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NEWS.md

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jackalope 1.1.4

  • Added required jackalope-package man file
  • Updated all docs with roxygen2 v7.2.3

jackalope 1.1.3

  • Remove one NULL_ENTRY to support STRICT_R_HEADERS

jackalope 1.1.2

  • Updated CITATION
  • Fixed some links in docs
  • Fixed unnecessary copying in HapSet class

jackalope 1.1.1

  • Updated src/Makevars to be compatible with using OpenMP on macOS with R >= 4.0.0
  • Updated CITATION
  • Replaced deprecated ape::is.binary.tree with ape::is.binary.phylo

jackalope 1.1.0

  • Fixed bug when scaling tree using theta parameter.
  • Using "haplotypes" instead of "variants" throughout.
  • Updated R6 class documentation for new roxygen2 methods.
  • Provide method to merge >1 chromosomes, but not the whole genome

jackalope 1.0.0

  • create_variants performs better with high mutation rates
  • Substitutions now use a random-site, discrete-Gamma model for among-site variability (optionally with invariant sites), rather than a fixed-sites model
  • No longer depends on vcfR package, instead using htslib for reading VCF files
  • Indel creation now uses "tau-leaping" approximation to the Doob-Gillespie algorithm
  • Substitutions are added by calculating transition-probability matrices and sampling for substitutions at each site