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adegenet version 2.0.1

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@zkamvar zkamvar released this 17 Feb 20:11
· 377 commits to master since this release

Adegenet version 2.0.1

This version contains a few new features, speedups, and bug fixes

NEW FEATURES

  • Hs() is now much faster and will scale better for large number of loci
  • Hs.test() allows for testing differences in expected heterozygosity between two
    groups of individuals
  • strata tutorial is now available via adegenetTutorial(which="strata")
  • repool can now handle objects with no population information, and can return a
    list of repooled genind (argument 'list' defauling to FALSE)
  • read.fstat() can now handle missing data coded by any number of "0"
  • scatter.dapc() function can now label individuals using orditorp() function
    from vegan package, which takes care of overlapping (See issue #100)
  • df2genind() is now faster at handling missing data (See issue #114)
  • the summary method has better formatting

BUG FIXES

  • Hs() no longer returns NaN if one locus has not been typed; instead,
    computations are done using all available loci
  • adegenetTutorial() now opens up-to-date tutorials
  • subsetting genlight objects now treats missing data appropriately when given
    logical, character, or negative subscripts. (See issue #83)
  • fixed occasional spurious warning about duplicated individual labels in
    df2genind()
  • fixed issues with mis-placed missing data in df2genind() when samples were
    labeled with numbers (See issue #96)
  • frequencies can now be obtained from P/A genpop objects (See issue #105)
  • Windows no longer throws an error with as.genlight() (See issue #109)
  • read.genpop() now returns individual names (See issue #117)