R Observatory: Metrics for scModels version 1.0.5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

scModels

1.0.5Package record

Fitting Discrete Distribution Models to Count Data

0packages depend

2Kdownloads / year

36.3%test coverage

13/13flavors OK

Overview

About

Maintained by Kumar HarshaCRAN 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.

Changes in 1.0.5

Drop C++11 specification
Update maintainer

From NEWS.md in the release

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. 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-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). 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: 4.5 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK7 OK2026-06-06

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.5

READMENoVignettesNoNEWSYes · 100% structured · mentions 1.0.5Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 6
Examples that run: 100%6 run in a plain check
Exported functions with examples: 100%
Documented parameters: 52%
Return-value docs: 0%
Help pages citing references: 0%

How these are measured

Downloads

2K

CRAN downloads in the past year

Rank #6,711 · ~5/day · ~164/mo

Releases R versions

Daily download trend is not available in this view yet.

43330 days

1.3K90 days

2K1 year

Compare downloads with other packages →

Also on364 r2u5 autocran100 c2d4u

How downloads are counted

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Installing scModels adds 2 packages (2 with compiled code, 3.3 MB of source tarballs). Heaviest: Rcpp 1.8 MB, gamlss.dist 1.5 MB.

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.

How these are counted

Code & Tests

People & History

People (4)

Kumar Harsha

Author, Maintainer since 1.0.5 (2026)

Lisa Amrhein

Author

Christiane Fuchs

Author

Pavel Holoborodko

Contributor

Author and copyright holder of 'mpreal.h'

Previously maintained by Lisa Amrhein (1.0.0 to 1.0.4).

Releases (6)

Pick two releases to compare their code metrics.

unarchivedReturned to CRAN
2026-06-05
1.0.5Latest
record
2026-06-05 · current release · diff ↗
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
record
2023-01-24 · diff ↗
R
R 4.2.0 released · 2022-04-22
unarchivedReturned to CRAN
2022-03-29
1.0.3
record
2022-03-29 · diff ↗
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
record
2021-02-26 · diff ↗ ·
added 11 exports
gmRNA_IGbasic_burst, gmRNA_basic_burst, nlogL_del, nlogL_del2, nlogL_pig, nlogL_pig2, nlogL_zidel, nlogL_zidel2, nlogL_zipig, nlogL_zipig2, rInvGaus
R
R 4.0.0 released · 2020-04-24
unarchivedReturned to CRAN
2019-09-03

Show 4 earlier eventsHide 4 earlier events

1.0.1
record
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
record
2019-06-13
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-06-13
Total releases: 6 / 7 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.1.0
Download size: 40 KB

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 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 scModels version 1.0.5 [Data set]. HJJB, LLC. Data release v2026-10-20. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-20, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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