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Recent Releases of adegenet

adegenet - 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()

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Published by zkamvar about 4 years ago

adegenet - adegenet 2.1.6

What's Changed

  • add sanity check to n.pca.max to default to max value if vector by @pdimens in https://github.com/thibautjombart/adegenet/pull/323
  • summmary.spca bug fix for matrices and data frames by @lvclark in https://github.com/thibautjombart/adegenet/pull/329

New Contributors

  • @pdimens made their first contribution in https://github.com/thibautjombart/adegenet/pull/323
  • @lvclark made their first contribution in https://github.com/thibautjombart/adegenet/pull/329

Full Changelog: https://github.com/thibautjombart/adegenet/compare/2.1.5...2.1.6

- R
Published by zkamvar about 4 years ago

adegenet - adegenet version 2.1.5

What's Changed

  • Set all parallel = FALSE by @zkamvar in https://github.com/thibautjombart/adegenet/pull/314
  • move spdep to suggests by @zkamvar in https://github.com/thibautjombart/adegenet/pull/316
  • fix bug in hybridize via tab method for genpop by @zkamvar in https://github.com/thibautjombart/adegenet/pull/317

Full Changelog: https://github.com/thibautjombart/adegenet/compare/2.1.4...2.1.5

- R
Published by zkamvar almost 5 years ago

adegenet - 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

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Published by zkamvar almost 5 years ago

adegenet - 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)

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Published by zkamvar about 6 years ago

adegenet - 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 https://github.com/thibautjombart/adegenet/issues/231 and https://github.com/thibautjombart/adegenet/pull/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 https://github.com/thibautjombart/adegenet/issues/234 for details.

  • seppop() will now take into account NA population assignments with the new keepNA argument. See https://github.com/thibautjombart/adegenet/pull/236 for details.

  • snapclust() likelihood calculation was incorrect for haploids. This has been fixed in commits 3a5f820db388c9821c3095cd29ad3cd3843237a5 and e41d2d598369bb5921465a60adffac9ecb61f86d.

MISC

  • snapclust() will give a better warning message when the number of samples in the dataset exceeds computer precision. See https://github.com/thibautjombart/adegenet/issues/221 for details.

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

- R
Published by zkamvar over 6 years ago

adegenet - 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.

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Published by zkamvar over 6 years ago

adegenet - adegenet version 2.1.0

This release contains several new features and bug fixes

- R
Published by zkamvar over 8 years ago

adegenet - 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)

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Published by zkamvar over 10 years ago

adegenet - New major version

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

- R
Published by thibautjombart about 11 years ago