ontophylo

1.1.3

Ontology-Informed Phylogenetic Comparative Analyses

0packages depend

2.2Kdownloads / year

22.4%test coverage

13/13checks pass

Overview

About

Maintained by Diego S. PortoFirst published 2023-12-202 releasesCRAN page ↗GitHub ↗

Provides new tools for analyzing discrete trait data integrating bio-ontologies and phylogenetics. It expands on the previous work of Tarasov et al. (2019) doi:10.1093/isd/ixz009. The PARAMO pipeline allows to reconstruct ancestral phenomes treating groups of morphological traits as a single complex character. The pipeline incorporates knowledge from ontologies during the amalgamation of individual character stochastic maps. Here we expand the current PARAMO functionality by adding new statistical methods for inferring evolutionary phenome dynamics using non-homogeneous Poisson process (NHPP). The new functionalities include: (1) reconstruction of evolutionary rate shifts of phenomes across lineages and time; (2) reconstruction of morphospace dynamics through time; and (3) estimation of rates of phenome evolution at different levels of anatomical hierarchy (e.g., entire body or specific regions only). The package also includes user-friendly tools for visualizing evolutionary rates of different anatomical regions using vector images of the organisms of interest.

Install

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

install.packages("ontophylo", 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("diegosasso/ontophylo")

Development version from diegosasso/ontophylo. 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-ontophylo

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-ontophylo

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-ontophylo

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

Health

CRAN checks

13OK

Slowest check: 4.5 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.22

22.4%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 54 wordsVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 98%
Documented parameters: 99%
Return-value docs: 100%
References docs: 18%

Downloads

2.2K

CRAN downloads in the past year

Rank #17,488 · ~6/day · ~187/mo

Releases R versions

Daily download trend is not available in this view yet.

23230 days

63890 days

2.2K1 year

Compare downloads with other packages →

Also on165 r2u33 autocran

Repository

GitHub ↗ diegosasso/ontophylo

2Stars

1Forks

1Open issues

0Open PRs

6Releases

15Commits

1Contributors

15 commits · Last activity 2024-01-17

Stars over time

2025-04-14 · 22026-07-07 · 2

Repository practices

Upstream repositoryBeta

Checks run against github.com/diegosasso/ontophylo on 2026-07-26.

No development-tooling practices detected in the upstream repository.

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

Dependencies

Declared dependencies

19 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (15)

magrittr dplyr tidyr purrr tibble ggplot2 stringdist ape phytools ontologyIndex RColorBrewergridtruncnorm fANCOVA grImport

LinkingTo (0)

none

Suggests (5)

rmarkdown knitr roxygen2 testthat stringr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (2)

Maintainer (1)

Diego S. Porto

Author, Maintainer

Authors (2)

Diego S. Porto

Author, Maintainer

Sergei Tarasov

Author

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.1.3Latest
2024-01-10 · current release · diff ↗
1.1.2
2023-12-20
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2023-12-20
Total releases: 2 / 3 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.5.0
Bundled data: 2.6 MB / 12 files
Download size: 2.7 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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