simfam: Simulate and Model Family Pedigrees with Structured Founders

The focus is on simulating and modeling families with founders drawn from a structured population (for example, with different ancestries or other potentially non-family relatedness), in contrast to traditional pedigree analysis that treats all founders as equally unrelated. Main function simulates a random pedigree for many generations, avoiding close relatives, pairing closest individuals according to a 1D geography and their randomly-drawn sex, and with variable children sizes to result in a target population size per generation. Auxiliary functions calculate kinship matrices, admixture matrices, and draw random genotypes across arbitrary pedigree structures starting from the corresponding founder values. The code is built around the plink FAM table format for pedigrees. Partially described in Yao and Ochoa (2019) <doi:10.1101/858399>.

Version: 1.0.3
Imports: Rcpp, stats, tibble
LinkingTo: Rcpp
Suggests: testthat (≥ 3.0.0), popkin, bnpsd (≥ 1.3.2), kinship2, RColorBrewer, knitr, rmarkdown
Published: 2021-10-05
Author: Alejandro Ochoa ORCID iD [aut, cre]
Maintainer: Alejandro Ochoa <alejandro.ochoa at duke.edu>
BugReports: https://github.com/OchoaLab/simfam/issues
License: GPL (≥ 3)
URL: https://github.com/OchoaLab/simfam
NeedsCompilation: yes
Materials: README NEWS
CRAN checks: simfam results

Downloads:

Reference manual: simfam.pdf
Vignettes: 'simfam': simulate and model family pedigrees with structured founders
Package source: simfam_1.0.3.tar.gz
Windows binaries: r-devel: simfam_1.0.3.zip, r-devel-UCRT: simfam_1.0.3.zip, r-release: simfam_1.0.3.zip, r-oldrel: simfam_1.0.3.zip
macOS binaries: r-release (arm64): simfam_1.0.2.tgz, r-release (x86_64): simfam_1.0.3.tgz, r-oldrel: simfam_1.0.3.tgz
Old sources: simfam archive

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