Package: NeighborFinder
Title: Find Neighbor Species of a Bacteria of Interest in the Human Gut
        Microbiota
Version: 1.0.1
Authors@R: c(
    person("Mathilde", "Sola", , "mathilde.sola@inrae.fr", role = c("aut", "cre"),
           comment = c(ORCID = "0009-0009-0436-5078")),
    person("Mahendra", "Mariadassou", , "mahendra.mariadassou@inrae.fr", role = "aut",
           comment = c(ORCID = "0000-0003-2986-354X")),
    person("Magali", "Berland", , "magali.berland@inrae.fr", role = "aut",
           comment = c(ORCID = "0000-0002-6762-5350"))
  )
Description: Implementation of the local approach described in Sola et
    al., 2026 <doi:10.64898/2025.12.05.692507> to identify companion
    species of a bacteria of interest. From several abundance tables of
    metagenomic data, 'NeighborFinder' suggests a shortlist of companion
    species based on the integration of results. A visualization via a
    network is proposed.
License: MIT + file LICENSE
Depends: R (>= 3.5.0)
Imports: dplyr, GGally, glmnet, glue, igraph, magrittr, Matrix,
        mvtnorm, network, purrr, rlang, sna, stats, stringr, tibble,
        tidyr, utils
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
Config/fusen/version: 0.7.2
Config/roxygen2/version: 8.0.0
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.3.3
NeedsCompilation: no
Packaged: 2026-06-24 15:05:58 UTC; mmariadasso
Author: Mathilde Sola [aut, cre] (ORCID:
    <https://orcid.org/0009-0009-0436-5078>),
  Mahendra Mariadassou [aut] (ORCID:
    <https://orcid.org/0000-0003-2986-354X>),
  Magali Berland [aut] (ORCID: <https://orcid.org/0000-0002-6762-5350>)
Maintainer: Mathilde Sola <mathilde.sola@inrae.fr>
Repository: CRAN
Date/Publication: 2026-06-30 12:20:32 UTC
Built: R 4.5.3; ; 2026-07-04 05:31:05 UTC; windows
