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) ), 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: ), Stéphane Dray [aut] (ORCID: ), Théo Tricou [aut] (ORCID: ), Aurélie Siberchicot [ctb, cre] (ORCID: ) Maintainer: Aurélie Siberchicot