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nimble
View on CRAN: Click
here
Download and install nimble package within the R console
Install from CRAN:
install.packages("nimble")
Install from Github:
library("remotes")
install_github("cran/nimble")
Install by package version:
library("remotes")
install_version("nimble", "1.1.0")
Attach the package and use:
library("nimble")
Maintained by
Christopher Paciorek
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2016-03-29
Latest Update: 2023-06-15
Description:
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, 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 .
How to cite:
Christopher Paciorek (2016). nimble: MCMC, Particle Filtering, and Programmable Hierarchical Modeling. R package version 1.1.0, https://cran.r-project.org/web/packages/nimble
Previous versions and publish date:
0.5 (2016-03-29 10:50), 0.6-1 (2016-10-11 18:56), 0.6-2 (2016-11-23 17:12), 0.6-3 (2016-12-14 23:15), 0.6-4 (2017-04-25 16:33), 0.6-5 (2017-06-07 00:14), 0.6-6 (2017-07-29 00:57), 0.6-7 (2017-11-15 10:18), 0.6-8 (2017-11-22 11:13), 0.6-9 (2018-02-07 00:06), 0.6-10 (2018-03-25 17:44), 0.6-11 (2018-06-14 09:49), 0.6-12 (2018-07-27 22:50), 0.6.13 (2019-01-26 00:50), 0.6 (2016-09-02 23:22), 0.7.0.1 (2019-03-01 08:07), 0.7.0 (2019-02-01 16:20), 0.7.1 (2019-03-12 10:50), 0.8.0 (2019-06-02 21:00), 0.9.0 (2019-12-18 22:10), 0.9.1 (2020-05-22 11:00), 0.10.0 (2020-10-10 19:40), 0.10.1 (2020-11-23 21:30), 0.11.0 (2021-04-17 19:20), 0.11.1 (2021-05-23 11:50), 0.12.0 (2021-09-28 18:50), 0.12.1 (2021-10-09 23:10), 0.12.2 (2022-02-24 12:00), 0.13.0 (2022-11-15 19:20), 0.13.1 (2022-12-14 18:10), 0.13.2 (2023-05-14 07:00), 1.0.0 (2023-05-23 21:42), 1.0.1 (2023-06-15 21:50)
Other packages that cited nimble R package
View nimble citation profile
Other R packages that nimble depends,
imports, suggests or enhances
Functions, R codes and Examples using
the nimble R package
Some associated functions: ADNimbleList . ADbreak . ADproxyModelClass-class . BUGSdeclClass-class . CAR-Normal . CAR-Proper . CAR_calcNumIslands . Categorical . ChineseRestaurantProcess . CmodelBaseClass-class . CnimbleFunctionBase-class . Constraint . Dirichlet . Double-Exponential . Exponential . Interval . Inverse-Gamma . Inverse-Wishart . LKJ . MCMCconf-class . MCMCsuite . Multinomial . Multivariate-t . MultivariateNormal . Rmatrix2mvOneVar . RmodelBaseClass-class . StickBreakingFunction . Wishart . any_na . as.carAdjacency . as.carCM . asRow . autoBlock . buildAuxiliaryFilter . buildBootstrapFilter . buildEnsembleKF . buildIteratedFilter2 . buildLiuWestFilter . buildMCEM . buildMCMC . calculateWAIC . carBounds . carMaxBound . carMinBound . checkInterrupt . clearCompiled . codeBlockClass-class . compareMCMCs . compileNimble . configureMCMC . configureRJ . decide . decideAndJump . declare . deregisterDistributions . distributionInfo . eigenNimbleList . extractControlElement . flat . getBUGSexampleDir . getBound . getConditionallyIndependentSets . getDefinition . getMacroParameters . getNimbleOption . getParam . getSamplesDPmeasure . getsize . identityMatrix . initializeModel . is.nf . is.nl . laplace . makeBoundInfo . makeModelDerivsInfo . makeParamInfo . modelBaseClass-class . modelDefClass-class . modelInitialization . modelValues . modelValuesBaseClass-class . modelValuesConf . model_macro_builder . nfMethod . nfVar . nimCat . nimCopy . nimDerivs . nimDim . nimEigen . nimIntegrate . nimMatrix . nimNumeric . nimOptim . nimOptimDefaultControl . nimPrint . nimStop . nimSvd . nimble-R-functions . nimble-internal . nimble-math . nimble-package . nimbleCode . nimbleExternalCall . nimbleFunction . nimbleFunctionBase-class . nimbleFunctionList-class . nimbleFunctionVirtual . nimbleList . nimbleMCMC . nimbleModel . nimbleOptions . nimbleRcall . nimbleType-class . nodeFunctions . optimControlNimbleList . optimDefaultControl . optimResultNimbleList . parameterTransform . pow_int . printErrors . rankSample . readBUGSmodel . registerDistributions . resize . run.time . runCrossValidate . runMCMC . samplers . setAndCalculate . setAndCalculateOne . setSize . setupMargNodes . setupOutputs . simNodes . simNodesMV . singleVarAccessClass-class . summaryLaplace . svdNimbleList . t . testBUGSmodel . valueInCompiledNimbleFunction . values . waic . waicDetailsNimbleList . waicNimbleList . withNimbleOptions .
Some associated R codes: BNP_distributions.R . BNP_samplers.R . BUGS_BUGSdecl.R . BUGS_contexts.R . BUGS_getDependencies.R . BUGS_graphNodeMaps.R . BUGS_macros.R . BUGS_mathCompatibility.R . BUGS_model.R . BUGS_modelDef.R . BUGS_nimbleGraph.R . BUGS_readBUGS.R . BUGS_testBUGS.R . BUGS_utils.R . CAR.R . Laplace.R . MCEM_build.R . MCMC_RJ.R . MCMC_WAIC.R . MCMC_autoBlock.R . MCMC_build.R . MCMC_configuration.R . MCMC_conjugacy.R . MCMC_run.R . MCMC_samplers.R . MCMC_utils.R . NF_utils.R . RCfunction_compile.R . RCfunction_core.R . all_utils.R . config.R . cppDefs_ADtools.R . cppDefs_BUGSmodel.R . cppDefs_RCfunction.R . cppDefs_core.R . cppDefs_cppProject.R . cppDefs_modelValues.R . cppDefs_namedObjects.R . cppDefs_nimbleFunction.R . cppDefs_nimbleList.R . cppDefs_outputCppFromRparseTree.R . cppDefs_utils.R . cppDefs_variables.R . cppInterfaces_modelValues.R . cppInterfaces_models.R . cppInterfaces_nimbleFunctions.R . cppInterfaces_otherTypes.R . cppInterfaces_utils.R . crossValidation.R . distributions_implementations.R . distributions_inputList.R . distributions_processInputList.R . externalCalls.R . genCpp_RparseTree2exprClasses.R . genCpp_addDebugMarks.R . genCpp_buildIntermediates.R . genCpp_eigenization.R . genCpp_exprClass.R . genCpp_generateCpp.R . genCpp_initSizes.R . genCpp_insertAssertions.R . genCpp_liftMaps.R . genCpp_maps.R . genCpp_operatorLists.R . genCpp_processSpecificCalls.R . genCpp_sizeProcessing.R . genCpp_toEigenize.R . initializeModel.R . makevars.R . miscFunctions.R . nimbleFunction_Rderivs.R . nimbleFunction_Rexecution.R . nimbleFunction_compile.R . nimbleFunction_core.R . nimbleFunction_keywordProcessing.R . nimbleFunction_nodeFunction.R . nimbleFunction_nodeFunctionNew.R . nimbleFunction_util.R . nimbleList_core.R . nimbleProject.R . options.R . parameterTransform.R . registration.R . setNimbleInternalFunctions.R . types_modelValues.R . types_modelValuesAccessor.R . types_modelVariableAccessor.R . types_nimbleFunctionList.R . types_nodeFxnVector.R . types_numericLists.R . types_symbolTable.R . types_util.R . zzz.R . Full nimble package functions and examples
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