R Observatory: Metrics for propr version 4.2.6

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

This package was removed from CRAN on 2022-11-10. Its history is shown below.

Reason: issues were not corrected in time

Details below reflect version 4.2.6, its last release before removal.

propr

4.2.6

Calculating Proportionality Between Vectors of Compositional Data

0packages depend

–downloads / year

–test coverage

–checks pass

Overview

About

Maintained by Thomas Quinn21 releasesCRAN page ↗GitHub ↗

The bioinformatic evaluation of gene co-expression often begins with correlation-based analyses. However, correlation lacks validity when applied to relative data, including count data generated by next-generation sequencing. This package implements several metrics for proportionality, including phi [Lovell et al (2015) DOI:10.1371/journal.pcbi.1004075] and rho [Erb and Notredame (2016) DOI:10.1007/s12064-015-0220-8]. This package also implements several metrics for differential proportionality. Unlike correlation, these measures give the same result for both relative and absolute data.

Install

R (source archive)pak (dev)Ubuntu (r2u)openSUSE (OBS)

url <- "https://cran.r-project.org/src/contrib/Archive/propr/propr_4.2.6.tar.gz"
pkgFile <- "propr_4.2.6.tar.gz"
download.file(url, pkgFile)
install.packages(pkgFile, type = "source", repos = NULL)

This package is no longer on CRAN, so install.packages() cannot fetch it by name. This downloads the last archived source (4.2.6) and builds it locally. Install its dependencies first, and note that building from source needs the usual compiler toolchain.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("tpq/propr")

Development version from tpq/propr. 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-propr

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

# 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-propr

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

Health

CRAN checks

CRAN check results are not tracked yet.

Code health

Yes

Tests · ratio 0.24

not tracked

Coverage

100%

Documentation · exports

8

Dependencies · direct

Documentation

READMEYes · 491 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: not tracked
Documented parameters: 97%
Return-value docs: 96%
References docs: 0%

Downloads

Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

Also on320 r2u15 autocran12.3K conda_forge

Dependencies

Declared dependencies

20 external dependencies (excludes base and recommended)

Depends (2)

R >= 3.2.2methods

Imports (7)

fastcluster ggplot2grDevicesigraph Rcppstatsutils

LinkingTo (1)

Rcpp

Suggests (18)

ALDEx2 Biobase cccrm compositions data.tabledatasetsgridggdendro knitr limmaparallelplotly reshape2 rgl rmarkdown SDMTools testthat vegan

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (6)

Maintainer (1)

Thomas Quinn

Author, Maintainer

Authors (3)

Thomas Quinn

Author, Maintainer

David Lovell

Author

Ionas Erb

Author · added in 2.1.1

Contributors (3)

Anders Bilgrau

Contributor · added in 2.1.1

Greg Gloor

Contributor · added in 2.1.8

Ryan Moore

Contributor · added in 4.2.6

Package Timeline

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

R
R 4.3.0 released · 2023-04-21
archivedRemoved from CRAN
2022-11-10
issues were not corrected in time
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
4.2.6
2019-12-16 · diff ↗
4.1.6
2019-07-10 · diff ↗
R
R 3.6.0 released · 2019-04-26
4.1.1
2018-11-19 · diff ↗
4.0.0
2018-07-25 · diff ↗
3.5.1
2018-05-09 · diff ↗
R
R 3.5.0 released · 2018-04-23
3.1.9
2018-04-19 · diff ↗
3.1.8
2018-03-21 · diff ↗
3.1.4
2018-01-18 · diff ↗
3.1.2
2017-12-14 · diff ↗

Show 14 earlier events

3.1.1
2017-11-13 · diff ↗
3.0.7
2017-09-07 · diff ↗
3.0.6
2017-08-01 · diff ↗
3.0.4
2017-06-02 · diff ↗
R
R 3.4.0 released · 2017-04-21
2.2.0
2017-04-19 · diff ↗
2.1.8
2017-03-09 · diff ↗
2.1.2
2017-02-02 · diff ↗
2.1.1
2016-12-21 · diff ↗
2.0.4
2016-10-31 · diff ↗
2.0.1
2016-09-30 · diff ↗
2.0.0
2016-08-27 · diff ↗
1.1.0
2016-07-06
R
R 3.3.0 released · 2016-05-03

Package metadata

Total releases: 21
License: GPL-2 OSI
Minimum R: ≥ 3.2.2
Bundled data: 1.2 MB / 9 files
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("propr")

Format

Quinn, T., Lovell, D., Erb, I., Bilgrau, A., Gloor, G., & Moore, R. (n.d.). propr: Calculating Proportionality Between Vectors of Compositional Data (Version 4.2.6) [Computer software]. Retrieved August 13, 2026, from https://CRAN.R-project.org/package=propr

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 propr version 4.2.6 [Data set]. HJJB, LLC. Data release v2026-08-13. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-13, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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