purgeR: Inbreeding-Purging Estimation in Pedigreed Populations

Inbreeding-purging analysis of pedigreed populations, including the computation of the inbreeding coefficient, partial, ancestral and purged inbreeding coefficients, and measures of the opportunity of purging related to the individual reduction of inbreeding load. In addition, functions to calculate the effective population size and other parameters relevant to population genetics are included. Caballero A. and Toro M.A. (2000) <doi:10.1017/s0016672399004449>. García-Dorado A., Wang J. and López-Cortegano E. (2016) <doi:10.1534/g3.116.032425>. Gulisija D. and Crow J.F. (2007) <doi:10.1111/j.1558-5646.2007.00088.x>. Gutiérrez J.P., Cervantes I., Goyache F. (2009) <doi:10.1111/j.1439-0388.2009.00810.x>. López-Cortegano E., Bersabé D., Wang J., García-Dorado A. (2018) <doi:10.1038/s41437-017-0045-y>.

Version: 1.2
Depends: R (≥ 3.5.0)
Imports: doSNOW (≥ 1.0.19), foreach (≥ 1.5.1), parallel, progress (≥ 1.2.2), Rcpp (≥ 1.0.5), RcppProgress (≥ 0.4.2)
LinkingTo: Rcpp, RcppProgress
Suggests: caret (≥ 6.0-86), coda (≥ 0.19-4), dplyr (≥ 1.0.0), e1071 (≥ 1.7-4), ggplot2 (≥ 3.3.1), glmnet (≥ 4.0-2), gtable (≥ 0.3.0), knitr (≥ 1.28), magrittr (≥ 1.5), pander (≥ 0.6.3), plyr (≥ 1.8.6), purrr (≥ 0.3.4), rmarkdown (≥ 2.2), scales (≥ 1.1.1), stringr (≥ 1.4.0), testthat (≥ 2.3.2), tibble (≥ 3.0.1), tidyr (≥ 1.1.0), tidyselect (≥ 1.1.0)
Published: 2021-07-12
Author: Eugenio López-Cortegano ORCID iD [aut, cre]
Maintainer: Eugenio López-Cortegano <elcortegano at gmail.com>
BugReports: https://gitlab.com/elcortegano/purgeR/-/issues/
License: GPL-2
URL: https://gitlab.com/elcortegano/purgeR/
NeedsCompilation: yes
Materials: NEWS
CRAN checks: purgeR results

Downloads:

Reference manual: purgeR.pdf
Vignettes: Inbreeding and Purging Estimates
purgeR tutorial
Package source: purgeR_1.2.tar.gz
Windows binaries: r-devel: purgeR_1.2.zip, r-devel-UCRT: purgeR_1.2.zip, r-release: purgeR_1.2.zip, r-oldrel: purgeR_1.2.zip
macOS binaries: r-release (arm64): purgeR_1.2.tgz, r-release (x86_64): purgeR_1.2.tgz, r-oldrel: purgeR_1.2.tgz
Old sources: purgeR archive

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