R Observatory: Metrics for PhylogeneticEM version 1.8.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

PhylogeneticEM

1.8.1

Automatic Shift Detection using a Phylogenetic EM

0packages depend

3.7Kdownloads / year

77.6%test coverage

13/13checks pass

Overview

About

Maintained by Paul BastideFirst published 2017-01-3111 releasesCRAN page ↗GitHub ↗

Implementation of the automatic shift detection method for Brownian Motion (BM) or Ornstein–Uhlenbeck (OU) models of trait evolution on phylogenies. Some tools to handle equivalent shifts configurations are also available. See Bastide et al. (2017) doi:10.1111/rssb.12206 and Bastide et al. (2018) doi:10.1093/sysbio/syy005.

Install

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

install.packages("PhylogeneticEM", 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("pbastide/PhylogeneticEM")

Development version from pbastide/PhylogeneticEM. 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-phylogeneticem

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-PhylogeneticEM

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-PhylogeneticEM

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

Health

CRAN checks

13OK

Slowest check: 12.7 min · r-devel-windows-x86_64

Code health

Yes

Tests · ratio 0.28

77.6%

Coverage · measured lines

100%

Documentation · exports

16

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
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
NOTE2026-06-08
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 3 earlier snapshots

NOTE2026-04-22
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 67%
Documented parameters: 95%
Return-value docs: 98%
References docs: 1%

Downloads

3.7K

CRAN downloads in the past year

Rank #11,345 · ~10/day · ~310/mo

Releases R versions

Daily download trend is not available in this view yet.

21030 days

87990 days

3.7K1 year

Compare downloads with other packages →

Also on407 r2u28 autocran4.9K conda_forge

Repository

GitHub ↗ pbastide/phylogeneticem

19Stars

4Forks

4Open issues

0Open PRs

11Releases

838Commits

4Contributors

License GPL-2.0 · 838 commits · Last activity 2025-09-24 · 0% stars, 30d

Stars over time

2025-05-17 · 182026-07-07 · 19

Repository practices

Upstream repositoryBeta

4 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/pbastide/phylogeneticem on 2026-08-23.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

18 external dependencies (excludes base and recommended)

Depends (3)

R >= 3.6.0apeMatrix

Imports (14)

capushe foreach gglasso glmnetgraphicsgrDevicesLINselectMASSmethodsplyr Rcpp robustbasestatsutils

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (7)

combinat doParallel phytools (>= 0.5.38)testthat TreeSim knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (2)

Maintainer (1)

Paul Bastide

Author, Maintainer

Authors (1)

Paul Bastide

Author, Maintainer

Contributors (1)

Mahendra Mariadassou

Contributor

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.8.1Latest
2025-09-23 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
1.8.0
2025-02-15 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.7.0
2024-01-31 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.6.0
2022-08-31 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.5.0
2021-09-16 · diff ↗
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
1.4.0
2020-02-11 · diff ↗
1.3.0
2019-10-03 · diff ↗
R
R 3.6.0 released · 2019-04-26
1.2.1
2018-09-11 · diff ↗

Show 6 earlier events

R
R 3.5.0 released · 2018-04-23
1.1.0
2017-09-08 · diff ↗
1.0.1
2017-05-01 · diff ↗
R
R 3.4.0 released · 2017-04-21
1.0.0
2017-01-31
R
R 3.3.0 released · 2016-05-03

Package metadata

First published: 2017-01-31
Total releases: 11 / 9 yrs
License: GPL (>= 2) | file LICENSE OSI
Minimum R: ≥ 3.6.0
Bundled data: 2.6 KB / 1 file
Download size: 628 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("PhylogeneticEM")

Format

Bastide, P., & Mariadassou, M. (2025). PhylogeneticEM: Automatic Shift Detection using a Phylogenetic EM (Version 1.8.1) [Computer software]. https://doi.org/10.32614/CRAN.package.PhylogeneticEM

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for PhylogeneticEM version 1.8.1 [Data set]. HJJB, LLC. Data release v2026-08-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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