Package: phylter
Title: Detect and Remove Outliers in Phylogenomics Datasets
Version: 0.9.12
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
NeedsCompilation: yes
Packaged: 2025-07-29 13:30:16 UTC; siberchicot
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>
Repository: CRAN
Date/Publication: 2025-07-29 19:20:09 UTC
Built: R 4.6.0; x86_64-w64-mingw32; 2026-04-06 03:11:48 UTC; windows
Archs: x64
