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.
- fixed typo in one of the examples
- cleaned up cpp code to comply with linting guidelines
- improved code coverage in tests
- updated tbb::task_scheduler_init to tbb::global_control
- improved linting of cpp code
- sped up tests
- added CITATION file
- added NEWS file
- simplified some tests
- merged many functions with similar functionality
- added vignette that provides overview of all functionality.
- added c++ versions of the unphased and phased likelihoods.
- added multithreading using the TBB / RcppParallel library.
- further improved the recombination function following Hanno Hildenbrandt's suggestions
- improved the recombination function to run twice as fast
- added option to track the true number of junctions
- 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).
- 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.
- 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.
- added support for estimating the expected number of junctions for arbitrarily distributed markers.
- 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.