phylter

0.9.12

Detect and Remove Outliers in Phylogenomics Datasets

0packages depend

2.7Kdownloads / year

–test coverage

12/13checks pass

Overview

About

Maintained by Aurélie SiberchicotFirst published 2023-01-204 releasesCRAN page ↗GitHub ↗

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.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("phylter", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("damiendevienne/phylter")

Development version from damiendevienne/phylter. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-phylter

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-phylter

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-phylter

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

1NOTE12OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 4.2 min · r-devel-linux-x86_64-fedora-clang

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 21%

Downloads

2.7K

CRAN downloads in the past year

Rank #13,705 · ~7/day · ~227/mo

Releases R versions

Daily download trend is not available in this view yet.

24130 days

74890 days

2.7K1 year

Compare downloads with other packages →

Also on413 r2u

Repository

GitHub ↗ damiendevienne/phylter

19Stars

5Forks

0Open issues

0Open PRs

4Releases

447Commits

4Contributors

phylogenetic-treesphylogeneticsphylogenomics

447 commits · Last activity 2025-12-14 · +5.6% stars, 30d

Stars over time

2025-04-11 · 112026-07-07 · 19

Repository practices

Upstream repositoryBeta

2 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/damiendevienne/phylter on 2026-08-02.

Continuous integration (1)

GitHub Actions

Research and citation (1)

codemeta.json

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

10 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.0

Imports (7)

ape ggplot2 reshape2 Rfast RSpectrastatsutils

LinkingTo (3)

RcppEigen Rcpp RcppArmadillo

Suggests (2)

knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (4)

Maintainer (1)

Aurélie Siberchicot

Contributor, Maintainer

Authors (3)

Stéphane Dray

Author

Théo Tricou

Author · added in 0.9.7

Damien M. de Vienne

Author

Contributors (1)

Aurélie Siberchicot

Contributor, Maintainer

Package Timeline

4 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.9.12Latest
2025-07-29 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
0.9.11
2023-08-24 · diff ↗
R
R 4.3.0 released · 2023-04-21
0.9.7
2023-02-27 · diff ↗
0.9.6
2023-01-20
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2023-01-20
Total releases: 4 / 3 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 4.0
Bundled data: 123 KB / 1 file
Download size: 4.3 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Anomaly Detection

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