NEWS
jackalope 1.1.4 (2023-10-15)
- Added required jackalope-package man file
- Updated all docs with roxygen2 v7.2.3
jackalope 1.1.3 (2021-07-06)
- Remove one NULL_ENTRY to support STRICT_R_HEADERS
jackalope 1.1.2 (2021-02-10)
- Updated CITATION
- Fixed some links in docs
- Fixed unnecessary copying in
HapSet class
jackalope 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
jackalope 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
jackalope 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