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adegenet version 2.1.2

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@zkamvar zkamvar released this 21 Jan 09:46
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This version of adegenet introduces several bugfixes (including a fix for mis-calculation of likelihood for haploids in snapclust) including a large speedup in the df2genind() function thanks to Klaus Schliep.

This version also introduces Zhian N. Kamvar as the acting maintainer

NEW MANAGEMENT

  • Zhian N. Kamvar is now the acting maintainer of the package.

NEW FEATURES

  • While creating genind from dataframe, it is now possible to skip
    the test of the ploidy that was added in 2.1.1 by passing the option
    check.ploidy = FALSE to the function df2genind. Thanks to Frederic Michaud
    for the fix. See #231 and
    #232 for details

  • showmekittens() has gained several new kittens thanks to @rdecamp

  • A new data set called swallowtails has been added to demonstrate the
    export to MVmapper functionality.

BUG FIXES

  • A bug where the number of alleles per locus was unaffected after subsetting
    a population with drop = FALSE has been fixed. Now, by default, the
    @loc.n.all slot (accessor: nAll()) will store the number of observed
    alleles in the current data set, regardless of whether or not these were
    dropped from the data matrix.
    See #234 for details.

  • seppop() will now take into account NA population assignments with the
    new keepNA argument.
    See #236 for details.

  • snapclust() likelihood calculation was incorrect for haploids. This has
    been fixed in commits 3a5f820 and
    e41d2d5.

MISC