adegenet 2.1.7

This is a minor update that removes the soft dependencies tripack and akima in favour of interp.

This also allows as.matrix() for genind objects to take arguments to tab()

adegenet 2.1.6

What's Changed

• add sanity check to n.pca.max to default to max value if vector by @pdimens in #323
• summmary.spca bug fix for matrices and data frames by @lvclark in #329

New Contributors

• @pdimens made their first contribution in #323
• @lvclark made their first contribution in #329

Full Changelog: 2.1.5...2.1.6

adegenet version 2.1.5

What's Changed

• Set all parallel = FALSE by @zkamvar in #314
• move spdep to suggests by @zkamvar in #316
• fix bug in hybridize via tab method for genpop by @zkamvar in #317

Full Changelog: 2.1.4...2.1.5

adegenet version 2.1.4

This maintenance release includes an updated version of the snapclust documentation pointing to the correct reference for citation. It also removes an invalid URL from the README

adegenet version 2.1.3

BUG FIX

• seppop() correctly subsets genlight objects now. (@rdinnager, #270)

MISC

• A bug in the scaleGen() example has been fixed and a minor spelling
  mistake was corrected (@courtiol, #273)
• find.clusters() gains a missing parenthesis in the user prompt (@knausb, #283 )
• Warning messages for missing loci and individuals have been made clearer (@zkamvar, #276)
• DESCRIPTION file now uses Authors@R syntax

CRAN MAINTENANCE

• DNAbin2genind() now checks for matrices by using inherits() instead of class(x) == "matrix" (@zkamvar, #275)

adegenet version 2.1.2

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

• snapclust() will give a better warning message when the number of
  samples in the dataset exceeds computer precision. See
  #221 for details.

• df2genind() now imports data >100x faster
  (@KlausVigo, https://github.com/thibautjombart/adegenet/pulls/260)

Version 2.1.1 (estimated)

I'm tagging the last commit that occurred before version 2.1.1 hit CRAN. I can only assume that this was the state when it was sent.

adegenet version 2.1.0

This release contains several new features and bug fixes

adegenet version 2.0.1

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)

New major version

This is adegenet 2.0.0 as submitted to CRAN on the 07-07-2015