Package: simfam
Title: Simulate and Model Family Pedigrees with Structured Founders
Version: 1.1.16.9000
Authors@R: 
    person(given = "Alejandro",
	   family = "Ochoa",
	   role = c("aut", "cre"),
	   email = "alejandro.ochoa@duke.edu",
           comment = c(ORCID = "0000-0003-4928-3403"))
Description: 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.  There are functions that simulate independent
        loci and also functions that use an explicit recombination
        model to simulate linkage disequilibrium (LD) in the pedigree,
        as well as population analogs resembling the Li-Stephens model.
        Described in Yao and Ochoa (2023) <doi:10.7554/eLife.79238>.
License: GPL (>= 3)
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Imports: Rcpp, stats, tibble, dplyr, tidyselect, rlang, Matrix, methods
Suggests: testthat (>= 3.0.0), popkin, bnpsd (>= 1.3.2), genio,
        BEDMatrix, kinship2, RColorBrewer, knitr, rmarkdown
Config/testthat/edition: 3
VignetteBuilder: knitr
LinkingTo: Rcpp
URL: https://github.com/OchoaLab/simfam
BugReports: https://github.com/OchoaLab/simfam/issues
Depends: R (>= 2.10)
LazyData: true
Repository: https://ochoalab.r-universe.dev
Date/Publication: 2025-01-08 18:08:26 UTC
RemoteUrl: https://github.com/ochoalab/simfam
RemoteRef: HEAD
RemoteSha: 5cd929803cd0ceaf68e3bcfc2f7a3c63a4a33e24
NeedsCompilation: yes
Packaged: 2026-06-05 07:53:53 UTC; root
Author: Alejandro Ochoa [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-4928-3403>)
Maintainer: Alejandro Ochoa <alejandro.ochoa@duke.edu>