R Observatory: Metrics for PHENIX version 1.3.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

PHENIX

1.3.2Package record

Phenotypic Integration Index

0packages depend

2.4Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by A. J. Muñoz-PajaresCRAN page ↗

Provides functions to estimate the size-controlled phenotypic integration index, a novel method by Torices & Méndez (2014) doi:10.1086/676622 to solve problems due to individual size when estimating integration (namely, larger individuals have larger components, which will drive a correlation between components only due to resource availability that might obscure the observed measures of integration). In addition, the package also provides the classical estimation by Wagner (1984) doi:10.1007/BF00275224, bootstrapping and jackknife methods to calculate confidence intervals and a significance test for both integration indices. Further details can be found in Torices & Muñoz-Pajares doi:10.3732/apps.1400104.

Install

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

install.packages("PHENIX", 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-phenix

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-PHENIX

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-PHENIX

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: 1.2 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.3.2

READMENoVignettesNoNEWSNoCitation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 12includes a package overview page
Examples that run: 100%11 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 75%

How these are measured

Downloads

2.4K

CRAN downloads in the past year

Rank #19,660 · ~7/day · ~200/mo

Releases R versions

Daily download trend is not available in this view yet.

23930 days

67690 days

2.4K1 year

Compare downloads with other packages →

Also on67 r2u2 autocran

How downloads are counted

Dependencies

Declared dependencies

2 external dependencies (excludes base and recommended)

Installing PHENIX adds 2 packages (1 with compiled code, 140 KB of source tarballs). Heaviest: SuppDists 137 KB, ppcor 3.4 KB.

Depends (0)

none

Imports (2)

ppcor SuppDists

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (2)

A. J. Muñoz-Pajares

Author, Maintainer since 1.0 (2014)

R. Torices

Author

Listed in earlier versions (1)

Muñoz-Pajares

no longer listed · 1.3.2

Releases (8)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
unarchivedReturned to CRAN
2025-09-25
1.3.2Latest
record
2025-09-25 · current release · diff ↗
archivedRemoved from CRAN
2025-06-13
issues were not corrected despite reminders
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
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
1.3.1
record
2017-06-02 · diff ↗
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
1.3
record
2016-04-27 · diff ↗

Show 7 earlier eventsHide 7 earlier events

1.2.2
record
2016-03-03 · diff ↗
1.2.1
record
2016-01-28 · diff ↗
1.2
record
2015-04-29 · diff ↗ ·
added 2 exports
pint.jack, pintsc.jack
R
R 3.2.0 released · 2015-04-16
1.1
record
2015-01-27 · diff ↗ ·
removed 4 exports
int, int.boot, intsc, intsc.boot

added 6 exports
pint, pint.boot, pint.p, pintsc, pintsc.boot, pintsc.p
1.0
record
2014-10-24
R
R 3.1.0 released · 2014-04-10

Package metadata

First published: 2014-10-24
Total releases: 8 / 12 yrs
License: GPL (>= 2) OSI
Bundled data: 1.0 KB / 2 files
Download size: 12 KB

Cite

Cite this package

Run in R for the authors' entry:

citation("PHENIX")

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

It points to 10.3732/apps.1400104.

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 PHENIX version 1.3.2 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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