GillespieSSA2

0.3.0

Gillespie's Stochastic Simulation Algorithm for Impatient People

1packages depend

7.8Kdownloads / year

92.6%test coverage

11/13checks pass

Overview

About

Maintained by Robrecht CannoodtFirst published 2019-08-057 releasesCRAN page ↗GitHub ↗

A fast, scalable, and versatile framework for simulating large systems with Gillespie's Stochastic Simulation Algorithm ('SSA'). This package is the spiritual successor to the 'GillespieSSA' package originally written by Mario Pineda-Krch. Benefits of this package include major speed improvements (>100x), easier to understand documentation, and many unit tests that try to ensure the package works as intended. Cannoodt and Saelens et al. (2021) doi:10.1038/s41467-021-24152-2.

Install

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

install.packages("GillespieSSA2", 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("rcannood/GillespieSSA2")

Development version from rcannood/GillespieSSA2. 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-gillespiessa2

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-GillespieSSA2

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-GillespieSSA2

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

Health

CRAN checks

2NOTE11OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 11.9 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.94

92.6%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-06-09
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
11 OK · 1 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-04-22
10 OK · 4 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
9 OK · 4 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
10 OK · 4 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 312 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 50%
Documented parameters: 100%
Return-value docs: 89%
References docs: 27%

Downloads

7.8K

CRAN downloads in the past year

Rank #9,482 · ~21/day · ~646/mo

Releases R versions

Daily download trend is not available in this view yet.

38730 days

1.2K90 days

7.8K1 year

Compare downloads with other packages →

Also on468 r2u36 autocran

Repository

GitHub ↗ rcannood/gillespiessa2

9Stars

0Forks

2Open issues

0Open PRs

5Releases

275Commits

4Contributors

275 commits · Last activity 2023-01-23 · +12.5% stars, 30d

Stars over time

2024-11-26 · 72026-07-07 · 9

Repository practices

Upstream repositoryBeta

6 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/rcannood/gillespiessa2 on 2026-07-19.

Continuous integration (1)

GitHub Actions

CRAN release process (2)

cran-comments.mdrevdep/

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

Show all practices

Coverage (1)

Codecov

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

Dependencies

Declared dependencies

17 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.3

Imports (12)

assertthat dplyr dynutilsMatrixmethodspurrr Rcpp (>= 0.12.3)RcppXPtrUtils readr rlang stringr tidyr

LinkingTo (1)

Rcpp

Suggests (6)

covr ggplot2 GillespieSSA knitr rmarkdown testthat (>= 2.1.0)

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

dyngen

Code & Tests

Code Composition

R 1,760 (42%)Vignettes 1,004 (24%)C++ 927 (22%)Rd 480 (11%)C 34 (1%)

Code characteristics

Object systems

S32

Cyclomatic complexity: 1.0 median / 8 max
Test cases: 16 / 0.94 per code line

Test coverage

Line coverage

93%

Expression

93.6%

Tests / Examples

92.6% / 13% ex

Functions

55 8 exported

Complexity

2.1 avg / 8 max

Call network

55 nodes / 24 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

55 functions

Function	Cyclo	Coverage
port_reactions exp	1	0%
print.SSA_method	2	0%
print.SSA_reaction	2	0%
plot_ssa exp	8	90%
compile_reactions exp	8	99%
ode_em exp	1	100%

People & History

People (2)

Maintainer (1)

Robrecht Cannoodt

Author, Maintainer

Authors (2)

Robrecht Cannoodt

Author, Maintainer

Wouter Saelens

Author · added in 0.2.5

Package Timeline

7 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
0.3.0Latest
2023-01-23 · current release · diff ↗
0.2.10
2022-09-23 · diff ↗
R
R 4.2.0 released · 2022-04-22
0.2.8
2021-05-18 · diff ↗
R
R 4.1.0 released · 2021-05-18
0.2.7
2020-07-14 · diff ↗
R
R 4.0.0 released · 2020-04-24
0.2.6.1
2020-03-14 · diff ↗
0.2.5
2019-08-22 · diff ↗
0.2.4
2019-08-05
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-08-05
Total releases: 7 / 7 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 3.3
Download size: 1.5 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Report a problem with this page →