Releases: thibautjombart/adegenet
adegenet 2.1.7
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
Full Changelog: 2.1.5...2.1.6
adegenet version 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
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 withdrop = 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 accountNA
population assignments with the
newkeepNA
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 lociHs.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 usingorditorp()
function
fromvegan
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 returnsNaN
if one locus has not been typed; instead,
computations are done using all available lociadegenetTutorial()
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