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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

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.