nh_analysis_generateR: NewHybrids analysis file maker

In bwringe/hybriddetective: Automates the process of detecting hybrids from genetic data

NewHybrids analysis file maker

Description

nh_analysis_GenerateR Merges simulated genotypes with the genotypes of unknown/experimental individuals, producing a file to be analyzed by NewHybrids. Will also output a dataframe containing the names of the individuals (including those that were simulated) in the NewHybrids formatted file.

Usage

nh_analysis_generateR(ReferencePopsData, UnknownIndivs,
  sim.pops.include = c("Pure1", "Pure2"), output.name)

Arguments

ReferencePopsData	A file path to a either a NewHybrids or GENEPOP formatted file containing genotypes from the simulated ancestral populations. This can be the result of any of the freqbasedsim functions, or a file created using the function genepop_newhybrids from the package genepopedit
UnknownIndivs	A file path to a file containing the genotypes of the individuals to be analyzed for possible hybrid ancestry. This can either be a genepop format file, or a NewHybrids format file. Note - the number of loci and the names of the loci in ReferencePopsData and UnknownIndivs must be the same
sim.pops.include	Optional character vector list denoting which hybrid categories from the simulated data should be included in the output. The default is Pure Population 1 and Pure Population 2.
output.name	A character vector to be applied as the name of the output.

bwringe/hybriddetective documentation built on March 22, 2023, 6:52 a.m.