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)