R Observatory: Metrics for BiDAG version 2.1.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

BiDAG

2.1.4Package record

Bayesian Inference for Directed Acyclic Graphs

2packages depend

6.4Kdownloads / year

–test coverage

9/13flavors OK

Overview

About

Maintained by Polina SuterCRAN page ↗

Implementation of a collection of MCMC methods for Bayesian structure learning of directed acyclic graphs (DAGs), both from continuous and discrete data. For efficient inference on larger DAGs, the space of DAGs is pruned according to the data. To filter the search space, the algorithm employs a hybrid approach, combining constraint-based learning with search and score. A reduced search space is initially defined on the basis of a skeleton obtained by means of the PC-algorithm, and then iteratively improved with search and score. Search and score is then performed following two approaches: Order MCMC, or Partition MCMC. The BGe score is implemented for continuous data and the BDe score is implemented for binary data or categorical data. The algorithms may provide the maximum a posteriori (MAP) graph or a sample (a collection of DAGs) from the posterior distribution given the data. All algorithms are also applicable for structure learning and sampling for dynamic Bayesian networks. References: J. Kuipers, P. Suter, G. Moffa (2022) doi:10.1080/10618600.2021.2020127, N. Friedman and D. Koller (2003) doi:10.1023/A:1020249912095, J. Kuipers and G. Moffa (2017) doi:10.1080/01621459.2015.1133426, M. Kalisch et al. (2012) doi:10.18637/jss.v047.i11, D. Geiger and D. Heckerman (2002) doi:10.1214/aos/1035844981, P. Suter, J. Kuipers, G. Moffa, N.Beerenwinkel (2023) doi:10.18637/jss.v105.i09.

Install

R (CRAN)Ubuntu (r2u)

install.packages("BiDAG", 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-bidag

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

Health

CRAN checks

4NOTE9OK

Check messages

NOTECRAN incoming feasibilityr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Maintainer: ‘Polina Suter <polina.suter@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Polina",
                      family = "Suter",
                      role = c("aut", "cre"),
                      email = "polina.suter@gmail.com"),
               person(given = "Jack",
                      family = "Kuipers",
                      role = "aut"))
as necessary.

NOTEdependencies in R coder-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Namespace in Imports field not imported from:
  ‘RBGL’
All declared Imports should be used.

CRAN check page ↗

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

Status changes

NOTE9 OK, 4 NOTENow
NOTE10 OK, 4 NOTE2026-04-22
ERROR9 OK, 4 NOTE, 1 ERROR2026-04-18
NOTE10 OK, 4 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.1.4

READMENoVignettesNoNEWSNoCitation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Cites a JSS article

Help pages: 54
Examples that run: 80%28 run in a plain check · 7 never run
Exported functions with examples: 95%
Documented parameters: 97%
Return-value docs: 97%
Help pages citing references: 28%

How these are measured

Downloads

6.4K

CRAN downloads in the past year

Rank #4,258 · ~17/day · ~531/mo

Releases R versions

Daily download trend is not available in this view yet.

85830 days

2.1K90 days

6.4K1 year

Compare downloads with other packages →

Also on426 r2u

How downloads are counted

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Installing BiDAG adds 28 packages (16 with compiled code, 36 MB of source tarballs). Heaviest: BH 14 MB, igraph 4.8 MB, pcalg 3.9 MB. 3 more not on CRAN are not measured.

Depends (1)

R >= 3.5.0

Imports (9)

Rcppmethodsgraph Rgraphviz RBGL pcalggraphicsMatrixcoda

LinkingTo (1)

Rcpp

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

2direct

0indirect

Imports 2

Depends, Imports or LinkingTo, most downloaded first

clustNet Bestie

How these are counted

Code & Tests

Datasets

People & History

People (from the free-text Author field) (2)

Polina Suter

Author, Maintainer · added in 1.0.2

Jack Kuipers

Author

Maintainer since 1.0.0 (2017)

Listed in earlier versions (1)

Polina Minkina

no longer listed · 1.0.0 to 1.0.1

Releases (23)

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
R
R 4.4.0 released · 2024-04-24
2.1.4Latest
record
2023-05-16 · current release · diff ↗
R
R 4.3.0 released · 2023-04-21
2.1.3
record
2023-01-23 · diff ↗
2.1.2
record
2022-12-21 · diff ↗ ·
added 1 export
getRuntime
2.1.1
record
2022-08-05 · diff ↗
2.1.0
record
2022-06-27 · diff ↗
2.0.9
record
2022-06-20 · diff ↗
2.0.7
record
2022-05-16 · diff ↗
2.0.6
record
2022-05-09 · diff ↗ ·
added 4 exports
bidag2coda, bidag2codalist, learnBN, sampleBN
R
R 4.2.0 released · 2022-04-22
2.0.5
record
2022-04-13 · diff ↗
2.0.4
record
2021-11-30 · diff ↗ ·
added 1 export
scoreagainstDBN
2.0.3
record
2021-07-28 · diff ↗ ·
removed 1 export
plotdiffs.DBN

added 5 exports
getDAG, getMCMCscore, getSpace, getTrace, plotdiffsDBN

Show 17 earlier eventsHide 17 earlier events

R
R 4.1.0 released · 2021-05-18
2.0.2
record
2021-04-30 · diff ↗
2.0.1
record
2021-04-28 · diff ↗ ·
removed 12 exports
iterations.check, plot.MCMCmult, plot.MCMCres, print.MCMCmult, print.MCMCres, print.MCMCscoretab, print.scoreparameters, sample.check, summary.MCMCmult, summary.MCMCres, summary.MCMCscoretab, summary.scoreparameters

added 4 exports
itercomp, plot2in1, samplecomp, scorespace
2.0.0
record
2021-02-15 · diff ↗ ·
removed 2 exports
dag.threshold, edges.posterior

added 15 exports
connectedSubGraph, edgep, getSubGraph, modelp, plot.MCMCmult, plot.MCMCres, print.MCMCmult, print.MCMCres, print.MCMCscoretab, print.scoreparameters, string2mat, summary.MCMCmult, summary.MCMCres, summary.MCMCscoretab, summary.scoreparameters
1.4.1
record
2020-07-14 · diff ↗ ·
added 2 exports
plotdiffs, plotdiffs.DBN
R
R 4.0.0 released · 2020-04-24
1.3.4
record
2020-04-12 · diff ↗ ·
removed 2 exports
plotdiffs, plotdiffs.DBN
1.3.0
record
2020-02-19 · diff ↗ ·
removed 4 exports
adjacency2dag, dag2adjacencymatrix, dag2skeletonadjacency, iterativeMCMCsearch

added 12 exports
DBNscore, compact2full, compareDBNs, full2compact, graph2m, iterativeMCMC, m2graph, plotDBN, plotdiffs, plotdiffs.DBN, plotpcor, plotpedges
1.2.0
record
2019-08-19 · diff ↗
R
R 3.6.0 released · 2019-04-26
1.1.2
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2018-05-24 · diff ↗
R
R 3.5.0 released · 2018-04-23
1.1.1
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2018-03-16 · diff ↗
1.0.2
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2017-09-08 · diff ↗
1.0.1
record
2017-07-26 · diff ↗
1.0.0
record
2017-07-19
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2017-07-19
Total releases: 23 / 9 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 3.5.0
Bundled data: 915 KB / 13 files
Download size: 1.0 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("BiDAG")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.18637/jss.v105.i09.

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 BiDAG version 2.1.4 [Data set]. HJJB, LLC. Data release v2026-10-26. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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