PhylogeneticEM

1.8.1

Automatic Shift Detection using a Phylogenetic EM

0packages depend

3.8Kdownloads / year

–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: 12.2 min · r-devel-linux-x86_64-fedora-gcc

Code health

Yes

Tests · ratio 0.28

not tracked

Coverage

100%

Documentation · exports

Yes

Vignettes

README

Dependencies · direct

Check history

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
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

Show 1 earlier snapshots

NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Downloads

3.8K

CRAN downloads in the past year

Rank #12,329 · ~11/day · ~320/mo

PhylogeneticEM Releases R versions

Daily download trend is not available in this view yet.

39930 days

86490 days

3.8K1 year

Compare downloads with other packages →

Also on424 r2u23 autocran4.8K conda_forge

Repository

GitHub ↗ pbastide/phylogeneticem

19Stars

4Forks

4Open issues

0Open PRs

11Releases

License GPL-2.0

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

Code Composition

R 19,318 (73%)Rd 5,518 (21%)C++ 854 (3%)Vignettes 558 (2%)C 191 (1%)

Code characteristics

Object systems

S327

Cyclomatic complexity: 2.0 median / 74 max
Test cases: 53 / 0.28 per code line
Documented parameters: 95%

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

350 40 exported

Complexity

4 avg / 74 max

Call network

350 nodes / 371 edges

Test coverage has not been measured for this package yet; nodes fall back to a neutral fill.

Call graph

Open call graph →

Loading call graph…

Lowest coverage

Per-function coverage is not measured for this package yet.

People & History

People (2)

Maintainer (1)

Paul Bastide

Author, Maintainer

Authors (1)

Paul Bastide

Author, Maintainer

Contributors (1)

Mahendra Mariadassou

Contributor

Release 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