R package for analysing inbreeding based on SNP and microsatellite data
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README.md

inbreedR

CRAN_Status_Badge Build Status

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