gpSampler

A character string pointing to a genepop input file. If the file exists in the current working directory, only the file name is required. If the file resides elsewhere, the entire file path is required.

infile

This argument specifies the number of individuals to be randomly sampled from each population sample in the input file. Either a single numeric argument can be passed or a numeric vector of length equal to the number of population samples in the genepop file.

samp_size

A character string specifying the prefix name for the resulting file. This string will be suffixed with ".gen". The file will be written to the working directory, unless a properly formatted path is passed to <code>outfile</code>

outfile


Randomly re-samples population samples from a genepop file for user defined sizes and returns a new genepop file containing the sub-sample data. The function can easily be integrated into simulation pipelines when exploring sample size effects.


Allows the calculation of both genetic diversity partition
statistics, genetic differentiation statistics, and locus informativeness
for ancestry assignment.
It also provides users with various option to calculate
bootstrapped 95\% confidence intervals both across loci,
for pairwise population comparisons, and to plot these results interactively.
Parallel computing capabilities and pairwise results without
bootstrapping are provided.
Weir and Cockerham's 1984 F-statistics are also calculated.
Various plotting features are also provided, as well as Chi-square tests of
genetic heterogeneity are also provided.
Functionality for the calculation of various diversity parameters is
possible for RAD-seq derived SNP data sets containing thousands of marker loci.
A shiny application for the development of microsatellite multiplexes is
also available.

gpSampler: Randomly sample a genepop file

Description

Usage

Arguments