R Observatory: Metrics for nimble version 1.4.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

nimble

1.4.3Package record

MCMC, Particle Filtering, and Programmable Hierarchical Modeling

27packages dependsuggested by 10

76.7Kdownloads / year

0.1%test coverage

13/13flavors OK

Overview

About

Maintained by Christopher PaciorekCRAN page ↗GitHub ↗Website ↗Issues ↗

A system for writing hierarchical statistical models largely compatible with 'BUGS' and 'JAGS', writing nimbleFunctions to operate models and do basic R-style math, and compiling both models and nimbleFunctions via custom-generated C++. 'NIMBLE' includes default methods for MCMC, Laplace Approximation, deterministic nested approximations, Monte Carlo Expectation Maximization, and some other tools. The nimbleFunction system makes it easy to do things like implement new MCMC samplers from R, customize the assignment of samplers to different parts of a model from R, and compile the new samplers automatically via C++ alongside the samplers 'NIMBLE' provides. 'NIMBLE' extends the 'BUGS'/'JAGS' language by making it extensible: New distributions and functions can be added, including as calls to external compiled code. Although most people think of MCMC as the main goal of the 'BUGS'/'JAGS' language for writing models, one can use 'NIMBLE' for writing arbitrary other kinds of model-generic algorithms as well. A full User Manual is available at https://r-nimble.org.

Changes in 1.4.3

USER LEVEL CHANGES

Improve warning message about bad pWAIC values to make clear that

individual pWAIC values can be obtained via getWAICdetails (Issue 1626).

Modify how getParents handles self=FALSE to avoid returning any of the

input nodes. Formerly if multiple inputs were provided and one of the provided

inputs was the parent of another, this would be returned (PR #1633).

BUG FIXES

Fix prior_samples MCMC sampler. Formerly this sampler gave incorrect

results as it did not account for the density of dependent variables and

simply iterated through the prior samples (PR #1624).

Fix/robustify dimension checking to avoid warning about dimension of

right-hand side-only dynamically-indexed variables (PR #1632).

Show all changes in 1.4.3Hide the rest of the changes in 1.4.3

Allow constants whose names start with a period (PR #1629).
Fix corner case in getConditionallyIndepedentSets when nodes is

provided and givenNodes is not (Issue #1625).

DEVELOPER LEVEL CHANGES

Update handling of various cases in setupMargNodes to fix some

inconsistencies in corner cases (PR #1633).

Fix UBSAN issue as requested by CRAN, avoiding std::copy calls that

make zero-length copy (PR #1627).

From inst/NEWS.md in the release

Install

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

install.packages("nimble", 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("nimble-dev/nimble")

Development version from nimble-dev/nimble. 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-nimble

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-nimble

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-nimble

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: 18.6 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-26
NOTE12 OK, 1 NOTE2026-07-11
OK13 OK2026-05-02
NOTE10 OK, 4 NOTE2026-04-09
WARNING6 OK, 5 NOTE, 3 WARNING2026-03-21

Show 1 earlier changeHide 1 earlier change

NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.4.3

READMEYes · 177 wordsVignettesNoNEWSYes · 100% structured · mentions 1.4.3Citation fileYes · cites a publicationWebsiteYes

Help pages: 153 (1 internal)includes a package overview page
Examples that run: 78%56 run in a plain check · 15 never run · 1 hold no code
Exported functions with examples: 50%
Documented parameters: 99%
Return-value docs: 42%
Help pages citing references: 16%

How these are measured

Downloads

76.7K

CRAN downloads in the past year

Rank #1,533 · ~210/day · ~6.4K/mo

Releases R versions

Daily download trend is not available in this view yet.

5.4K30 days

15.7K90 days

76.7K1 year

Compare downloads with other packages →

Also on1.6K r2u15 autocran8.1K conda_forge248 c2d4u

How downloads are counted

Repository

nimble-dev/nimble ↗Organization: nimble-dev

198Stars

27Forks

98Open issues

0Open PRs

30Releases

5,197Commits

44Commit identities

bayesian-inferencemcmchierarchical-modelsprobabilistic-programmingbayesian-methodsr

License file reads as BSD-3-Clause · 5,197 commits · Last activity 2026-08-31 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 90%
Median days to close, 50 most recently updated closed issues: 52
Median days to close, 50 most recently updated closed PRs: 14

Stars over time

2025-09-01 · 1802026-09-09 · 198

How these are measured

PracticesBeta

5 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/nimble-dev/nimble on 2026-10-11.

Continuous integration (2)

GitHub ActionsAppVeyor

Governance and community (2)

Code of conductContributing guide

Research and citation (1)

Zenodo

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Installing nimble adds 13 packages (6 with compiled code, 8.5 MB of source tarballs). Heaviest: igraph 4.8 MB, vctrs 1.0 MB, rlang 766 KB.

Depends (1)

R >= 3.1.2

Imports (6)

methodsigraph coda R6 pracma numDeriv

LinkingTo (0)

none

Suggests (4)

testthat mcmcse nloptr nimbleQuad

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

27direct

0indirect

Depends 19 · Imports 8

Suggested by 10

Show all 37 packagesHide all 37 packages

Depends, Imports or LinkingTo, most downloaded first

Suggests, most downloaded first

bridgesampling priorsense camtrapR occumb runMCMCbtadjust saeHB rjuliabugs ct prova postpack

How these are counted

Code & Tests

People & History

People (16)

Christopher Paciorek

Author, Maintainer since 0.5 (2016)

Cliff Anderson-Bergman

Author

Joshua Hug

Author · added in 0.12.0

WAIC

Nick Michaud

Author · added in 0.6-5

Fritz Obermeyer

Author · added in 0.6-5

Sally Paganin

Author · added in 0.8.0

reversible jump MCMC

Abel Rodríguez

Author

Bayesian nonparametrics system

Duncan Temple Lang

Author

packaging configuration

Daniel Turek

Author

Claudia Wehrhahn Cortes

Author · added in 0.6.13

Bayesian nonparametrics system

Wei Zhang

Author · added in 1.0.0

node marginalization

Perry de Valpine

Author

Paul van Dam-Bates

Author · added in 1.1.0

Pólya-Gamma sampler, nimIntegrate, matrix exponential

Jagadish Babu

Contributor · added in 0.8.0

code for the compilation system for an early version of NIMBLE

Lauren Ponisio

Contributor · added in 0.8.0

contributions to the cross-validation code

Peter Sujan

Contributor · added in 0.8.0

multivariate t distribution code

Listed in earlier versions (5)

Show 5 peopleHide 5 people

Cliff Anderson- Bergman

no longer listed · 0.6 to 0.6-6

see AUTHORS file for additional contributors.

no longer listed · 0.6-7 to 0.7.1

Abel Rodriguez

no longer listed · 0.6.13 to 0.9.0

Dao Nguyen

no longer listed · 0.9.0 to 0.9.1

Abel Rodrìguez

no longer listed · 0.9.1 to 0.13.2

Releases (41)

Pick two releases to compare their code metrics.

1.4.3Latest
record
2026-08-22 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
1.4.2
record
2026-04-01 · diff ↗
1.4.1
record
2026-02-13 · diff ↗ ·
added 1 export
sampler_partial_mvn
1.4.0
record
2025-12-13 · diff ↗ ·
added 17 exports
calc_dmnorm_inv_ld_AltParams, PDinverse_logdet, derived_BASE, derived_logProb, derived_mean, derived_predictive, derived_variance, dmnorm_inv_ld, emptyParam, expAv, expm, gaussParam, getParam_BASE, multiGaussParam, rmnorm_inv_ld, sampler_barker, splitLatents
R
R 4.5.0 released · 2025-04-11
1.3.0
record
2024-12-17 · diff ↗ ·
removed 1 export
model_macro_builder

added 1 export
buildMacro
1.2.1
record
2024-07-30 · diff ↗ ·
added 1 export
sampler_RW_multinomial
1.2.0
record
2024-06-09 · diff ↗ ·
removed 2 exports
MCMCsuite, compareMCMCs

added 8 exports
MCEM_mcse, buildAGHQ, nimOptimMethod, runAGHQ, runLaplace, sampler_noncentered, sampler_polyagamma, summaryAGHQ
R
R 4.4.0 released · 2024-04-24
1.1.0
record
2024-01-31 · diff ↗ ·
removed 1 export
sampler_RW_multinomial

added 3 exports
getMacroParameters, nimIntegrate, sampler_prior_samples
1.0.1
record
2023-06-15 · diff ↗
1.0.0
record
2023-05-23 · diff ↗ ·
removed 2 exports
waicDetailsList, waicList

added 15 exports
mcmc_createModelObject, ADbreak, ADproxyModelClass, AGHQuad_params, AGHQuad_summary, buildLaplace, clearCompiled, getConditionallyIndependentSets, makeModelDerivsInfo, parameterTransform, pow_int, setupMargNodes, summaryLaplace, waicDetailsNimbleList, waicNimbleList
0.13.2
record
2023-05-14 · diff ↗
R
R 4.3.0 released · 2023-04-21
0.13.1
record
2022-12-14 · diff ↗

Show 39 earlier eventsHide 39 earlier events

0.13.0
record
2022-11-15 · diff ↗ ·
removed 1 export
sampler_posterior_predictive_branch
R
R 4.2.0 released · 2022-04-22
0.12.2
record
2022-02-24 · diff ↗ ·
added 2 exports
messageIfVerbose, sampler_slice_CRP_base_param
0.12.1
record
2021-10-09 · diff ↗
0.12.0
record
2021-09-28 · diff ↗ ·
added 7 exports
dlkj_corr_cholesky, rlkj_corr_cholesky, sampler_RW_block_lkj_corr_cholesky, sampler_RW_lkj_corr_cholesky, waicList, waicDetailsList, calculateWAIC
0.11.1
record
2021-05-23 · diff ↗
R
R 4.1.0 released · 2021-05-18
0.11.0
record
2021-04-17 · diff ↗ ·
added 1 export
sampler_posterior_predictive_branch
0.10.1
record
2020-11-23 · diff ↗
0.10.0
record
2020-10-10 · diff ↗ ·
removed 4 exports
getLoadingNamespace, sampler_CRP_old, sampler_RW_PF, sampler_RW_PF_block

added 5 exports
calcAdaptationFactor, is.nfGenerator, nimbleFunctionList, extractControlElement, nf_preProcessMemberDataObject
0.9.1
record
2020-05-22 · diff ↗
R
R 4.0.0 released · 2020-04-24
0.9.0
record
2019-12-18 · diff ↗ ·
removed 2 exports
sampler_RJ, sampler_toggled

added 5 exports
any_na, any_nan, buildIteratedFilter2, sampler_RJ_fixed_prior, sampler_RJ_toggled
0.8.0
record
2019-06-02 · diff ↗ ·
removed 5 exports
combine_MCMC_comparison_results, make_MCMC_comparison_pages, rename_MCMC_comparison_method, reshape_comparison_results, updateMCMCcomparisonWithHighOrderESS

added 4 exports
configureRJ, sampler_RJ, sampler_RJ_indicator, sampler_toggled
R
R 3.6.0 released · 2019-04-26
0.7.1
record
2019-03-12 · diff ↗
0.7.0.1
record
2019-03-01 · diff ↗
0.7.0
record
2019-02-01 · diff ↗
0.6.13
record
2019-01-26 · diff ↗ ·
added 7 exports
ddexp, pdexp, printErrors, qdexp, rdexp, sampler_CRP_old, sampler_RW_wishart
0.6-12
record
2018-07-27 · diff ↗
0.6-11
record
2018-06-14 · diff ↗ ·
added 7 exports
cc_getNodesInExpr, dCRP, getSamplesDPmeasure, rCRP, sampler_CRP, sampler_CRP_concentration, stick_breaking
R
R 3.5.0 released · 2018-04-23
0.6-10
record
2018-03-25 · diff ↗
unarchivedReturned to CRAN
2018-02-07
0.6-9
record
2018-02-07 · diff ↗
archivedRemoved from CRAN
2018-02-01
policy violation Forces the use of '-fPIC', whereas some Linux compilers use '-KPIC' and overriding the user's settings is not acceptable There were also pragmas suppressing warnings
0.6-8
record
2017-11-22 · diff ↗
0.6-7
record
2017-11-15 · diff ↗ ·
added 22 exports
calc_dcatConjugacyContributions, CAR_calcM, CAR_calcC, CAR_calcCmatrix, CAR_calcEVs2, CAR_calcEVs3, as.carCM, carBounds, carMaxBound, carMinBound, dcar_proper, is.Cmodel, is.Cnf, is.Rmodel, is.model, model_macro_builder, nimbleMCMC, rcar_proper, runCrossValidate, sampler_CAR_proper, samplesSummary, withNimbleOptions
0.6-6
record
2017-07-29 · diff ↗ ·
added 11 exports
ADNimbleList, CAR_calcNumIslands, as.carAdjacency, dcar_normal, nimDerivs, nimbleExternalCall, nimbleRcall, optimDefaultControl, rcar_normal, sampler_CAR_normal, sampler_categorical
0.6-5
record
2017-06-07 · diff ↗ ·
added 13 exports
calc_dwishAltParams, dflat, dhalfflat, dinvwish_chol, dsqrtinvgamma, nimOptim, nimOptimDefaultControl, optimControlNimbleList, optimResultNimbleList, rflat, rhalfflat, rinvwish_chol, rsqrtinvgamma
0.6-4
record
2017-04-25 · diff ↗ ·
added 18 exports
nimbleType, dinvgamma, eigenNimbleList, is.nl, nimC, nimEigen, nimLogical, nimRep, nimRound, nimSeq, nimSvd, nimbleList, pinvgamma, qinvgamma, rinvgamma, sampler_AF_slice, sampler_RW_dirichlet, svdNimbleList
R
R 3.4.0 released · 2017-04-21
0.6-3
record
2016-12-14 · diff ↗
0.6-2
record
2016-11-23 · diff ↗ ·
added 9 exports
getBound, getDimension, getDistributionInfo, getParamNames, getType, isDiscrete, isUserDefined, makeBoundInfo, pqDefined
0.6-1
record
2016-10-11 · diff ↗ ·
added 2 exports
nimbleUserNamespace, Rmatrix2mvOneVar
0.6
record
2016-09-02 · diff ↗ ·
removed 327 exports
accessorVectorLength_setupCodeTemplate, activeBindingTemplateLength1NonScalar, addArg, addBlockFromCppName, addDistKeywordProcessors, addDistList2matchFunctions, addNecessarySetupCode, addNewCode, addNodeFxn, addNodeFxn_LOOP, addSamplerToSpec, addSetupCodeNames, addSingleModelValuesAccess, addSingleVarAccess, allLHSNodes_SetupTemplate, allModelNodes_SetupTemplate, allModelValuesVars_SetupTemplate, argInfo2PointerStaticCast, assignNumberedObject, autoBlockClass, autoBlockModel, autoBlockParamDefaults, BUGScode, BUGScontextClass, BUGSdeclClass, BUGSsingleContextClass, buildConjugateSamplerFunctions, buildModelInterface, buildNeededObjects, buildNimbleFxnInterface and 297 more

added 25 exports
calc_dmnormConjugacyContributions, getNodeFunctionIndexedInfo, nimbleInternalFunctions, nfVar<-, values<-, buildAuxiliaryFilter, buildBootstrapFilter, buildEnsembleKF, buildLiuWestFilter, dmvt_chol, identityMatrix, modelValuesConf, nimCat, nimInteger, nimMatrix, nimNumeric, rmvt_chol, run.time, runMCMC, sampler_RW_PF, sampler_RW_PF_block, sampler_RW_llFunction_block, sampler_RW_multinomial, sampler_binary, sampler_posterior_predictive
R
R 3.3.0 released · 2016-05-03
0.5
record
2016-03-29
R
R 3.2.0 released · 2015-04-16

Package metadata

First published: 2016-03-29
Total releases: 41 / 10 yrs
License: BSD_3_clause + file LICENSE | GPL (>= 2) OSI · relicensed from BSD_3_clause + file LICENSE in 0.6-7
Copyright: See COPYRIGHTS file.
Minimum R: ≥ 3.1.2
Download size: 3.2 MB

Appears in task views

Bayesian Inference Mixed, Multilevel, and Hierarchical Models in R

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("nimble")

The package provides a citation file that builds its entry when R runs it. Run citation() to see it.

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 nimble version 1.4.3 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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