R Observatory: Metrics for LDAcoop version 0.1.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

LDAcoop

0.1.2Package record

Analysis of Data from Limiting Dilution Assay (LDA) with or without Cellular Cooperation

0packages depend

2.1Kdownloads / year

100.0%test coverage

13/13flavors OK

Overview

About

Maintained by Daniel SamagaCRAN page ↗GitHub ↗Issues ↗

Cellular cooperation compromises the established method of calculating clonogenic activity from limiting dilution assay (LDA) data. This tool provides functions that enable robust analysis in presence or absence of cellular cooperation. The implemented method incorporates the same cooperativity module to model the non-linearity associated with cellular cooperation as known from the colony formation assay (Brix et al. (2021) doi:10.1038/s41596-021-00615-0: "Analysis of clonogenic growth in vitro." Nature protocols).

Install

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

install.packages("LDAcoop", 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/LDAcoop")

Development version from ZytoHMGU/LDAcoop. 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-ldacoop

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-LDAcoop

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-LDAcoop

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

13OK

CRAN check page ↗

Slowest check: 2.1 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.2

READMEYes · 7 wordsVignettesYes · 1 · dynamicNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 10
Examples that run: 100%10 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

LDAcoop HTML

How these are measured

Downloads

2.1K

CRAN downloads in the past year

Rank #22,812 · ~6/day · ~174/mo

Releases R versions

Daily download trend is not available in this view yet.

20930 days

55690 days

2.1K1 year

Compare downloads with other packages →

Also on69 r2u6 autocran

How downloads are counted

Repository

zytohmgu/ldacoop ↗Account: ZytoHMGU

0Stars

0Forks

0Open issues

0Open PRs

0Releases

Last activity 2024-07-17

Responsiveness

not measured

How these are measured

PracticesBeta

3 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/zytohmgu/ldacoop on 2026-10-11.

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

4 external dependencies (excludes base and recommended)

Installing LDAcoop adds 51 packages (26 with compiled code, 52 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

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.

How these are counted

Code & Tests

Datasets

People & History

People (5)

Daniel Samaga

Maintainer since 0.1.1 (2023), Author

Author

Author

Author

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
0.1.2Latest
record
2024-07-17 · current release · diff ↗
R
R 4.4.0 released · 2024-04-24
0.1.1
record
2023-10-09
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2023-10-09
Total releases: 2 / 3 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Bundled data: 2.7 KB / 1 file
Download size: 479 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("LDAcoop")

Format

Samaga, D., Brix, N., Danko, B., Lauber, K., & Zitzelsberger, H. (2024). LDAcoop: Analysis of Data from Limiting Dilution Assay (LDA) with or without Cellular Cooperation (Version 0.1.2) [Computer software]. https://doi.org/10.32614/CRAN.package.LDAcoop

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 LDAcoop version 0.1.2 [Data set]. HJJB, LLC. Data release v2026-10-17. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-17, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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