ticphasetype

This package implements core functions from phase-type theory that are useful in the analysis of biological data. It includes easy-to-use functions for modelling common statistics in evolutionary genetics, as well as a flexible high-level interface for more advanced users. You can learn more about the package in vignette('ticphasetype').

Details

ticphasetype contains several functions for representing statistics that are commonly used in population genomics. t_mrca() and t_total() can be used for modelling the time until the most recent common ancestor and the total tree length for Kingman's coalescence using a user-friendly interface. These two quantities are represented using a discrete phase-type distribution (the cont_phase_type class). The user can use the generator function for this class if they want phase-type representations based on other coalescent models.

On the other hand, ticphasetype can also model the mutational process. The package contains a generator function for the block counting process of Kingsman's coalescent (kingsman()). By reward-transfor ming this continuous phase-type representation, ticphasetype creates discrete phase-type distributions of singletons, doubletons and related statistics (itons()), for the total number of segregating sites (segsites()), and for the tail statistic (tailstat()). All these quantities are represented using the disc_phase_type() class, whose generator function can also be used for user-tailored discrete phase-type distributions.

The mean and the variance of the any phase-type representation can easily be computed using mean() and var() respectively. Moreover, a readable summary of a distribution can be obtained using the generic function summary().

This package also contains functions for the density (dphtype()), quantiles (qphtype()), distribution (pphtype()) and random draw generator (rphtype()) for both discrete and continuous phase-type distributions. Additionally, the user can calculate and plot the site-frequency spectrum using sfs().

The vignette for the package can be consulted here. For a quick overview of all included functions, please visit this link .

Installation

If you install devtools in your R environment install.packages("devtools"), our package will install with the following command.

devtools::install_github("aumath-advancedr2019/ticphasetype")

Please be aware that our package depends on the R partitions package, which is only supported by R version >= 3.6.0.