BASiCStan
Bioc currentStan implementation of BASiCS
Release Lineage
Entered 3.16 · Nov 2, 2022
Current · Requires R 4.6
Description
Provides an interface to infer the parameters of BASiCS using the variational inference (ADVI), Markov chain Monte Carlo (NUTS), and maximum a posteriori (BFGS) inference engines in the Stan programming language. BASiCS is a Bayesian hierarchical model that uses an adaptive Metropolis within Gibbs sampling scheme. Alternative inference methods provided by Stan may be preferable in some situations, for example for particularly large data or posterior distributions with difficult geometries.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
10 2 exported
Complexity
2.9 avg / 9 max
Call network
10 nodes / 4 edges
Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.
Call graph
Open call graph →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
760
Files
21
Compiled share
3.6%
Has compiled src
Yes
Language breakdown
API
Exported functions
2
Internal functions
7
Testing
Has tests
Yes
Test-to-code ratio
0.33
testthat edition
3
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
30.8%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.2
System requirements
1 externalGNU make
C++ standard
C++17
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
8
First release
2022-11-01
Latest release
2026-06-30
Avg cadence
182 days
Cold removal rate
–
Dep drift
0
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 3includes a package overview page
- Examples that run
- 100%2 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 70%
- Return-value docs
- 100%
- Help pages citing references
- 33%
Repository practices
3 development-tooling and community-health practices detected across 2 families in the upstream repository
Checks run against github.com/alanocallaghan/basicstan on 2026-10-21.
The R CMD check workflow runs on Linux, macOS and Windows
Topics
People
- Alan O'Callaghan author maintainer
- Catalina Vallejos author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("BASiCStan")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.
From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.