There is a newer version of this record available.

Software Open Access

adegenet: adegenet version 2.0.1

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


MARC21 XML Export

<?xml version='1.0' encoding='UTF-8'?>
<record xmlns="http://www.loc.gov/MARC21/slim">
  <leader>00000nmm##2200000uu#4500</leader>
  <controlfield tag="005">20210717181048.0</controlfield>
  <controlfield tag="001">46188</controlfield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">Oregon State University</subfield>
    <subfield code="a">Zhian N. Kamvar</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">PhD student</subfield>
    <subfield code="a">Roman Luštrik</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="a">Klaus Schliep</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">IPAE</subfield>
    <subfield code="a">Vladimir Mikryukov</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">USDA-Agricultural Research Service</subfield>
    <subfield code="a">Brian Knaus</subfield>
  </datafield>
  <datafield tag="856" ind1="4" ind2=" ">
    <subfield code="s">10078223</subfield>
    <subfield code="z">md5:9b13f2ede4049462c7a941b261a61d2c</subfield>
    <subfield code="u">https://zenodo.org/record/46188/files/adegenet-2.0.1.zip</subfield>
  </datafield>
  <datafield tag="542" ind1=" " ind2=" ">
    <subfield code="l">open</subfield>
  </datafield>
  <datafield tag="260" ind1=" " ind2=" ">
    <subfield code="c">2016-02-17</subfield>
  </datafield>
  <datafield tag="909" ind1="C" ind2="O">
    <subfield code="p">software</subfield>
    <subfield code="p">user-zenodo</subfield>
    <subfield code="o">oai:zenodo.org:46188</subfield>
  </datafield>
  <datafield tag="100" ind1=" " ind2=" ">
    <subfield code="u">Imperial College London</subfield>
    <subfield code="a">Thibaut Jombart</subfield>
  </datafield>
  <datafield tag="245" ind1=" " ind2=" ">
    <subfield code="a">adegenet: adegenet version 2.0.1</subfield>
  </datafield>
  <datafield tag="980" ind1=" " ind2=" ">
    <subfield code="a">user-zenodo</subfield>
  </datafield>
  <datafield tag="540" ind1=" " ind2=" ">
    <subfield code="a">Other (Open)</subfield>
  </datafield>
  <datafield tag="650" ind1="1" ind2="7">
    <subfield code="a">cc-by</subfield>
    <subfield code="2">opendefinition.org</subfield>
  </datafield>
  <datafield tag="520" ind1=" " ind2=" ">
    <subfield code="a">&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;</subfield>
  </datafield>
  <datafield tag="773" ind1=" " ind2=" ">
    <subfield code="n">url</subfield>
    <subfield code="i">isSupplementTo</subfield>
    <subfield code="a">https://github.com/thibautjombart/adegenet/tree/2.0.1</subfield>
  </datafield>
  <datafield tag="773" ind1=" " ind2=" ">
    <subfield code="n">doi</subfield>
    <subfield code="i">isVersionOf</subfield>
    <subfield code="a">10.5281/zenodo.592811</subfield>
  </datafield>
  <datafield tag="024" ind1=" " ind2=" ">
    <subfield code="a">10.5281/zenodo.46188</subfield>
    <subfield code="2">doi</subfield>
  </datafield>
  <datafield tag="980" ind1=" " ind2=" ">
    <subfield code="a">software</subfield>
  </datafield>
</record>
1,472
54
views
downloads
All versions This version
Views 1,472331
Downloads 5417
Data volume 551.6 MB171.3 MB
Unique views 887252
Unique downloads 4717

Share

Cite as