Changes in version 1.1.6 (2025-09-29) - Removed zlibbioc requirement Changes in version 1.1.4 (2023-10-15) - Added required jackalope-package man file - Updated all docs with roxygen2 v7.2.3 Changes in version 1.1.3 (2021-07-06) - Remove one NULL_ENTRY to support STRICT_R_HEADERS Changes in version 1.1.2 (2021-02-10) - Updated CITATION - Fixed some links in docs - Fixed unnecessary copying in HapSet class Changes in version 1.1.1 (2020-06-15) - 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 Changes in version 1.1.0 (2020-02-28) - 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 Changes in version 1.0.0 (2019-11-22) - 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