R Observatory: Metrics for phyr version 1.1.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

phyr

1.1.3Package record

Model Based Phylogenetic Analysis

2packages dependsuggested by 1

144.4Kdownloads / year

51.4%test coverage

13/13flavors OK

Overview

About

Maintained by Daijiang LiCRAN page ↗GitHub ↗Website ↗Issues ↗

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. 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-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). 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: 9.9 min · r-release-macos-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK13 OK2026-06-02

Show 7 earlier changesHide 7 earlier changes

NOTE12 OK, 1 NOTE2026-05-29
OK13 OK2026-05-02
NOTE12 OK, 2 NOTE2026-04-22
ERROR11 OK, 2 NOTE, 1 ERROR2026-04-18
NOTE8 OK, 6 NOTE2026-04-06
ERROR8 OK, 5 NOTE, 1 ERROR2026-04-05
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1.3

READMEYes · 377 wordsVignettesYes · 3 · dynamicNEWSYes · 100% structured · does not mention 1.1.3Citation fileNoWebsiteYes · pkgdown

Help pages: 41
Examples that run: 80%4 run in a plain check · 1 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 21%
Documented parameters: 97%
Return-value docs: 100%
Help pages citing references: 12%

Vignettes (3)

How these are measured

Downloads

144.4K

CRAN downloads in the past year

Rank #1,166 · ~395/day · ~12K/mo

Releases R versions

Daily download trend is not available in this view yet.

7.1K30 days

29.3K90 days

144.4K1 year

Compare downloads with other packages →

Also on569 r2u7 autocran149 c2d4u

How downloads are counted

Repository

daijiang/phyr ↗Account: daijiang

36Stars

11Forks

34Open issues

0Open PRs

3Releases

583Commits

11Commit identities

rrpackageglmmbayesianphylogenyinlaspecies-distribution-modeling

License file reads as GPL-3.0 · 583 commits · Last activity 2026-05-18 · Default branch at 1.2.1, ahead of CRAN 1.1.3 (checked 2026-10-11)

Responsiveness

How these are sampled

PRs merged (all time): 96%
Median days to close, 50 most recently updated closed issues: 26
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-09-03 · 362026-07-07 · 36

How these are measured

PracticesBeta

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

Checks run against github.com/daijiang/phyr on 2026-10-11.

Continuous integration (3)

GitHub ActionsR CMD check workflowTravis CI (config file)

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

Governance and community (1)

Code of conduct

Docs source (3)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-05-18

Coverage (1)

Coverage reporting (Codecov)

Show all practicesHide 3 practices

Reproducibility and dev environment (1)

data-raw/

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v3 (2026-09-26)

AI coding toolsBeta

This repository shows signs of AI coding tools.

Claude Codefirst seen 2026-04-29
Named in .Rbuildignore: .claude
Named in .gitignore: .claude
Commits: at least 1 crediting it in the message

Models named in its commits

Claude Sonnet 4.61 commit · Apr 2026

Counts are commits, not lines of code. Commits by a tool's accounts count once across all of its accounts. Commits crediting it are the largest count among its credit lines, a minimum.How this is detected·Detection ruleset v4 (updated 2026-09-27)

Dependencies

Declared dependencies

27 external dependencies (excludes base and recommended)

Installing phyr adds 40 packages (26 with compiled code, 36 MB of source tarballs). Heaviest: stringi 11 MB, lme4 4.1 MB, nloptr 2.1 MB.

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

2direct

1indirect

Imports 2

Suggested by 1

Depends, Imports or LinkingTo, most downloaded first

rr2 invasible

Suggests, most downloaded first

phylosem

How these are counted

Code & Tests

Datasets

People & History

People (5)

Daijiang Li

Author, Maintainer since 1.0.0 (2019)

Author

Author

Author

Author

Listed in earlier versions (1)

Lucas A.

no longer listed · 1.0.0 to 1.1.3

Releases (5)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.1.3Latest
record
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
record
2020-12-18 · diff ↗ ·
removed 6 exports
pglmm.compare, pglmm.matrix.structure, pglmm.plot.ranef, pglmm.plot.re, pglmm.predicted.values, pglmm.profile.LRT

added 8 exports
pglmm_compare, pglmm_matrix_structure, pglmm_plot_ranef, pglmm_plot_re, pglmm_predicted_values, pglmm_profile_LRT, plot_bayes, plot_data
R
R 4.0.0 released · 2020-04-24
1.0.2
record
2019-11-13 · diff ↗
1.0.1
record
2019-11-10 · diff ↗ ·
removed 1 export
binaryPGLMM

added 1 export
pglmm.compare
1.0.0
record
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

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 package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 v2026-10-17. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-17, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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