R Observatory: Metrics for pez version 1.2-5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

pez

1.2-5Package record

Phylogenetics for the Environmental Sciences

0packages dependsuggested by 1

24.2Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by William D. PearseCRAN 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. 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-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). 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: 4.4 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-04-10
ERROR13 OK, 1 ERROR2026-04-09
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.2-5

READMENoVignettesYes · 2 · dynamicNEWSYes · 33% structuredCitation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 29 (1 internal)includes a package overview page
Examples that run: 91%21 run in a plain check · 2 never run
Exported functions with examples: 80%
Documented parameters: 97%
Return-value docs: 80%
Help pages citing references: 59%

Vignettes (2)

pez-intro PDF
pez-pglmm-overview PDF

How these are measured

Downloads

24.2K

CRAN downloads in the past year

Rank #2,983 · ~66/day · ~2K/mo

Releases R versions

Daily download trend is not available in this view yet.

1.5K30 days

4.5K90 days

24.2K1 year

Compare downloads with other packages →

Also on170 r2u2 autocran84 c2d4u

How downloads are counted

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Installing pez adds 52 packages (29 with compiled code, 39 MB of source tarballs). Heaviest: igraph 4.8 MB, magick 4.4 MB, sp 4.3 MB.

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

0direct

0indirect

Suggested by 1

Suggests, most downloaded first

phyr

How these are counted

Code & Tests

Datasets

People & History

People (7)

William D. Pearse

Author, Maintainer since 0.9-0 (2014)

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)

Show 5 peopleHide 5 people

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

Releases (10)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.2-5Latest
record
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
record
2022-08-31 · diff ↗
R
R 4.2.0 released · 2022-04-22
unarchivedReturned to CRAN
2021-06-17
1.2-3
record
2021-06-17 · diff ↗
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
record
2020-10-12 · diff ↗ ·
removed 1 export
.colless
1.2-1
record
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
record
2019-02-27 · diff ↗ ·
removed 1 export
bind.replace

added 9 exports
.bed, .pe, .ses.vntd, .ses.vpd, .vntd, .vpd, congeneric.impute, fibre.plot, pez.endemism

Show 9 earlier eventsHide 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
record
2016-01-15 · diff ↗
1.1-0
record
2015-08-06 · diff ↗ ·
removed 5 exports
dispersion, dissimilarity, evenness, print.phy.structure, shape

added 48 exports
.aed, .colless, .comdist, .d, .delta, .dist.fd, .eaed, .eco.null, .eed, .eigen.sum, .gamma, .haed, .hed, .iac, .innd, .kappa, .lambda, .metric.null, .mipd, .mntd, .mpd, .pae, .pcd, .pd, .phylo.entropy, .phylosor, .pse, .psr, .psv, .rao and 18 more
R
R 3.2.0 released · 2015-04-16
1.0-0
record
2015-02-11 · diff ↗ ·
added 17 exports
comm<-, env<-, phy<-, traits<-, tree<-, comm, communityPGLMM, communityPGLMM.binary, communityPGLMM.binary.LRT, communityPGLMM.gaussian, communityPGLMM.matrix.structure, communityPGLMM.predicted.values, env, phy, print.phy.structure, traits, tree
0.9-0
record
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

Appears in task views

Mixed, Multilevel, and Hierarchical Models in R

Cite

Cite this package

Run in R for the authors' entry:

citation("pez")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1093/bioinformatics/btv277.

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 v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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