The hardware and bandwidth for this mirror is donated by METANET, the Webhosting and Full Service-Cloud Provider.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]metanet.ch.

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 2.1.1

• 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.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.