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PopGenHelpR version 1.4.0

What is PopGenHelpR?

PopGenHelpR is an R package designed to estimate commonly used population genomic statistics and to generate publication quality figures. The current version of PopGenHelpR uses vcf, geno (012), and csv files to generate output, however, future implementations will expand the input file type options. Please see the vignette and other articles for examples.

We plan to continue developing the package to include more functions, feel free to reach out to Keaka Farleigh if you have any suggestions or would like to collaborate.

Do you use PopGenHelpR in your research or class and want to be kept up to date?

Please email Keaka Farleigh (farleik@miamioh.edu) to be informed about any updates or pending changes to PopGenHelpR.

Installation

You can install PopGenHelpR using:

install.packages("PopGenHelpR")

You can install the development version of PopGenHelpR using devtools:

devtools::install_github("kfarleigh/PopGenHelpR")

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Version

Install

install.packages('PopGenHelpR')

Monthly Downloads

231

Version

1.4.0

License

GPL (>= 3)

Maintainer

Keaka Farleigh

Last Published

July 2nd, 2025

Functions in PopGenHelpR (1.4.0)

Private.alleles

A function to estimate the number of private alleles in each population.
Differentiation

A function to estimate three measures of genetic differentiation using geno files, vcf files, or vcfR objects. Data is assumed to be bi-allelic.
Network_map

A function to map statistics (i.e., genetic differentiation) between points as a network on a map.
PCA

A function to perform principal component analysis (PCA) on genetic data. Loci with missing data will be removed prior to PCA.
Ancestry_barchart

Plot an ancestry matrix for individuals and(or) populations.
HornedLizard_VCF

A vcfR object to be used in Heterozygosity and Differentiation.
Heterozygosity

A function to estimate seven measures of heterozygosity using geno files, vcf files, or vcfR objects. Data is assumed to be bi-allelic.
Pairwise_heatmap

A function to plot a heatmap from a symmetric matrix.
Piechart_map

Plot a map of ancestry pie charts.
Point_map

A function to map statistics as colored points on a map.
Plot_coordinates

A function to plot coordinates on a map.
Fst_dat

A genetic differentiation matrix and locality information for each population. This data was generated by subsetting data of Farleigh et al., 2021.
HornedLizard_Pop

A population assignment data frame to be used in Heterozygosity and Differentiation.
Het_dat

A data frame of hypothetical heterozygosity data produced by Heterozygosity.
Q_dat

A list representing a q-matrix and the locality information associated with the qmatrix