R Observatory: Metrics for scModels version 1.0.5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

scModels

1.0.5

Fitting Discrete Distribution Models to Count Data

0packages depend

961downloads / year

36.3%test coverage

13/13checks pass

Overview

About

Maintained by Kumar HarshaFirst published 2026-06-056 releasesCRAN page ↗

Provides functions for fitting discrete distribution models to count data. Included are the Poisson, the negative binomial, the Poisson-inverse gaussian and, most importantly, a new implementation of the Poisson-beta distribution (density, distribution and quantile functions, and random number generator) together with a needed new implementation of Kummer's function (also: confluent hypergeometric function of the first kind). Three different implementations of the Gillespie algorithm allow data simulation based on the basic, switching or bursting mRNA generating processes. Moreover, likelihood functions for four variants of each of the three aforementioned distributions are also available. The variants include one population and two population mixtures, both with and without zero-inflation. The package depends on the 'MPFR' libraries (https://www.mpfr.org/) which need to be installed separately (see description at https://github.com/fuchslab/scModels). This package is supplement to the paper "A mechanistic model for the negative binomial distribution of single-cell mRNA counts" by Lisa Amrhein, Kumar Harsha and Christiane Fuchs (2019) doi:10.1101/657619 available on bioRxiv.

Install

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

install.packages("scModels", 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-scmodels

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-scModels

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-scModels

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

Health

CRAN checks

13OK

Slowest check: 4.5 min · r-devel-windows-x86_64

Code health

Yes

Tests · ratio 0.08

36.3%

Coverage · measured lines

100%

Documentation · exports

2

Dependencies · direct

Check history

OK2026-08-04
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-06
7 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 52%
Return-value docs: 0%
References docs: 0%

Downloads

961

CRAN downloads in the past year

Rank #10,189 · ~3/day · ~80/mo

Releases R versions

Daily download trend is not available in this view yet.

23130 days

93490 days

9611 year

Compare downloads with other packages →

Also on391 r2u16 autocran47 c2d4u

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.1.0

Imports (2)

Rcpp gamlss.dist

LinkingTo (1)

Rcpp

Suggests (3)

knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (4)

Maintainer (1)

Kumar Harsha

Author, Maintainer

Authors (3)

Kumar Harsha

Author, Maintainer

Lisa Amrhein

Author

Christiane Fuchs

Author

Contributors (1)

Pavel Holoborodko

Contributor

Package Timeline

6 releases. Pick two to compare their code metrics. R releases are shown for context.

1.0.5Latest
2026-06-05 · current release · diff ↗
unarchivedReturned to CRAN
2026-06-05
R
R 4.6.0 released · 2026-04-24
archivedRemoved from CRAN
2026-03-09
issues were not corrected despite reminders
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
1.0.4
2023-01-24 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.0.3
2022-03-29 · diff ↗
unarchivedReturned to CRAN
2022-03-29
archivedRemoved from CRAN
2022-03-17
check problems were not corrected in time Does not install with current (trunk) mpfr headers
R
R 4.1.0 released · 2021-05-18
1.0.2
2021-02-26 · diff ↗
R
R 4.0.0 released · 2020-04-24
unarchivedReturned to CRAN
2019-09-03

Show 4 earlier events

1.0.1
2019-09-02 · diff ↗
archivedRemoved from CRAN
2019-09-01
installation warnings were not corrected Warnings with mpfr 4.x, which is an undeclared and untested 'SystemRequirements'
1.0.0
2019-06-13
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2026-06-05
Total releases: 6 / 1 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.1.0
Download size: 40 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Probability Distributions

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("scModels")

Format

Harsha, K., Amrhein, L., Fuchs, C., & Holoborodko, P. (2026). scModels: Fitting Discrete Distribution Models to Count Data (Version 1.0.5) [Computer software]. https://doi.org/10.32614/CRAN.package.scModels

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 scModels version 1.0.5 [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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