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 2.1.0

• 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.