phylter: Detect and Remove Outliers in Phylogenomics Datasets

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.

Version:	0.9.11
Depends:	R (≥ 4.0)
Imports:	ape, ggplot2, reshape2, Rfast, RSpectra, stats, utils
LinkingTo:	RcppEigen (≥ 0.3.2.9.0), Rcpp (≥ 0.12.6), RcppArmadillo (≥ 0.7.600.1.0)
Suggests:	knitr, rmarkdown
Published:	2023-08-24
Author:	Damien M. de Vienne [aut], Stéphane Dray [aut], Théo Tricou [aut], Aurélie Siberchicot [aut, cre]
Maintainer:	Aurélie Siberchicot <aurelie.siberchicot at univ-lyon1.fr>
BugReports:	https://github.com/damiendevienne/phylter/issues
License:	GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
NeedsCompilation:	yes
CRAN checks:	phylter results

Documentation:

Reference manual:	phylter.pdf
Vignettes:	2-PhylteR in a container 1-Use of phylter

Downloads:

Package source:	phylter_0.9.11.tar.gz
Windows binaries:	r-devel: phylter_0.9.11.zip, r-release: phylter_0.9.11.zip, r-oldrel: phylter_0.9.11.zip
macOS binaries:	r-release (arm64): phylter_0.9.11.tgz, r-oldrel (arm64): phylter_0.9.11.tgz, r-release (x86_64): phylter_0.9.11.tgz, r-oldrel (x86_64): phylter_0.9.11.tgz
Old sources:	phylter archive

Linking:

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