coda4microbiome

0.2.4

Compositional Data Analysis for Microbiome Studies

0packages depend

4.6Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Toni SusinFirst published 2022-03-179 releasesCRAN page ↗GitHub ↗

Functions for microbiome data analysis that take into account its compositional nature. Performs variable selection through penalized regression for both, cross-sectional and longitudinal studies, and for binary and continuous outcomes.

Install

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

install.packages("coda4microbiome", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("malucalle/coda4microbiome")

Development version from malucalle/coda4microbiome. 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-coda4microbiome

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-coda4microbiome

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-coda4microbiome

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

Health

CRAN checks

13OK

Slowest check: 6.3 min · r-devel-linux-x86_64-fedora-clang

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

None

Vignettes

README

Dependencies · direct

Check history

OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Downloads

4.6K

CRAN downloads in the past year

Rank #10,016 · ~13/day · ~381/mo

coda4microbiome Releases R versions

Daily download trend is not available in this view yet.

47030 days

1.1K90 days

4.6K1 year

Compare downloads with other packages →

Also on111 r2u25 autocran

Repository

GitHub ↗ malucalle/coda4microbiome

10Stars

0Forks

4Open issues

0Open PRs

0Releases

Dependencies

Declared dependencies

10 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (10)

corrplot glmnet plyr pROC ggpubr ggplot2 ComplexHeatmap circlizesurvivalsurvminer

LinkingTo (0)

none

Suggests (1)

rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

R 3,121 (67%)Rd 1,515 (33%)

Code characteristics

Cyclomatic complexity: 7.0 median / 32 max
Documented parameters: 100%

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

23 19 exported

Complexity

10.3 avg / 32 max

Call network

23 nodes / 28 edges

Test coverage has not been measured for this package yet; nodes fall back to a neutral fill.

Call graph

Open call graph →

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Lowest coverage

Per-function coverage is not measured for this package yet.

People & History

People (3)

Maintainer (1)

Toni Susin

Author, Maintainer

Authors (3)

Toni Susin

Author, Maintainer

Malu Calle

Author

Meritxell Pujolassos

Author

Release timeline

9 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
0.2.4Latest
2024-07-17 · current release · diff ↗
R
R 4.4.0 released · 2024-04-24
0.2.3
2024-02-21 · diff ↗
0.2.2
2024-01-26 · diff ↗
0.2.1
2023-12-21 · diff ↗
R
R 4.3.0 released · 2023-04-21
0.1.4
2023-02-09 · diff ↗
0.1.3
2022-12-19 · diff ↗
0.1.2
2022-11-07 · diff ↗
R
R 4.2.0 released · 2022-04-22
0.1.1
2022-03-31 · diff ↗
0.1.0
2022-03-17
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2022-03-17
Total releases: 9 / 4 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.5.0
Bundled data: 183 KB / 5 files
Download size: 212 KB
Installed size: not tracked yet
With dependencies: not tracked yet