R Observatory: Metrics for PhylogeneticEM version 1.8.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

PhylogeneticEM

1.8.1Package record

Automatic Shift Detection using a Phylogenetic EM

0packages depend

3.7Kdownloads / year

77.6%test coverage

13/13flavors OK

Overview

About

Maintained by Paul BastideCRAN page ↗GitHub ↗Website ↗Issues ↗

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.

Changes in 1.8.1

Deprecation fix:
change arma::is_finite(val) to std::isfinite(val)

From NEWS.md in the release

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. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 10.1 min · r-oldrel-macos-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
NOTE12 OK, 1 NOTE2026-06-08
OK12 OK2026-04-25

Show 3 earlier changesHide 3 earlier changes

NOTE12 OK, 2 NOTE2026-04-22
ERROR11 OK, 2 NOTE, 1 ERROR2026-04-18
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.8.1

README· In the repository, left out of the releaseVignettesYes · 2 · dynamicNEWSYes · 100% structured · mentions 1.8.1Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 143 (89 internal)
Examples that run: 67%6 run in a plain check (2 of them under a condition) · 3 never run
Exported functions with examples: 23%
Documented parameters: 95%
Return-value docs: 98%
Help pages citing references: 1%

Vignettes (2)

How these are measured

Downloads

3.7K

CRAN downloads in the past year

Rank #9,411 · ~10/day · ~306/mo

Releases R versions

Daily download trend is not available in this view yet.

38830 days

1K90 days

3.7K1 year

Compare downloads with other packages →

Also on367 r2u6 autocran4.6K conda_forge

How downloads are counted

Repository

pbastide/phylogeneticem ↗Account: pbastide

19Stars

4Forks

4Open issues

0Open PRs

11Releases

838Commits

4Commit identities

License file reads as GPL-2.0 · 838 commits · Last activity 2025-09-23 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 5
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-05-17 · 182026-07-07 · 19

How these are measured

PracticesBeta

9 development-tooling and community-health practices detected across 6 families in the upstream repository

Checks run against github.com/pbastide/phylogeneticem on 2026-10-21.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Docs source (3)

pkgdown

GitHub Pages site last deployed 2025-09-24 · The repository has a site deploy workflow

Coverage (1)

Coverage reporting

Reproducibility and dev environment (1)

data-raw/

Show all practicesHide 2 practices

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

18 external dependencies (excludes base and recommended)

Installing PhylogeneticEM adds 21 packages (13 with compiled code, 19 MB of source tarballs). Heaviest: pls 4.2 MB, glmnet 2.7 MB, robustbase 2.2 MB.

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.

How these are counted

Code & Tests

Datasets

People & History

People (2)

Paul Bastide

Author, Maintainer since 1.0.0 (2017)

Mahendra Mariadassou

Contributor

Releases (11)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.8.1Latest
record
2025-09-23 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
1.8.0
record
2025-02-15 · diff ↗ ·
added 1 export
merge_alpha_grids
R
R 4.4.0 released · 2024-04-24
1.7.0
record
2024-01-31 · diff ↗ ·
added 1 export
node_optimal_values
R
R 4.3.0 released · 2023-04-21
1.6.0
record
2022-08-31 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.5.0
record
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
record
2020-02-11 · diff ↗
1.3.0
record
2019-10-03 · diff ↗
R
R 3.6.0 released · 2019-04-26
1.2.1
record
2018-09-11 · diff ↗ ·
added 4 exports
find_rotation, get_criterion, merge_rotations, plot_criterion

Show 6 earlier eventsHide 6 earlier events

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

Cite

Cite this package

Run in R for the authors' entry:

citation("PhylogeneticEM")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1111/rssb.12206.

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 v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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