R Observatory: Metrics for CoDiNA version 1.1.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

CoDiNA

1.1.2Package record

Co-Expression Differential Network Analysis

0packages dependsuggested by 1

3.5Kdownloads / year

–test coverage

11/13flavors OK

Overview

About

Maintained by Deisy Morselli GysiCRAN page ↗

Categorize links and nodes from multiple networks in 3 categories: Common links (alpha) specific links (gamma), and different links (beta). Also categorizes the links into sub-categories and groups. The package includes a visualization tool for the networks. More information about the methodology can be found at: Gysi et. al., 2018 arXiv:1802.00828.

Install

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

install.packages("CoDiNA", 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-codina

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-CoDiNA

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-CoDiNA

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: ‘Deisy Morselli Gysi <deisy.ccnr@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Deisy", "Morselli"),
                      family = "Gysi",
                      role = c("aut", "cre"),
                      email = "deisy.ccnr@gmail.com"),
               person(given = c("Tiago", "de", "Miranda"),
                      family = "Fragoso",
                      role = "aut"),
               person(given = "Eivind",
                      family = "Almaas",
                      role = "aut"),
               person(given = "Katja",
                      family = "Nowick.",
                      role = "aut"))
as necessary.

The Description field contains
  <arXiv:1802.00828>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.

CRAN check page ↗

Slowest check: 1.4 min · r-oldrel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTENow
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1.2

READMENoVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 17 (4 internal)
Examples that run: 100%12 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 67%
Help pages citing references: 24%

How these are measured

Downloads

3.5K

CRAN downloads in the past year

Rank #11,248 · ~10/day · ~289/mo

Releases R versions

Daily download trend is not available in this view yet.

31530 days

95390 days

3.5K1 year

Compare downloads with other packages →

Also on91 r2u10 autocran

How downloads are counted

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Installing CoDiNA adds 39 packages (23 with compiled code, 48 MB of source tarballs). Heaviest: stringi 11 MB, data.table 5.7 MB, bslib 5.6 MB.

Depends (1)

R >= 3.1

Imports (6)

data.table igraph magrittr plyr visNetwork reshape2

LinkingTo (0)

none

Suggests (3)

knitr rmarkdown wTO

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Suggested by 1

Suggests, most downloaded first

NetSci

How these are counted

Code & Tests

Datasets

People & History

People (from the free-text Author field) (4)

Deisy Morselli Gysi

Tiago de Miranda Fragoso

Eivind Almaas

Katja Nowick.

Maintainer since 1.0.0 (2018)

Releases (4)

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
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
1.1.2Latest
record
2020-07-15 · current release · diff ↗
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
1.1.1
record
2019-03-06 · diff ↗
1.1
record
2018-07-06 · diff ↗ ·
removed 1 export
makeDiffNet

added 2 exports
ClusterNodes, MakeDiffNet
R
R 3.5.0 released · 2018-04-23
1.0.0
record
2018-02-08
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2018-02-08
Total releases: 4 / 8 yrs
License: GPL-2 OSI
Minimum R: ≥ 3.1
Bundled data: 429 KB / 4 files
Download size: 443 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("CoDiNA")

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 CoDiNA version 1.1.2 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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