This package provides individual based simulations in order to
simulate the accumulation of junctions over time, both for chromosomes
with a finite and an infinite number of recombination sites.
Furthermore, the package provides mathematical tools to verify the
outcomes of the individual based simulations.
version 2.1.4
replaced Rf_error with Rcpp::stop()
Added optional support for TBB (e.g. also support for machines that
don’t have TBB installed, such as musl based linux)
version 2.1.1
fixed typo in one of the examples
cleaned up cpp code to comply with linting guidelines
improved code coverage in tests
version 2.1.0
updated tbb::task_scheduler_init to tbb::global_control
improved linting of cpp code
sped up tests
added CITATION file
added NEWS file
version 2.0.2
simplified some tests
version 2.0
merged many functions with similar functionality
added vignette that provides overview of all functionality.
version 1.9
added c++ versions of the unphased and phased likelihoods.
version 1.8
added multithreading using the TBB / RcppParallel library.
version 1.7
further improved the recombination function following Hanno
Hildenbrandt’s suggestions
version 1.6
improved the recombination function to run twice as fast
version 1.5.1
added option to track the true number of junctions
version 1.5
added support for inferring the time since admixture based on phased
and unphased data.
included simulation functions to simulate appropriate data
(e.g. phased and unphased).
version 1.4
added support for estimating the number of junctions under a
backcrossing scheme
added support for simulating the number of junctions under a
backcrossing scheme
both based on the code supplied in Lavretsky et al. 2019.
version 1.3
added support for estimating the time since admixture using unphased
data.
added individual based simulations returning phased and unphased
data.
Updated entire package to Roxygen.
version 1.2
added support for estimating the expected number of junctions for
arbitrarily distributed markers.
version 1.1
updated underlying random number generator for picking recombination
sites. The previous generator had limited precision, which could
generate duplicate recombination sites. This update fixes that.