R Observatory: Metrics for codacore version 0.0.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

codacore

0.0.4

Learning Sparse Log-Ratios for Compositional Data

0packages depend

2.7Kdownloads / year

0.0%test coverage

11/13checks pass

Overview

About

Maintained by Elliott Gordon-RodriguezFirst published 2022-01-072 releasesCRAN page ↗

In the context of high-throughput genetic data, CoDaCoRe identifies a set of sparse biomarkers that are predictive of a response variable of interest (Gordon-Rodriguez et al., 2021) doi:10.1093/bioinformatics/btab645. More generally, CoDaCoRe can be applied to any regression problem where the independent variable is Compositional (CoDa), to derive a set of scale-invariant log-ratios (ILR or SLR) that are maximally associated to a dependent variable.

Install

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

install.packages("codacore", 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-codacore

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-codacore

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-codacore

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

Health

CRAN checks

2NOTE11OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 2.8 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.09

0.0%

Coverage · measured lines

100%

Documentation · exports

5

Dependencies · direct

Check history

NOTE2026-06-09
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
11 OK · 1 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 205 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 0%
Documented parameters: 100%
Return-value docs: 91%
References docs: 26%

Downloads

2.7K

CRAN downloads in the past year

Rank #15,131 · ~7/day · ~226/mo

Releases R versions

Daily download trend is not available in this view yet.

18030 days

68690 days

2.7K1 year

Compare downloads with other packages →

Also on146 r2u17 autocran

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.6.0

Imports (5)

tensorflow keras pROC R6 (>= 2.5)gtools

LinkingTo (0)

none

Suggests (4)

zCompositions testthat knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (2)

Maintainer (1)

Elliott Gordon-Rodriguez

Author, Maintainer

Authors (2)

Elliott Gordon-Rodriguez

Author, Maintainer

Thomas Quinn

Author

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
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
0.0.4Latest
2022-08-29 · current release · diff ↗
R
R 4.2.0 released · 2022-04-22
0.0.3
2022-01-07
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2022-01-07
Total releases: 2 / 4 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.6.0
Bundled data: 75 KB / 3 files
Download size: 1.3 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Compositional Data Analysis

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("codacore")

Format

Gordon-Rodriguez, E., & Quinn, T. (2022). codacore: Learning Sparse Log-Ratios for Compositional Data (Version 0.0.4) [Computer software]. https://doi.org/10.32614/CRAN.package.codacore

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 codacore version 0.0.4 [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.

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