polyfreqs is an R package for the estimation of biallelic SNP frequencies in populations of polyploids. It uses a hierarchical Bayesian model to integrate over genotype uncertainty . The package implements a Gibbs sampler to draw from the joint posterior distribution of allele frequencies and genotypes: \(P(\,p,G|\,R,\epsilon)\).

Dependencies

polyfreqs uses C++ code to implement its Gibbs sampling algorithm which will usually require the installation of additional software (depending on the operating system [OS] being used). Windows users will need to install Rtools. MacOSX users will need to install the Xcode Command Line Tools. Linux users will need an up-to-date version of the GNU C Compiler (gcc), which typically comes installed with most Linux distributions.

polyfreqs relies on two other R packages: Rcpp and RcppArmadillo. These are both available on CRAN and can be installed in the usual way using install.packages():

install.packages("Rcpp")
install.packages("RcppArmadillo")

Note that Rcpp and RcppArmadillo also require the compilation of C++ code so make sure that the necessary compilers are installed appropriately for your OS.

Installation

Installing polyfreqs can be done using the devtools package and the install_github() command. Install devtools using install.packages("devtools"). polyfreqs can then be installed as follows:

devtools::install_github("pblischak/polyfreqs")