adegenet: adegenet version 2.0.1</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2016</publicationYear>
  <dates>
    <date dateType="Issued">2016-02-17</date>
  </dates>
  <resourceType resourceTypeGeneral="Software"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/46188</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsSupplementTo">https://github.com/thibautjombart/adegenet/tree/2.0.1</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.592811</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsPartOf">https://zenodo.org/communities/zenodo</relatedIdentifier>
  </relatedIdentifiers>
  <version>2.0.1</version>
  <rightsList>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&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;</description>
  </descriptions>
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