Population Assignment using Genetic, Non-Genetic or Integrated Data in a Machine Learning Framework


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Documentation for package ‘assignPOP’ version 1.2.2

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accuracy.kfold Estimate assignment accuracies of K-fold cross-validation results
accuracy.MC Estimate assignment accuracies of Monte-Carlo cross-validation results
accuracy.plot Make a boxplot (ggplot2 style) of assignment accuracy from cross-validation results
assign.kfold Population assignment test using K-fold cross-validation
assign.matrix Make an assignment maxtrix from cross-validation results
assign.MC Population assignment test using Monte-Carlo cross-validation
assign.X Perform a population assignment test on unknown individuals using known data
check.loci Check which loci frequently have high Fst across training sets
compile.data Compile genetic and other non-genetic data
membership.plot Make a membership probability plot using results from K-fold cross-validation (ggplot2 style)
read.Genepop Read GENEPOP format file
read.Structure Read Structure format file
reduce.allele Remove low variance alleles (dimensionality reduction)