R Observatory: Metrics for pez version 1.2-5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

pez

1.2-5

Phylogenetics for the Environmental Sciences

1packages depend

29Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by William D. PearseFirst published 2014-11-0810 releasesCRAN page ↗

Eco-phylogenetic and community phylogenetic analyses. Keeps community ecological and phylogenetic data matched up and comparable using 'comparative.comm' objects. Wrappers for common community phylogenetic indices ('pez.shape', 'pez.evenness', 'pez.dispersion', and 'pez.dissimilarity' metrics). Implementation of Cavender-Bares (2004) correlation of phylogenetic and ecological matrices ('fingerprint.regression'). Phylogenetic Generalised Linear Mixed Models (PGLMMs; 'pglmm') following Ives & Helmus (2011) and Rafferty & Ives (2013). Simulation of null assemblages, traits, and phylogenies ('scape', 'sim.meta.comm').

Install

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

install.packages("pez", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

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-pez

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-pez

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-pez

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

Health

CRAN checks

13OK

Slowest check: 4.7 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

12

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
OK2026-04-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-09
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 33% structuredCode of conductNoContributing guideNo

Examples that run: 91%
Documented parameters: 97%
Return-value docs: 80%
References docs: 59%

Downloads

29K

CRAN downloads in the past year

Rank #2,654 · ~79/day · ~2.4K/mo

Releases R versions

Daily download trend is not available in this view yet.

1.8K30 days

6.7K90 days

29K1 year

Compare downloads with other packages →

Also on136 r2u1 autocran44 c2d4u

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Depends (1)

ape

Imports (11)

caper picante quantreg mvtnorm vegan ade4 FD (>= 1.0-12)Matrixmethodsanimation (>= 2.4-0)phytools

LinkingTo (0)

none

Suggests (3)

knitr lme4 formatR

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

phyr

Code & Tests

Datasets

People & History

People (7)

Maintainer (1)

William D. Pearse

Author, Maintainer

Authors (7)

William D. Pearse

Author, Maintainer

Marc W. Cadotte

Author

Jeannine Cavender-Bares

Author

Matthew R. Helmus

Author

Anthony R. Ives

Author · added in 1.0-0

Caroline Tucker

Author

Steve C. Walker

Author

Listed in earlier versions (5)

Cadotte

no longer listed · 1.2-5

Helmus

no longer listed · 1.2-5

Ives

no longer listed · 1.2-5

Pearse

no longer listed · 1.2-5

Walker

no longer listed · 1.2-5

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.2-5Latest
2025-08-28 · 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
1.2-4
2022-08-31 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.2-3
2021-06-17 · diff ↗
unarchivedReturned to CRAN
2021-06-17
archivedRemoved from CRAN
2021-06-16
check problems were not corrected in time
R
R 4.1.0 released · 2021-05-18
1.2-2
2020-10-12 · diff ↗
1.2-1
2020-07-26 · diff ↗
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
1.2-0
2019-02-27 · diff ↗

Show 9 earlier events

R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
1.1-1
2016-01-15 · diff ↗
1.1-0
2015-08-06 · diff ↗
R
R 3.2.0 released · 2015-04-16
1.0-0
2015-02-11 · diff ↗
0.9-0
2014-11-08
R
R 3.1.0 released · 2014-04-10

Package metadata

First published: 2014-11-08
Total releases: 10 / 12 yrs
License: GPL-3 OSI
Bundled data: 2.8 KB / 1 file
Download size: 617 KB
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("pez")

Format

Pearse, W. D., Cadotte, M. W., Cavender-Bares, J., Helmus, M. R., Ives, A. R., Tucker, C., & Walker, S. C. (2025). pez: Phylogenetics for the Environmental Sciences (Version 1.2-5) [Computer software]. https://doi.org/10.32614/CRAN.package.pez

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 pez version 1.2-5 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →