Package: pgacmdr
Title: Interactive Shiny Application for Population Genetics
Version: 0.1.0
Authors@R: c(
    person("Naffiou", "Kadiri",
           email = "naffiou.kadiri@ird.fr",
           role = c("aut", "cre")),
    person("Vincent", "Manzanilla",
           email = "vincent.manzanilla@ird.fr",
           role = "aut"),
    person("Thierry", "de Meeûs",
           email = "thierry.demeeus@ird.fr",
           role = "aut"),
    person("INTERTRYP, IRD, CIRAD",
           role = "cph")
    )
BugReports: https://github.com/KadNaf/PGA-cmdr/issues
URL: https://github.com/KadNaf/PGA-cmdr
Description: PGA-cmdr is an interactive 'shiny' application for
        population genetics analyses of multilocus individual genotype
        data from codominant markers (microsatellites, allozymes,
        SNPs). It covers data import and formatting, allele frequencies
        and missing data, observed and expected heterozygosity,
        F-statistics (FIS, FST, FIT) following Weir and Cockerham
        (1984) <doi:10.1111/j.1558-5646.1984.tb05657.x>, and gene
        diversities (HS, HT) following Nei and Chesser (1983)
        <doi:10.1111/j.1469-1809.1983.tb00993.x>. Analyses include
        local and global panmixia tests, population subdivision with a
        G-based test of genotypic differentiation, pairwise linkage
        disequilibrium tests, null allele frequency estimation with the
        ENA correction of Chapuis and Estoup (2007)
        <doi:10.1093/molbev/msl191>, and isolation by distance using
        the regression of Rousset (1997)
        <doi:10.1093/genetics/145.4.1219> and a Mantel test. Confidence
        intervals are obtained by bootstrap over individuals,
        sub-samples or loci, and p-values by Monte Carlo permutation,
        computed in parallel in C++ via 'Rcpp' and 'OpenMP'. All
        computations run locally and no data leave the user's computer.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 4.1.0)
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
Imports: shiny (>= 1.7.0), bslib (>= 0.9.0), shinydashboard,
        shinyWidgets, shinyalert, dplyr, tidyr, kableExtra, knitr, Rcpp
        (>= 1.0.0), tibble, waiter, parallel, stats, utils, graphics,
        duckdb, DBI, jsonlite, htmltools, magrittr, zip
LinkingTo: Rcpp
VignetteBuilder: knitr
SystemRequirements: C++17, OpenMP
Suggests: testthat (>= 3.0.0), digest, golem (>= 0.4.0), knitr,
        rmarkdown, hierfstat
Config/testthat/edition: 3
Config/pak/sysreqs: cmake libfontconfig1-dev libfreetype6-dev
        libfribidi-dev make libharfbuzz-dev libicu-dev libpng-dev
        libuv1-dev libxml2-dev xz-utils zlib1g-dev
Repository: https://kadnaf.r-universe.dev
Date/Publication: 2026-10-20 01:48:47 UTC
RemoteUrl: https://github.com/KadNaf/PGA-cmdr
RemoteRef: HEAD
RemoteSha: 31045c1cabdd0a519c3408ad1644b785de02eac9
NeedsCompilation: yes
Packaged: 2026-10-20 05:12:25 UTC; root
Author: Naffiou Kadiri [aut, cre],
  Vincent Manzanilla [aut],
  Thierry de Meeûs [aut],
  INTERTRYP, IRD, CIRAD [cph]
Maintainer: Naffiou Kadiri <naffiou.kadiri@ird.fr>