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NEWS.md

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admixr 0.7.1

  • Parse admixture proportions from the "best coefficients" line of the qpAdm output file.

admixr 0.7.0

  • Fixed handling of warnings when dealing with duplicated populations.
  • 9s are now replaced with NAs in read_geno() and write_geno(), which makes it more convenient to write custom analytic code working on data.frames.
  • Renamed qpAdm() output elements and changed its function signature.

admixr 0.6.3

  • Rename keep_transversions() to 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.
  • Printing EIGENSTRAT objects now also shows "group" and "exclude" modifiers only if present.

admixr 0.6.2

  • read_output() made public.
  • Fixed issues with parsing of mis-formatted ind files (tabs at the ends of lines etc.).

admixr 0.6.1

  • 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.

admixr 0.6.0

  • Conversion of VCF to EIGENSTRAT format is now implemented in C++ and should be approximately infinitely faster than the old conversion function written in pure R.
  • Conversion of EIGENSTRAT into VCF has been removed.

admixr 0.5.0

  • Added full implementations of qpWave() and qpAdm() functions.
  • filter_bed() now implemented simply by calling bedtools in the background. This turned out to be way faster and memory efficient than the previous data.table-based solution.

admixr 0.4.1

  • Fixed missing group_labels() update.
  • Removed the huge built-in data set. Implemented download_data() function that fetches the example data set from the web.

admixr 0.4.0

  • The package now has a tutorial vignette describing the main functionality.
  • Simple SNP dataset is now included with the package.
  • The API of many utility functions has been simplified and their internals re-written.
  • filter_sites is now implemented using data.table and allows overlap with an arbitrary BED file.

admixr 0.3.0

  • All wrappers have been given simpler names (qpDstat() -> d(), qpF4ratio() -> f4ratio(), etc).
  • F4 statistic can now be calculated using a separate f4() function (f4mode parameter remains in the d() function though, as f4() calls d() internally).
  • All tests are performed on Travis CI using installed and compiled ADMIXTOOLS software.

admixr 0.2.0

  • The package now includes qpAdm functionality.

  • Formal tests for all implemented wrapper functions have been implemented.

admixr 0.1.0

Implemented:

  • D statistic as qpDstat,
  • f4 statistic as qpDstat(f4mode = TRUE),
  • f4-ratio statistic as qpF4Ratio,
  • f3 statistic as qp3Pop.