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, particle filtering,
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>.
c(
person("Perry", "de Valpine", role = "aut"),
person("Christopher", "Paciorek", , "paciorek@stat.berkeley.edu", role = c("aut", "cre")),
person("Daniel", "Turek", role = "aut"),
person("Nick", "Michaud", role = "aut"),
person("Cliff", "Anderson-Bergman", role = "aut"),
person("Fritz", "Obermeyer", role = "aut"),
person("Claudia", "Wehrhahn Cortes", role = "aut", comment = "Bayesian nonparametrics system"),
person("Abel", "Rodriguez", role = "aut", comment = "Bayesian nonparametrics system"),
person("Sally", "Paganin", role = "aut", comment = "reversible jump MCMC"),
person("Jagadish", "Babu", role = "ctb", comment = "code for the compilation system for an early version of NIMBLE"),
person("Dao", "Nguyen", role = "ctb", comment = "contributions to the IF2 code"),
person("Lauren", "Ponisio", role = "ctb", comment = "contributions to the cross-validation code"),
person("Peter", "Sujan", role = "ctb", comment = "multivariate t distribution code")
)
config.R all_utils.R options.R distributions_inputList.R
distributions_processInputList.R
distributions_implementations.R BUGS_BUGSdecl.R BUGS_contexts.R
BUGS_nimbleGraph.R BUGS_modelDef.R BUGS_model.R
BUGS_graphNodeMaps.R BUGS_readBUGS.R BUGS_macros.R
BUGS_testBUGS.R BUGS_getDependencies.R BUGS_utils.R
BUGS_mathCompatibility.R externalCalls.R genCpp_exprClass.R
genCpp_operatorLists.R genCpp_RparseTree2exprClasses.R
genCpp_initSizes.R genCpp_buildIntermediates.R
genCpp_processSpecificCalls.R genCpp_sizeProcessing.R
genCpp_toEigenize.R genCpp_insertAssertions.R genCpp_maps.R
genCpp_liftMaps.R genCpp_eigenization.R genCpp_addDebugMarks.R
genCpp_generateCpp.R RCfunction_core.R RCfunction_compile.R
nimbleFunction_util.R nimbleFunction_core.R
nimbleFunction_nodeFunction.R nimbleFunction_nodeFunctionNew.R
nimbleFunction_Rexecution.R nimbleFunction_compile.R
nimbleFunction_keywordProcessing.R nimbleList_core.R
types_util.R types_symbolTable.R types_modelValues.R
types_modelValuesAccessor.R types_modelVariableAccessor.R
types_nimbleFunctionList.R types_nodeFxnVector.R
types_numericLists.R cppDefs_utils.R cppDefs_variables.R
cppDefs_core.R cppDefs_namedObjects.R cppDefs_ADtools.R
cppDefs_BUGSmodel.R cppDefs_RCfunction.R
cppDefs_nimbleFunction.R cppDefs_nimbleList.R
cppDefs_modelValues.R cppDefs_cppProject.R
cppDefs_outputCppFromRparseTree.R cppInterfaces_utils.R
cppInterfaces_models.R cppInterfaces_modelValues.R
cppInterfaces_nimbleFunctions.R cppInterfaces_otherTypes.R
nimbleProject.R initializeModel.R CAR.R MCMC_utils.R
MCMC_configuration.R MCMC_build.R MCMC_run.R MCMC_samplers.R
MCMC_conjugacy.R MCMC_autoBlock.R MCMC_RJ.R MCEM_build.R
crossValidation.R filtering_resamplers.R filtering_auxiliary.R
filtering_liuwest.R filtering_IF2.R filtering_enkf.R
filtering_bootstrap.R filtering_utils.R BNP_distributions.R
BNP_samplers.R NF_utils.R miscFunctions.R makevars.R
setNimbleInternalFunctions.R registration.R nimble-package.r
zzz.R
Perry de Valpine [aut],
Christopher Paciorek [aut, cre],
Daniel Turek [aut],
Nick Michaud [aut],
Cliff Anderson-Bergman [aut],
Fritz Obermeyer [aut],
Claudia Wehrhahn Cortes [aut] (Bayesian nonparametrics system),
Abel Rodriguez [aut] (Bayesian nonparametrics system),
Sally Paganin [aut] (reversible jump MCMC),
Jagadish Babu [ctb] (code for the compilation system for an early
version of NIMBLE),
Dao Nguyen [ctb] (contributions to the IF2 code),
Lauren Ponisio [ctb] (contributions to the cross-validation code),
Peter Sujan [ctb] (multivariate t distribution code)