Package: pooledpeaks
Title: Genetic Analysis of Pooled Samples
Version: 1.2.2
Authors@R: c( 
    person("Kathleen", "Kuesters", email = "kathleen.kuesters@gmail.com", 
       role = c("aut", "cre", "cph"), comment = c(ORCID = "0000-0003-0238-7889")),
    person("Jeffrey", "Long", role = c("aut")),
    person("Jessica", "Blanton", role = c("aut")),
    person("Walter", "Blank", role = c("ctb")),
    person("Jeffrey", "Kovach", role = c("ctb")),
    person("Ronald", "Blanton", role = c("ctb")))
Description: Analyzing genetic data obtained from pooled samples. This
        package can read in Fragment Analysis output files, process the
        data, and score peaks, as well as facilitate various analyses,
        including cluster analysis, calculation of genetic distances
        and diversity indices, as well as bootstrap resampling for
        statistical inference. Specifically tailored to handle genetic
        data efficiently, researchers can explore population structure,
        genetic differentiation, and genetic relatedness among samples.
        We updated some functions from Covarrubias-Pazaran et al.
        (2016) <doi:10.1186/s12863-016-0365-6> to allow for the use of
        new file formats and referenced the following to write our
        genetic analysis functions: Long et al. (2022)
        <doi:10.1038/s41598-022-04776-0>, Jost (2008)
        <doi:10.1111/j.1365-294x.2008.03887.x>, Nei (1973)
        <doi:10.1073/pnas.70.12.3321>, Foulley et al. (2006)
        <doi:10.1016/j.livprodsci.2005.10.021>, Chao et al. (2008)
        <doi:10.1111/j.1541-0420.2008.01010.x>.
URL: https://github.com/kmkuesters/pooledpeaks
License: GPL (>= 3)
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Imports: ape, dplyr, Fragman, graphics, magrittr, pdftools, qpdf,
        rlang, stats, tibble, tidyr, utils
Suggests: knitr, plyr, rmarkdown, testthat (>= 3.0.0)
Config/testthat/edition: 3
BugReports: https://github.com/kmkuesters/pooledpeaks/issues
VignetteBuilder: knitr
Config/pak/sysreqs: libicu-dev libjpeg-dev libssl-dev
        libpoppler-cpp-dev poppler-data
Repository: https://kmkuesters.r-universe.dev
Date/Publication: 2025-05-09 00:12:14 UTC
RemoteUrl: https://github.com/kmkuesters/pooledpeaks
RemoteRef: HEAD
RemoteSha: 1bcc8b6fd48c2b1b7fafc587d2af8523a814da2b
NeedsCompilation: no
Packaged: 2026-09-27 11:30:02 UTC; root
Author: Kathleen Kuesters [aut, cre, cph] (ORCID:
    <https://orcid.org/0000-0003-0238-7889>),
  Jeffrey Long [aut],
  Jessica Blanton [aut],
  Walter Blank [ctb],
  Jeffrey Kovach [ctb],
  Ronald Blanton [ctb]
Maintainer: Kathleen Kuesters <kathleen.kuesters@gmail.com>