inbreedR

inbreedR provides functions and workflows for the analysis of inbreeding and heterozygosity-fitness correlations (HFCs) based on molecular markers such as microsatellites and SNPs. It has four main application areas:

• Quantifying variance in inbreeding through estimation of identitiy disequilibria (g2), heterozygosity-heterozygosity correlations (HHC) and variance in standardized multilocus heterozygosity (sMLH)

• Calculating g2 for small and large SNP datasets. The use of data.table and parallelization speed up bootstrapping and permutation tests

• Estimating central parameters within HFC theory, such as the influence of inbreeding on heterozygosity and fitness, and their confidence intervals.

• Exploring the sensitivity of these measures towards the number of genetic markers using simulations

You can install:

• the latest released version from CRAN with

  install.packages("inbreedR")

• the latest development version from github with

  if (packageVersion("devtools") < 1.6) {
    install.packages("devtools")
  }
  devtools::install_github("mastoffel/inbreedR", build_vignettes = TRUE)

If you encounter bug or if you have any suggestions for improvement, just contact me: martin.adam.stoffel[at]gmail.com

Get started with inbreedR

To get started read the vignette:

vignette("inbreedR_step_by_step", package = "inbreedR")

Citation

Stoffel, M. A., Esser, M., Kardos, M., Humble, E., Nichols, H., David, P., & Hoffman, J. I. (2016). inbreedR: an R package for the analysis of inbreeding based on genetic markers. Methods in Ecology and Evolution, 7(11), 1331-1339. doi:10.1111/2041-210X.12588