R Observatory: Metrics for CFAcoop version 1.0.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

CFAcoop

1.0.0

Colony Formation Assay: Taking into Account Cellular Cooperation

0packages depend

3.2Kdownloads / year

100.0%test coverage

13/13checks pass

Overview

About

Maintained by Daniel SamagaFirst published 2020-11-252 releasesCRAN page ↗GitHub ↗

Cellular cooperation compromises the plating efficiency-based analysis of clonogenic survival data. This tool provides functions that enable a robust analysis of colony formation assay (CFA) data in presence or absence of cellular cooperation. The implemented method has been described in Brix et al. (2020). (Brix, N., Samaga, D., Hennel, R. et al. "The clonogenic assay: robustness of plating efficiency-based analysis is strongly compromised by cellular cooperation." Radiat Oncol 15, 248 (2020). doi:10.1186/s13014-020-01697-y) Power regression for parameter estimation, calculation of survival fractions, uncertainty analysis and plotting functions are provided.

Install

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

install.packages("CFAcoop", 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("ZytoHMGU/CFAcoop")

Development version from ZytoHMGU/CFAcoop. 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-cfacoop

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-CFAcoop

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-CFAcoop

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

Health

CRAN checks

13OK

Slowest check: 2.5 min · r-release-macos-x86_64

Code health

Yes

Tests · ratio 0.39

100.0%

Coverage · measured lines

100%

Documentation · exports

1

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
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

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 17%

Downloads

3.2K

CRAN downloads in the past year

Rank #14,404 · ~9/day · ~263/mo

Releases R versions

Daily download trend is not available in this view yet.

16530 days

71790 days

3.2K1 year

Compare downloads with other packages →

Also on111 r2u30 autocran

Repository

GitHub ↗ zytohmgu/cfacoop

0Stars

1Forks

0Open issues

0Open PRs

0Releases

16Commits

1Contributors

16 commits · Last activity 2021-06-11

Repository practices

Upstream repositoryBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

Checks run against github.com/zytohmgu/cfacoop on 2026-08-16.

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

4 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (1)

Hmisc

LinkingTo (0)

none

Suggests (3)

knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (4)

Maintainer (1)

Daniel Samaga

Maintainer, Author

Authors (4)

Maintainer, Author

Author

Author

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
R
R 4.2.0 released · 2022-04-22
1.0.0Latest
2021-06-11 · current release · diff ↗
R
R 4.1.0 released · 2021-05-18
0.1.0
2020-11-25
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-11-25
Total releases: 2 / 6 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Bundled data: 4.4 KB / 1 file
Download size: 273 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("CFAcoop")

Format

Samaga, D., Brix, N., Lauber, K., & Zitzelsberger, H. (2021). CFAcoop: Colony Formation Assay: Taking into Account Cellular Cooperation (Version 1.0.0) [Computer software]. https://doi.org/10.32614/CRAN.package.CFAcoop

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 CFAcoop version 1.0.0 [Data set]. HJJB, LLC. Data release v2026-08-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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