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adegenet: adegenet version 2.0.1

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

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)

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