EvoPhylo

0.3.5

Pre- And Postprocessing of Morphological Data from Relaxed Clock Bayesian Phylogenetics

0packages depend

3.1Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Tiago SimoesFirst published 2022-05-174 releasesCRAN page ↗GitHub ↗

Performs automated morphological character partitioning for phylogenetic analyses and analyze macroevolutionary parameter outputs from clock (time-calibrated) Bayesian inference analyses, following concepts introduced by Simões and Pierce (2021) doi:10.1038/s41559-021-01532-x.

Install

R (CRAN)pak (dev)Ubuntu (r2u)

install.packages("EvoPhylo", 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("tiago-simoes/EvoPhylo")

Development version from tiago-simoes/EvoPhylo. 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-evophylo

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

Health

CRAN checks

13OK

Slowest check: 7.6 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

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
OK2026-05-10
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-05-03
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 1 earlier snapshots

NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 93%
Documented parameters: 98%
Return-value docs: 100%
References docs: 15%

Downloads

3.1K

CRAN downloads in the past year

Rank #12,695 · ~9/day · ~261/mo

Releases R versions

Daily download trend is not available in this view yet.

24930 days

84490 days

3.1K1 year

Compare downloads with other packages →

Also on209 r2u35 c2d4u

Repository

GitHub ↗ tiago-simoes/evophylo

4Stars

5Forks

3Open issues

1Open PRs

3Releases

154Commits

5Contributors

154 commits · Last activity 2025-08-27

Stars over time

2024-04-18 · 42026-07-07 · 4

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/tiago-simoes/evophylo on 2026-07-19.

Continuous integration (1)

GitHub Actions

CRAN release process (1)

cran-comments.md

Docs source (1)

README.Rmd

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 (1)

R >= 4.0.0

Imports (16)

ape dplyrclusterdeeptime ggplot2 ggrepel ggtree patchwork treeio Rtsne (>= 0.15)unglue tidyr tibbletoolsphangorn magrittr

LinkingTo (0)

none

Suggests (4)

devtools kableExtra knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (4)

Maintainer (1)

Tiago Simoes

Maintainer, Author

Authors (4)

Tiago Simoes

Maintainer, Author

Joelle Barido-Sottani

Author · added in 0.3

Noah Greifer

Author

Stephanie Pierce

Author

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
0.3.5Latest
2025-08-27 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
0.3.2
2022-11-03 · diff ↗
0.3
2022-08-19 · diff ↗
0.1
2022-05-17
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2022-05-17
Total releases: 4 / 4 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 4.0.0
Bundled data: 2.5 MB / 11 files
Download size: 5.2 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Phylogenetics

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