Package: BRCore
Title: A Unified Framework for Identification and Ecological
        Interpretation of Microbial Data from Bioenergy Research
        Centers
Version: 2.0.7.9000
Authors@R: c(
    person("Bolívar", "Aponte Rolón",
           email = "bolaponte@pm.me", 
           role = c("aut", "cre"),
           comment = c(ORCID = "0000-0002-2544-4551")),
    person("Gian Maria Niccolò", "Benucci",
           email = "benucci@msu.edu",
           role = "aut", 
           comment = c(ORCID = "0000-0003-1589-947X", "Co-maintainer")),
    person("Brandon", "Kristy", 
           role = "aut", 
           comment = c(ORCID = "0000-0003-2421-7143")),
    person("Ashley", "Shade", 
           role = "aut", 
           comment = c(ORCID = "0000-0002-7189-3067")),
    person("Nejc", "Stopnisek", 
           role = "aut", 
           comment = c(ORCID = "0000-0002-1532-6826")),
    person("Adina", "Howe", 
           role = "aut", 
           comment = c(ORCID = "0000-0002-7705-343X")),
    person("Center for Advanced Bioenergy and Bioproducts Innovation", 
           role = c("cph", "fnd")),
    person("Great Lakes Bioenergy Research Center", 
           role = c("cph", "fnd"))
  )
Description: A unified framework for identification and ecological
        interpretation of core microbiomes across time and space,
        enhancing robustness and reproducibility in microbiome data
        analysis. 'BRCore' implements the workflow proposed by Shade
        and Stopnisek (2019) and incorporates additional rarefaction
        steps. The proposed workflow aims to identify persistent
        microbiomes using abundance-occupancy distributions and neutral
        community model fitting. For more details on
        abundance-occupancy distributions see Shade A, Stopnisek N
        (2019) <doi:10.1016/j.mib.2019.09.008>, for neutral models, see
        Sloan et al. (2006) <doi:10.1111/j.1462-2920.2005.00956.x> and
        Burns et al. (2015) <doi:10.1038/ismej.2015.142>.
Depends: R (>= 4.4)
biocViews:
Imports: cli (>= 3.6.5), dplyr (>= 1.1.4), ggplot2 (>= 4.0.1), ggpubr
        (>= 0.6.2), ggrepel (>= 0.9.6), Hmisc (>= 5.2.4), magrittr (>=
        2.0.4), minpack.lm (>= 1.2.4), phyloseq, rlang (>= 1.1.6),
        scales (>= 1.4.0), stats4, tibble (>= 3.3.0), tidyr (>= 1.3.1),
        vegan (>= 2.7.2)
Suggests: knitr (>= 1.50), rmarkdown (>= 2.30), testthat (>= 3.2.3),
        tidyverse (>= 2.0.0), viridis (>= 0.6.5)
License: MIT + file LICENSE
Encoding: UTF-8
Language: en-US
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
Config/testthat/edition: 3
LazyData: true
VignetteBuilder: knitr
URL: https://github.com/germs-lab/BRCore,
        https://www.germslab.org/BRCore/
BugReports: https://github.com/germs-lab/BRCore/issues
Config/pak/sysreqs: cmake libglpk-dev make libicu-dev libuv1-dev
        libxml2-dev zlib1g-dev
Repository: https://germs-lab.r-universe.dev
Date/Publication: 2026-05-20 17:37:12 UTC
RemoteUrl: https://github.com/germs-lab/brcore
RemoteRef: HEAD
RemoteSha: b08c3c183ce71153685ef9ec9bba254a8dca6cb1
NeedsCompilation: no
Packaged: 2026-06-19 07:00:22 UTC; root
Author: Bolívar Aponte Rolón [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-2544-4551>),
  Gian Maria Niccolò Benucci [aut] (ORCID:
    <https://orcid.org/0000-0003-1589-947X>, Co-maintainer),
  Brandon Kristy [aut] (ORCID: <https://orcid.org/0000-0003-2421-7143>),
  Ashley Shade [aut] (ORCID: <https://orcid.org/0000-0002-7189-3067>),
  Nejc Stopnisek [aut] (ORCID: <https://orcid.org/0000-0002-1532-6826>),
  Adina Howe [aut] (ORCID: <https://orcid.org/0000-0002-7705-343X>),
  Center for Advanced Bioenergy and Bioproducts Innovation [cph, fnd],
  Great Lakes Bioenergy Research Center [cph, fnd]
Maintainer: Bolívar Aponte Rolón <bolaponte@pm.me>