R Observatory: Metrics for phyr version 1.1.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

phyr

1.1.3

Model Based Phylogenetic Analysis

3packages depend

164.1Kdownloads / year

51.4%test coverage

13/13checks pass

Overview

About

Maintained by Daijiang LiFirst published 2019-10-245 releasesCRAN page ↗GitHub ↗

A collection of functions to do model-based phylogenetic analysis. It includes functions to calculate community phylogenetic diversity, to estimate correlations among functional traits while accounting for phylogenetic relationships, and to fit phylogenetic generalized linear mixed models. The Bayesian phylogenetic generalized linear mixed models are fitted with the 'INLA' package (https://www.r-inla.org).

Install

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

install.packages("phyr", 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("daijiang/phyr")

Development version from daijiang/phyr. 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-phyr

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-phyr

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-phyr

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

Health

CRAN checks

13OK

Slowest check: 9.9 min · r-release-macos-x86_64

Code health

Yes

Tests · ratio 0.15

51.4%

Coverage · measured lines

97%

Documentation · exports

13

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
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-06-02
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 7 earlier snapshots

NOTE2026-05-29
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-05-02
13 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
NOTE2026-04-06
8 OK · 6 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-05
8 OK · 5 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 377 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 97%
Return-value docs: 100%
References docs: 12%

Downloads

164.1K

CRAN downloads in the past year

Rank #1,127 · ~450/day · ~13.7K/mo

Releases R versions

Daily download trend is not available in this view yet.

10.7K30 days

33.4K90 days

164.1K1 year

Compare downloads with other packages →

Also on534 r2u15 autocran68 c2d4u

Repository

GitHub ↗ daijiang/phyr

36Stars

11Forks

34Open issues

0Open PRs

3Releases

583Commits

11Contributors

rrpackageglmmbayesianphylogenyinlaspecies-distribution-modeling

License GPL-3.0 · 583 commits · Last activity 2026-05-18 · 0% stars, 30d

Stars over time

2025-07-15 · 352026-07-07 · 36

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/daijiang/phyr on 2026-08-09.

Continuous integration (2)

GitHub ActionsTravis CI

Reproducibility and dev environment (1)

data-raw/

CRAN release process (1)

cran-comments.md

Docs source (1)

README.Rmd

Show all practices

Lint, format, editor (1)

RStudio project

Coverage (1)

Codecov

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

Development tooling

AI-assisted toolingBeta

Uses AI-assisted development tooling (declared in repo)

Earliest detected marker: claude on 2026-04-29

claude

Most recent: claude on 2026-04-29

Evidence

claude: on 2026-04-29 · evidence B, D

How this is detected·Detection ruleset v2 (updated 2026-07-29)

Dependencies

Declared dependencies

27 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.1

Imports (13)

statsape RcppMatrixmethodsgraphicsdplyr lme4 nloptr gridExtra mvtnorm latticeExtra tidyr

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (16)

testthat pez knitr rmarkdown covr picante rbenchmark INLA MCMCglmm logistf phylolm ggplot2 ggridges DHARMa rr2 future.apply

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

3direct

1indirect

invasible rr2 phylosem

Code & Tests

Datasets

People & History

People (5)

Maintainer (1)

Daijiang Li

Author, Maintainer

Authors (5)

Author, Maintainer

Author

Author

Author

Author

Listed in earlier versions (1)

Lucas A.

no longer listed · 1.0.0 to 1.1.3

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.1.3Latest
2025-11-11 · 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
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
1.1.0
2020-12-18 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.0.2
2019-11-13 · diff ↗
1.0.1
2019-11-10 · diff ↗
1.0.0
2019-10-24
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-10-24
Total releases: 5 / 7 yrs
License: GPL-3 OSI
Additional repositories: inla.r-inla-download.org
Minimum R: ≥ 3.1
Bundled data: 7.2 KB / 6 files
Download size: 1.5 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Mixed, Multilevel, and Hierarchical Models in R

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("phyr")

Format

Li, D., Dinnage, R., Helmus, M., Ives, A., & Nell, L. A. (2025). phyr: Model Based Phylogenetic Analysis (Version 1.1.3) [Computer software]. https://doi.org/10.32614/CRAN.package.phyr

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 phyr version 1.1.3 [Data set]. HJJB, LLC. Data release v2026-08-15. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-15, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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