Package: hybridclock
Title: How Long Have Hybrids Been Forming? Hybrid Population Histories
        from Diagnostic Markers
Version: 0.1.1
Authors@R: 
    person("Paul A.", "Maier", , "maierpa@gmail.com", role = c("aut", "cre", "cph"),
           comment = c(ORCID = "0000-0003-0851-8827"))
Description: Estimates the history of hybrid populations from diagnostic
    markers, with or without a genetic map: the average age of the hybrids,
    how long ago the rarer species' ancestry entered, the number of
    backcrosses, and whether pure animals of the rarer species are still
    arriving. Population samples of
    hybrid index and interspecies heterozygosity, as defined by Fitzpatrick
    (2012) <doi:10.1186/1471-2148-12-131>, are compared with forward simulations
    that include drift, small breeding groups, sibling mating and separate
    breeding pools, so that inbreeding is not mistaken for age. Estimates
    come from 'Cubist' models with split-conformal intervals. Recent hybrids
    are also classified individually, and the number of markers needed to
    detect backcrossed hybrids follows Boecklen and Howard (1997)
    <doi:10.1890/0012-9658(1997)078[2611:GAOHZN]2.0.CO;2>.
License: MIT + file LICENSE
URL: https://github.com/paulmaier/hybridclock,
        https://paulmaier.github.io/hybridclock/
BugReports: https://github.com/paulmaier/hybridclock/issues
Depends: R (>= 4.1)
Imports: Cubist, graphics, grDevices, parallel, ranger, stats
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr
Config/testthat/edition: 3
Encoding: UTF-8
Config/roxygen2/version: 8.1.0
LazyData: true
NeedsCompilation: no
Packaged: 2026-10-14 13:59:47 UTC; paulm
Author: Paul A. Maier [aut, cre, cph] (ORCID:
    <https://orcid.org/0000-0003-0851-8827>)
Maintainer: Paul A. Maier <maierpa@gmail.com>
Repository: CRAN
Date/Publication: 2026-10-22 16:40:02 UTC
Built: R 4.6.1; ; 2026-10-22 19:38:49 UTC; unix
