transversions_only(). The old function is now deprecated.
print.EIGENSTRAT()now uses a pre-calculated numbers of removed/remaining sites, instead of calculating them each and every time.
It turned out that dragging along Rcpp and Boost dependencies just for the VCF -> EIGENSTRAT conversion function causes unnecessary complications in the installation process. It’s not worth having it in the package if it would be used only by a small fraction of potential users.
This function has been removed and the
vcf2eigenstrat program is maintained in its own repository.
download_data()function that fetches the example data set from the web.
filter_sitesis now implemented using
data.tableand allows overlap with an arbitrary BED file.
f4modeparameter remains in the
d()function though, as
The package now includes qpAdm functionality.
Formal tests for all implemented wrapper functions have been implemented.