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@thierrygosselin thierrygosselin released this 08 Jul 21:01
· 532 commits to master since this release

v.0.3.0

  • Update that makes my coding life easier.
  • Several internal functions to convert from a tidy dataframe to:
    vcf, plink, genind, genlight, gtypes, hierfstat, genepop, structure and betadiv
    are now separate modules available to users (look for write_... with the outputformat)
  • New function genomic_converter: If you want the to convert from the supported
    input file formats to many output formats, at once, this is the function.
    With the new function genomic_converter, import and imputations are only
    done once, saving time if you were generating different output WITH imputations.
  • Change: all the vcf2... functions (excep vcf2dadi) are now a shorcut of genomic_converter.
    This is particularly interesting and faster if you were generating different
    output WITH imputations. This makes the functions vcf2... and genomic_converter
    easier to debug for me and more stable for users.
  • Deprecated: the haplo2... functions are all deprecated and replaced by
    genomic_converter, except haplo2colony that requires so many arguments that it
    would be too complicated, for now, to integrate with genomic_converter.
  • New feature: when arguments pop.select, blacklist.id and imputation.method
    are used, the REF and ALT alleles are now re-computed to account for the filters
    and imputations.