Changelog

Source: NEWS.md

jackalope 1.1.62025-09-29

• Removed zlibbioc requirement

jackalope 1.1.42023-10-15

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

jackalope 1.1.32021-07-06

• Remove one NULL_ENTRY to support STRICT_R_HEADERS

jackalope 1.1.22021-02-10

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

jackalope 1.1.12020-06-15

• 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 1.1.02020-02-28

• 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 1.0.02019-11-22

• 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