R Observatory: Metrics for codacore version 0.0.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

codacore

0.0.4Package record

Learning Sparse Log-Ratios for Compositional Data

0packages depend

2.8Kdownloads / year

0.0%test coverage

11/13flavors OK

Overview

About

Maintained by Elliott Gordon-RodriguezCRAN 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.

Changes in 0.0.4

---------------------

Update vignette.
Fix title.
Add incremental fit for cts. target.
Minor clarifications.
Updated README to reflect CRAN latest.
Add cvParams default values to func documentation.
Add helper funcs getNumLogRatios() and getTidyTable()
Add getBinaryPartitions function to retrieve SBP-like representation of learned balances.
Allow tibble inputs.

From NEWS.md in the release

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. 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-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). 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

2NOTE11OK

Check messages

NOTECRAN incoming feasibilityr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Maintainer: ‘Elliott Gordon-Rodriguez <eg2912@columbia.edu>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

CRAN check page ↗

Slowest check: 2.9 min · r-devel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTE2026-06-09
ERROR11 OK, 1 NOTE, 1 ERROR2026-06-08
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.0.4

READMEYes · 205 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 0.0.4Citation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 19
Examples that run: 0%1 never run
Exported functions with examples: 9%
Documented parameters: 100%
Return-value docs: 91%
Help pages citing references: 26%

Vignettes (1)

my-vignette HTML

How these are measured

Downloads

2.8K

CRAN downloads in the past year

Rank #13,585 · ~8/day · ~235/mo

Releases R versions

Daily download trend is not available in this view yet.

35630 days

84890 days

2.8K1 year

Compare downloads with other packages →

Also on102 r2u9 autocran

How downloads are counted

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Installing codacore adds 33 packages (19 with compiled code, 15 MB of source tarballs). Heaviest: keras 3.4 MB, tfruns 1.9 MB, Rcpp 1.8 MB.

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.

How these are counted

Code & Tests

Datasets

People & History

People (2)

Elliott Gordon-Rodriguez

Author, Maintainer since 0.0.3 (2022)

Thomas Quinn

Author

Releases (2)

Pick two releases to compare their code metrics.

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
record
2022-08-29 · current release · diff ↗ ·
added 3 exports
getBinaryPartitions, getNumLogRatios, getTidyTable
R
R 4.2.0 released · 2022-04-22
0.0.3
record
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

Appears in task views

Compositional Data Analysis

Cite

Cite this package

Run in R for the authors' entry:

citation("codacore")

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

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 v2026-10-21. 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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