Package: phylter
Title: Detect and Remove Outliers in Phylogenomics Datasets
Version: 1.0.0
Imports: ape, ggplot2, reshape2, Rfast, RSpectra, stats, utils
Suggests: knitr, rmarkdown
LinkingTo: RcppEigen (>= 0.3.2.9.0), Rcpp (>= 0.12.6), RcppArmadillo
        (>= 0.7.600.1.0)
Authors@R: c(
    person("Damien M.", "de Vienne", role = "aut", email = "damien.de-vienne@univ-lyon1.fr", comment = c(ORCID = "0000-0001-9532-5251")),
    person("Stéphane", "Dray", role = "aut", email = "stephane.dray@univ-lyon1.fr", comment = c(ORCID = "0000-0003-0153-1105")),
    person("Théo", "Tricou", role = "aut", email = "treecou.theo@gmail.com", comment = c(ORCID = "0000-0002-4432-2680")),
    person("Aurélie", "Siberchicot", role = c("ctb", "cre"), email = "aurelie.siberchicot@univ-lyon1.fr", comment = c(ORCID = "0000-0002-7638-8318"))
    )
License: GPL (>= 2)
Description: Analyzis and filtering of phylogenomics datasets. It takes
        an input either a collection of gene trees (then transformed to
        matrices) or directly a collection of gene matrices and
        performs an iterative process to identify what species in what
        genes are outliers, and whose elimination significantly
        improves the concordance between the input matrices. The
        methods builds upon the Distatis approach (Abdi et al. (2005)
        <doi:10.1101/2021.09.08.459421>), a generalization of classical
        multidimensional scaling to multiple distance matrices.
LazyData: true
Depends: R (>= 4.0)
BugReports: https://github.com/damiendevienne/phylter/issues
URL: https://github.com/damiendevienne/phylter
Encoding: UTF-8
RoxygenNote: 7.3.2
VignetteBuilder: knitr
Config/pak/sysreqs: cmake libicu-dev
Repository: https://damiendevienne.r-universe.dev
Date/Publication: 2026-10-08 06:59:48 UTC
RemoteUrl: https://github.com/damiendevienne/phylter
RemoteRef: HEAD
RemoteSha: c57f25e910e38e335be3c1da2fac8d004c1bf815
NeedsCompilation: yes
Packaged: 2026-10-08 09:24:19 UTC; root
Author: Damien M. de Vienne [aut] (ORCID:
    <https://orcid.org/0000-0001-9532-5251>),
  Stéphane Dray [aut] (ORCID: <https://orcid.org/0000-0003-0153-1105>),
  Théo Tricou [aut] (ORCID: <https://orcid.org/0000-0002-4432-2680>),
  Aurélie Siberchicot [ctb, cre] (ORCID:
    <https://orcid.org/0000-0002-7638-8318>)
Maintainer: Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
