{ "_id": "6a1be9e41d7bb097a0a1db9c", "Package": "nimble", "Title": "MCMC, Particle Filtering, and Programmable Hierarchical Modeling", "Description": "A system for writing hierarchical statistical models\nlargely compatible with 'BUGS' and 'JAGS', writing\nnimbleFunctions to operate models and do basic R-style math,\nand compiling both models and nimbleFunctions via\ncustom-generated C++. 'NIMBLE' includes default methods for\nMCMC, Laplace Approximation, deterministic nested\napproximations, Monte Carlo Expectation Maximization, and some\nother tools. The nimbleFunction system makes it easy to do\nthings like implement new MCMC samplers from R, customize the\nassignment of samplers to different parts of a model from R,\nand compile the new samplers automatically via C++ alongside\nthe samplers 'NIMBLE' provides. 'NIMBLE' extends the\n'BUGS'/'JAGS' language by making it extensible: New\ndistributions and functions can be added, including as calls to\nexternal compiled code. Although most people think of MCMC as\nthe main goal of the 'BUGS'/'JAGS' language for writing models,\none can use 'NIMBLE' for writing arbitrary other kinds of\nmodel-generic algorithms as well. A full User Manual is\navailable at .", "Version": "1.4.2", "Date": "2026-04-01", "Maintainer": "Christopher Paciorek ", "Authors@R": "c(\nperson(\"Perry\", \"de Valpine\", role = \"aut\"),\nperson(\"Christopher\", \"Paciorek\", , \"paciorek@stat.berkeley.edu\", role = c(\"aut\", \"cre\")),\nperson(\"Daniel\", \"Turek\", role = \"aut\"),\nperson(\"Nick\", \"Michaud\", role = \"aut\"),\nperson(\"Cliff\", \"Anderson-Bergman\", role = \"aut\"),\nperson(\"Fritz\", \"Obermeyer\", role = \"aut\"),\nperson(\"Claudia\", \"Wehrhahn Cortes\", role = \"aut\", comment = \"Bayesian nonparametrics system\"),\nperson(\"Abel\", \"Rodr\\u00edguez\", role = \"aut\", comment = \"Bayesian nonparametrics system\"),\nperson(\"Duncan\", \"Temple Lang\", role = \"aut\", comment = \"packaging configuration\"),\nperson(\"Wei\", \"Zhang\", role = \"aut\", comment = \"node marginalization\"),\nperson(\"Sally\", \"Paganin\", role = \"aut\", comment = \"reversible jump MCMC\"),\nperson(\"Joshua\", \"Hug\", role = \"aut\", comment = \"WAIC\"),\nperson(\"Paul\", \"van Dam-Bates\", role = \"aut\", comment = \"P\\u00f3lya-Gamma sampler, nimIntegrate, matrix exponential\"),\nperson(\"Jagadish\", \"Babu\", role = \"ctb\", comment = \"code for the compilation system for an early version of NIMBLE\"),\nperson(\"Lauren\", \"Ponisio\", role = \"ctb\", comment = \"contributions to the cross-validation code\"),\nperson(\"Peter\", \"Sujan\", role = \"ctb\", comment = \"multivariate t distribution code\")\n)", "URL": "https://r-nimble.org, https://github.com/nimble-dev/nimble", "BugReports": "https://github.com/nimble-dev/nimble/issues", "SystemRequirements": "GNU make", "License": "BSD_3_clause + file LICENSE | GPL (>= 2)", "Copyright": "See COPYRIGHTS file.", "Note": "For convenience, the package includes the necessary header files\nfor the Eigen distribution. (This is all that is needed to use\nthat functionality.) You can use an alternative installation of\nEigen on your system or the one we provide. The license for the\nEigen code is very permissive and allows us to distribute it\nwith this package. See and also the License section on that page.", "Encoding": "UTF-8", "Collate": "config.R all_utils.R options.R distributions_inputList.R\ndistributions_processInputList.R\ndistributions_implementations.R BUGS_BUGSdecl.R BUGS_contexts.R\nBUGS_nimbleGraph.R BUGS_modelDef.R BUGS_model.R\nBUGS_graphNodeMaps.R BUGS_readBUGS.R BUGS_macros.R\nBUGS_testBUGS.R BUGS_getDependencies.R BUGS_utils.R\nBUGS_mathCompatibility.R externalCalls.R genCpp_exprClass.R\ngenCpp_operatorLists.R genCpp_RparseTree2exprClasses.R\ngenCpp_initSizes.R genCpp_buildIntermediates.R\ngenCpp_processSpecificCalls.R genCpp_sizeProcessing.R\ngenCpp_toEigenize.R genCpp_insertAssertions.R genCpp_maps.R\ngenCpp_liftMaps.R genCpp_eigenization.R genCpp_addDebugMarks.R\ngenCpp_generateCpp.R RCfunction_core.R RCfunction_compile.R\nnimbleFunction_util.R nimbleFunction_core.R\nnimbleFunction_nodeFunction.R nimbleFunction_nodeFunctionNew.R\nnimbleFunction_Rderivs.R nimbleFunction_Rexecution.R\nnimbleFunction_compile.R nimbleFunction_keywordProcessing.R\nnimbleList_core.R types_util.R types_symbolTable.R\ntypes_modelValues.R types_modelValuesAccessor.R\ntypes_modelVariableAccessor.R types_nimbleFunctionList.R\ntypes_nodeFxnVector.R types_numericLists.R cppDefs_utils.R\ncppDefs_variables.R cppDefs_core.R cppDefs_namedObjects.R\ncppDefs_ADtools.R cppDefs_BUGSmodel.R cppDefs_RCfunction.R\ncppDefs_nimbleFunction.R cppDefs_nimbleList.R\ncppDefs_modelValues.R cppDefs_cppProject.R\ncppDefs_outputCppFromRparseTree.R cppInterfaces_utils.R\ncppInterfaces_models.R cppInterfaces_modelValues.R\ncppInterfaces_nimbleFunctions.R cppInterfaces_otherTypes.R\nnimbleProject.R initializeModel.R parameterTransform.R CAR.R\nMCMC_utils.R MCMC_configuration.R MCMC_build.R MCMC_run.R\nMCMC_samplers.R MCMC_derived.R MCMC_conjugacy.R\nMCMC_autoBlock.R MCMC_RJ.R MCMC_WAIC.R MCEM_build.R\ncrossValidation.R BNP_distributions.R BNP_samplers.R\nsetupMargNodes.R NF_utils.R miscFunctions.R normTooling.R\nmiscAlgorithms.R makevars.R 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"waicNimbleList", "withNimbleOptions" ], "_help": [ { "page": "ADbreak", "title": "NIMBLE language function to break tracking of derivatives", "topics": [ "ADbreak" ] }, { "page": "ADNimbleList", "title": "Data type for the return value of 'nimDerivs'", "topics": [ "ADNimbleList" ] }, { "page": "ADproxyModelClass-class", "title": "create an ADproxyModelClass object", "topics": [ "ADproxyModelClass", "ADproxyModelClass-class" ] }, { "page": "any_na", "title": "Determine if any values in a vector are NA or NaN", "topics": [ "any_na", "any_nan" ] }, { "page": "as.carAdjacency", "title": "Convert CAR structural parameters to adjacency, weights, num format", "topics": [ "as.carAdjacency" ] }, { "page": "as.carCM", "title": "Convert weights vector to parameters of 'dcar_proper' distributio", "topics": [ "as.carCM" ] }, { "page": "asRow", "title": "Turn a numeric vector into a single-row or single-column matrix", "topics": [ "asCol", "asRow" ] }, { "page": "autoBlock", "title": "Automated 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"title": "Builds an MCEM algorithm for a given NIMBLE model", "topics": [ "buildMCEM" ] }, { "page": "buildMCMC", "title": "Create an MCMC object from a NIMBLE model, or an MCMC configuration object", "topics": [ "buildMCMC" ] }, { "page": "calculateWAIC", "title": "Calculating WAIC using an offline algorithm", "topics": [ "calculateWAIC" ] }, { "page": "CAR_calcNumIslands", "title": "Calculate number of islands based on a CAR adjacency matrix.", "topics": [ "CAR_calcNumIslands" ] }, { "page": "CAR-Normal", "title": "The CAR-Normal Distribution", "topics": [ "CAR-Normal", "dcar_normal", "rcar_normal" ] }, { "page": "CAR-Proper", "title": "The CAR-Proper Distribution", "topics": [ "CAR-Proper", "dcar_proper", "rcar_proper" ] }, { "page": "carBounds", "title": "Calculate bounds for the autocorrelation parameter of the 'dcar_proper' distribution", "topics": [ "carBounds" ] }, { "page": "carMaxBound", "title": "Calculate the upper bound for the autocorrelation parameter of the 'dcar_proper' distribution", "topics": [ "carMaxBound" ] }, { "page": "carMinBound", "title": "Calculate the lower bound for the autocorrelation parameter of the 'dcar_proper' distribution", "topics": [ "carMinBound" ] }, { "page": "Categorical", "title": "The Categorical Distribution", "topics": [ "Categorical", "dcat", "rcat" ] }, { "page": "checkInterrupt", "title": "Check for interrupt (e.g. Ctrl-C) during nimbleFunction execution. Part of the NIMBLE language.", "topics": [ "checkInterrupt" ] }, { "page": "ChineseRestaurantProcess", "title": "The Chinese Restaurant Process Distribution", "topics": [ "ChineseRestaurantProcess", "dCRP", "rCRP" ] }, { "page": "clearCompiled", "title": "Clear compiled objects from a project and unload shared library", "topics": [ "clearCompiled" ] }, { "page": "CmodelBaseClass-class", "title": "Class 'CmodelBaseClass'", "topics": [ "CmodelBaseClass", "CmodelBaseClass-class" ] }, { "page": "CnimbleFunctionBase-class", "title": "Class 'CnimbleFunctionBase'", "topics": [ "CnimbleFunctionBase", "CnimbleFunctionBase-class" ] }, { "page": "codeBlockClass-class", "title": "Class 'codeBlockClass'", "topics": [ "codeBlockClass", "codeBlockClass-class" ] }, { "page": "compileNimble", "title": "compile NIMBLE models and nimbleFunctions", "topics": [ "compileNimble" ] }, { "page": "configureMCMC", "title": "Build the MCMCconf object for construction of an MCMC object", "topics": [ "configureMCMC" ] }, { "page": "configureRJ", "title": "Configure Reversible Jump for Variable Selection", "topics": [ "configureRJ" ] }, { "page": "Constraint", "title": "Constraint calculations in NIMBLE", "topics": [ "Constraint", "dconstraint", "rconstraint" ] }, { "page": "decide", "title": "Makes the Metropolis-Hastings acceptance decision, based upon the input (log) Metropolis-Hastings ratio", "topics": [ "decide" ] }, { "page": "decideAndJump", "title": "Creates a nimbleFunction for executing the Metropolis-Hastings jumping decision, and updating values in the model, or in a carbon copy modelValues object, accordingly.", "topics": [ "decideAndJump" ] }, { "page": "declare", "title": "Explicitly declare a variable in run-time code of a nimbleFunction", "topics": [ "declare" ] }, { "page": "deregisterDistributions", "title": "Remove user-supplied distributions from use in NIMBLE BUGS models", "topics": [ "deregisterDistributions" ] }, { "page": "derived", "title": "MCMC Derived Quantities", "topics": [ "derived", "derived_BASE", "derived_logProb", "derived_mean", "derived_predictive", "derived_variance" ] }, { "page": "Dirichlet", "title": "The Dirichlet Distribution", "topics": [ "ddirch", "Dirichlet", "dirichlet", "rdirch" ] }, { "page": "distributionInfo", "title": "Get information about a distribution", "topics": [ "distributionInfo", "getDistributionInfo", "getParamNames", "getType", "isUserDefined", "pqDefined" ] }, { "page": "Double-Exponential", "title": "The Double Exponential (Laplace) Distribution", "topics": [ "ddexp", "Double-Exponential", "pdexp", "qdexp", "rdexp" ] }, { "page": "eigenNimbleList", "title": "eigenNimbleList definition", "topics": [ "eigenNimbleList" ] }, { "page": "expAv", "title": "Matrix Exponential times a vector", "topics": [ "expAv" ] }, { "page": "expm", "title": "Matrix Exponential", "topics": [ "expm" ] }, { "page": "Exponential", "title": "The Exponential Distribution", "topics": [ "dexp_nimble", "Exponential", "pexp_nimble", "qexp_nimble", "rexp_nimble" ] }, { "page": "extractControlElement", "title": "Extract named elements from MCMC sampler control list", "topics": [ "extractControlElement" ] }, { "page": "flat", "title": "The Improper Uniform Distribution", "topics": [ "dflat", "dhalfflat", "flat", "halfflat", "rflat", "rhalfflat" ] }, { "page": "getBound", "title": "Get value of bound of a stochastic node in a model", "topics": [ "getBound" ] }, { "page": "getBUGSexampleDir", "title": "Get the directory path to one of the classic BUGS examples installed with NIMBLE package", "topics": [ "getBUGSexampleDir" ] }, { "page": "getConditionallyIndependentSets", "title": "Get a list of conditionally independent sets of nodes in a nimble model", "topics": [ "getConditionallyIndependentSets" ] }, { "page": "getDefinition", "title": "Get nimbleFunction definition", "topics": [ "getDefinition" ] }, { "page": "getMacroParameters", "title": "EXPERIMENTAL: Get list of parameter names generated by model macros", "topics": [ "getMacroParameters" ] }, { "page": "getNimbleOption", "title": "Get NIMBLE Option", "topics": [ "getNimbleOption" ] }, { "page": "getParam", "title": "Get value of a parameter of a stochastic node in a model", "topics": [ "getParam" ] }, { "page": "getSamplesDPmeasure", "title": "Get posterior samples for a Dirichlet process distribution (measure)", "topics": [ "getSamplesDPmeasure" ] }, { "page": "getsize", "title": "Returns number of rows of modelValues", "topics": [ "getsize" ] }, { "page": "identityMatrix", "title": "Create an Identity matrix (Deprecated)", "topics": [ "identityMatrix" ] }, { "page": "initializeModel", "title": "Performs initialization of nimble model node values and log probabilities", "topics": [ "initializeModel" ] }, { "page": "Interval", "title": "Interval calculations", "topics": [ "dinterval", "Interval", "rinterval" ] }, { "page": "Inverse-Gamma", "title": "The Inverse Gamma Distribution", "topics": [ "dinvgamma", "Inverse-Gamma", "pinvgamma", "qinvgamma", "rinvgamma" ] }, { "page": "Inverse-Wishart", "title": "The Inverse Wishart Distribution", "topics": [ "dinvwish_chol", "Inverse-Wishart", "inverse-wishart", "rinvwish_chol" ] }, { "page": "is.nf", "title": "check if a nimbleFunction", "topics": [ "is.nf" ] }, { "page": "is.nl", "title": "check if a nimbleList", "topics": [ "is.nl" ] }, { "page": "LKJ", "title": "The LKJ Distribution for the Cholesky Factor of a Correlation Matrix", "topics": [ "dlkj", "dlkj_corr_cholesky", "LKJ", "lkj", "lkj_corr", "lkj_corr_cholesky", "rlkj", "rlkj_corr_cholesky" ] }, { "page": "makeBoundInfo", "title": "Make an object of information about a model-bound pairing for getBound. Used internally", "topics": [ "makeBoundInfo" ] }, { "page": "makeModelDerivsInfo", "title": "Information on model structure used for derivatives", "topics": [ "makeModelDerivsInfo" ] }, { "page": "makeParamInfo", "title": "Make an object of information about a model-parameter pairing for getParam. Used internally", "topics": [ "makeParamInfo" ] }, { "page": "MCMCconf-class", "title": "Class 'MCMCconf'", "topics": [ "addDerivedQuantity", "addMonitors", "addMonitors2", "addSampler", "getDerivedQuantities", "getDerivedQuantityDefinition", "getMonitors", "getMonitors2", "getSamplerExecutionOrder", "getSamplers", "MCMCconf", "MCMCconf-class", "printDerivedQuantities", "printMonitors", "printSamplers", "removeDerivedQuantities", "removeDerivedQuantity", "removeSamplers", "resetMonitors", "setMonitors", "setMonitors2", "setSamplerExecutionOrder", "setSamplers", "setThin", "setThin2" ] }, { "page": "modelBaseClass-class", "title": "Class 'modelBaseClass'", "topics": [ "checkConjugacy", "expandNodeNames", "getCode", "getConstants", "getDependencies", "getDependenciesList", "getDimension", "getDistribution", "getDownstream", "getMacroInits", "getNodeNames", "getParents", "getVarNames", "initializeInfo", "isBinary", "isData", "isDeterm", "isDiscrete", "isEndNode", "isMultivariate", "isStoch", "isTruncated", "isUnivariate", "modelBaseClass", "modelBaseClass-class", "newModel", "resetData", "setData", "setInits", "topologicallySortNodes", "[[,modelBaseClass-method", "[[<-,modelBaseClass-method" ] }, { "page": "modelDefClass-class", "title": "Class for NIMBLE model definition", "topics": [ "modelDefClass", "modelDefClass-class" ] }, { "page": "modelInitialization", "title": "Information on initial values in a NIMBLE model", "topics": [ "modelInitialization" ] }, { "page": "modelValues", "title": "Create a NIMBLE modelValues Object", "topics": [ "modelValues" ] }, { "page": "modelValuesBaseClass-class", "title": "Class 'modelValuesBaseClass'", "topics": [ "modelValuesBaseClass", "modelValuesBaseClass-class", "[,CmodelValues-method", "[,CmodelValues-method,ANY,ANY", "[,CmodelValues-method,character,missing", "[,CmodelValues-method,character,missing,ANY-method", "[,modelValuesBaseClass-method", "[<-,CmodelValues-method", "[<-,modelValuesBaseClass-method", "[[,CmodelValues-method", "[[<-,CmodelValues-method" ] }, { "page": "modelValuesConf", "title": "Create the confs for a custom NIMBLE modelValues object", "topics": [ "modelValuesConf" ] }, { "page": "Multinomial", "title": "The Multinomial Distribution", "topics": [ "dmulti", "Multinomial", "multinomial", "rmulti" ] }, { "page": "Multivariate-t", "title": "The Multivariate t Distribution", "topics": [ "dmvt_chol", "Multivariate-t", "multivariate-t", "mvt", "rmvt_chol" ] }, { "page": "MultivariateNormal", "title": "The Multivariate Normal Distribution", "topics": [ "dmnorm_chol", "dmnorm_inv_ld", "MultivariateNormal", "rmnorm_chol", "rmnorm_inv_ld" ] }, { "page": "nfMethod", "title": "access (call) a member function of a nimbleFunction", "topics": [ "nfMethod" ] }, { "page": "nfVar", "title": "Access or set a member variable of a nimbleFunction", "topics": [ "nfVar", "nfVar<-" ] }, { "page": "nimble-internal", "title": "Functions and Classes Internal to NIMBLE", "topics": [ "AGHQuad_params", "AGHQuad_summary", "as.list.modelValuesBaseClass-Class", "as.matrix.modelValuesBaseClass-Class", "autoBlockClass-Class", "BUGScontextClass-Class", "BUGSsingleContextClass-Class", "calcAdaptationFactor", "calc_dcatConjugacyContributions", "calc_dmnormAltParams", "calc_dmnormConjugacyContributions", "calc_dmnorm_inv_ld_AltParams", "calc_dwishAltParams", "CAR_calcC", "CAR_calcCmatrix", "CAR_calcEVs2", "CAR_calcEVs3", "CAR_calcM", "cc_getNodesInExpr", "CmultiNimbleFunctionClass-Class", "CmultiNimbleListClass-Class", "CmultiNimbleObjClass-Class", "conjugacyClass-Class", "conjugacyRelationshipsClass-Class", "copyExprClass-Class", "cppBUGSmodelClass-Class", "cppCodeFileClass-Class", "cppCPPfileClass-Class", "cppHfileClass-Class", "cppModelValuesClass-Class", "cppNamedObjectsClass-Class", "cppNimbleClassClass-Class", "cppNimbleFunctionClass-Class", "cppNimbleListClass-Class", "cppProjectClass-Class", "cppVirtualNimbleFunctionClass-Class", "dependentClass-Class", "distClass-Class", "distributionsClass-Class", "dsqrtinvgamma", "eigenize_nimbleNullaryClass-Class", "emptyParam", "exprClass-Class", "exprTypeInfoClass-Class", "findMethodsInExprClass-Class", "gaussParam", "getNimbleProject", "getNodeFunctionIndexedInfo", "getParam_BASE", "indexedNodeInfoTableClass-Class", "is.Cmodel", "is.Cnf", "is.model", "is.nfGenerator", "is.Rmodel", "keywordInfoClass-Class", "MakeCustomModelClass-Class", "makeCustomModelValuesClass-Class", "mapsClass-Class", "MCEM_mcse", "mcmc_createModelObject", "messageIfVerbose", "modelDefInfoClass-Class", "multiGaussParam", "mvInfoClass-Class", "nfCompilationInfoClass-Class", "nf_preProcessMemberDataObject", "nimbleGraphClass-Class", "nimbleInternalFunctions", "nimbleListDefClass-Class", "nimbleProjectClass-Class", "nimbleUserNamespace", "nimDerivsInfoClass-Class", "nlCompilationInfoClass-Class", "PDinverse_logdet", "posteriorClass-Class", "RCfunctionCompileClass-Class", "RCfunInfoClass-Class", "RMakeCustomModelClass-Class", "rsqrtinvgamma", "samplesSummary", "setupCodeTemplateClass-Class", "singleModelValuesAccess", "singleModelValuesAccessClass-Class", "splitLatents", "varInfoClass-Class", "[,distributionsClass-method", "[,numberedModelValuesAccessors-method", "[,numberedObjects-method", "[<-,numberedModelValuesAccessors-method", "[<-,numberedObjects-method", "[[,CNumericList-method", "[[,conjugacyRelationshipsClass-method", "[[,distributionsClass-method", "[[,nimPointerList-method", "[[,RNumericList-method", "[[<-,CNumericList-method", "[[<-,nimbleFunctionList-method", "[[<-,nimPointerList-method", "[[<-,RNumericList-method" ] }, { "page": "nimble-math", "title": "Mathematical functions for BUGS and nimbleFunction programming", "topics": [ "besselK", "cloglog", "cube", "expit", "icloglog", "ilogit", "inprod", "inverse", "iprobit", "logdet", "logfact", "loggam", "logit", "nimEquals", "nimRound", "nimStep", "nimSwitch", "phi", "pow", "probit" ] }, { "page": "nimble-R-functions", "title": "NIMBLE language functions for R-like vector construction", "topics": [ "all", "any", "c", "diag", "is.na", "is.nan", "length", "nimble-R-functions", "nimC", "nimRep", "nimSeq", "rep", "seq", "seq_along", "which" ] }, { "page": "nimbleCode", "title": "Turn BUGS model code into an object for use in 'nimbleModel' or 'readBUGSmodel'", "topics": [ "nimbleCode" ] }, { "page": "nimbleExternalCall", "title": "Create a nimbleFunction that wraps a call to external compiled code", "topics": [ "nimbleExternalCall" ] }, { "page": "nimbleFunction", "title": "create a nimbleFunction", "topics": [ "nimbleFunction" ] }, { "page": "nimbleFunctionBase-class", "title": "Class 'nimbleFunctionBase'", "topics": [ "nimbleFunctionBase", "nimbleFunctionBase-class" ] }, { "page": "nimbleFunctionList-class", "title": "Create a list of nimbleFunctions", "topics": [ "nimbleFunctionList", "nimbleFunctionList-class" ] }, { "page": "nimbleFunctionVirtual", "title": "create a virtual nimbleFunction, a base class for other nimbleFunctions", "topics": [ "nimbleFunctionVirtual" ] }, { "page": "nimbleList", "title": "create a nimbleList", "topics": [ "nimbleList" ] }, { "page": "nimbleMCMC", "title": "Executes one or more chains of NIMBLE's default MCMC algorithm, for a model specified using BUGS code", "topics": [ "nimbleMCMC" ] }, { "page": "nimbleModel", "title": "Create a NIMBLE model from model code", "topics": [ "nimbleModel" ] }, { "page": "nimbleOptions", "title": "NIMBLE Options Settings", "topics": [ "nimbleOptions" ] }, { "page": "nimbleRcall", "title": "Make an R function callable from compiled nimbleFunctions (including nimbleModels).", "topics": [ "nimbleRcall" ] }, { "page": "nimbleType-class", "title": "create a nimbleType object", "topics": [ "nimbleType", "nimbleType-class" ] }, { "page": "nimCat", "title": "cat function for use in nimbleFunctions", "topics": [ "cat", "nimCat" ] }, { "page": "nimCopy", "title": "Copying function for NIMBLE", "topics": [ "copy", "nimCopy" ] }, { "page": "nimDerivs", "title": "Nimble Derivatives", "topics": [ "AD", "derivs", "nimDerivs" ] }, { "page": "nimDim", "title": "return sizes of an object whether it is a vector, matrix or array", "topics": [ "dim", "nimDim" ] }, { "page": "nimEigen", "title": "Spectral Decomposition of a Matrix", "topics": [ "eigen", "nimEigen" ] }, { "page": "nimIntegrate", "title": "Integration of One-Dimensional Functions", "topics": [ "integrate", "nimIntegrate" ] }, { "page": "nimMatrix", "title": "Creates matrix or array objects for use in nimbleFunctions", "topics": [ "array", "matrix", "nimArray", "nimMatrix" ] }, { "page": "nimNumeric", "title": "Creates numeric, integer or logical vectors for use in nimbleFunctions", "topics": [ "integer", "logical", "nimInteger", "nimLogical", "nimNumeric", "numeric" ] }, { "page": "nimOptim", "title": "General-purpose Optimization", "topics": [ "nimOptim" ] }, { "page": "nimOptimDefaultControl", "title": "Creates a default 'control' argument for 'nimOptim'.", "topics": [ "nimOptimDefaultControl" ] }, { "page": "nimOptimMethod", "title": "Set or get an optimization function to be used by 'nimOptim'", "topics": [ "nimOptimMethod" ] }, { "page": "nimPrint", "title": "print function for use in nimbleFunctions", "topics": [ "nimPrint", "print" ] }, { "page": "nimStop", "title": "Halt execution of a nimbleFunction function method. Part of the NIMBLE language", "topics": [ "nimStop", "stop" ] }, { "page": "nimSvd", "title": "Singular Value Decomposition of a Matrix", "topics": [ "nimSvd", "svd" ] }, { "page": "nodeFunctions", "title": "calculate, calculateDiff, simulate, or get the current log probabilities (densities) a set of nodes in a NIMBLE model", "topics": [ "calculate", "calculateDiff", "getLogProb", "nodeFunctions", "simulate" ] }, { "page": "optimControlNimbleList", "title": "Data type for the 'control' parameter of 'nimOptim'", "topics": [ "optimControlNimbleList" ] }, { "page": "optimDefaultControl", "title": "Creates a deafult 'control' argument for 'optim' (just an empty list).", "topics": [ "optimDefaultControl" ] }, { "page": "optimResultNimbleList", "title": "Data type for the return value of 'nimOptim'", "topics": [ "optimResultNimbleList" ] }, { "page": "parameterTransform", "title": "Automated transformations of model nodes to unconstrained scales", "topics": [ "parameterTransform" ] }, { "page": "pow_int", "title": "Power function for integer-valued exponent", "topics": [ "pow_int" ] }, { "page": "printErrors", "title": "Print error messages after failed compilation", "topics": [ "printErrors" ] }, { "page": "rankSample", "title": "Generates a weighted sample (with replacement) of ranks", "topics": [ "rankSample" ] }, { "page": "readBUGSmodel", "title": "Create a NIMBLE BUGS model from a variety of input formats, including BUGS model files", "topics": [ "readBUGSmodel" ] }, { "page": "registerDistributions", "title": "Add user-supplied distributions for use in NIMBLE BUGS models", "topics": [ "registerDistributions" ] }, { "page": "resize", "title": "Resizes a modelValues object", "topics": [ "resize" ] }, { "page": "Rmatrix2mvOneVar", "title": "Set values of one variable of a modelValues object from an R matrix", "topics": [ "Rmatrix2mvOneVar" ] }, { "page": "RmodelBaseClass-class", "title": "Class 'RmodelBaseClass'", "topics": [ "RmodelBaseClass", "RmodelBaseClass-class" ] }, { "page": "run.time", "title": "Time execution of NIMBLE code", "topics": [ "run.time" ] }, { "page": "runCrossValidate", "title": "Perform k-fold cross-validation on a NIMBLE model fit by MCMC", "topics": [ "runCrossValidate" ] }, { "page": "runLaplace", "title": "Placeholder for runLaplace", "topics": [ "runLaplace" ] }, { "page": "runMCMC", "title": "Run one or more chains of an MCMC algorithm and return samples, summary and/or WAIC", "topics": [ "runMCMC" ] }, { "page": "samplers", "title": "MCMC Sampling Algorithms", "topics": [ "AF_slice", "barker", "binary", "categorical", "crossLevel", "CRP", "CRP_concentration", "DPmeasure", "partial_mvn", "posterior_predictive", "prior_samples", "RJ_fixed_prior", "RJ_indicator", "RJ_toggled", "RW", "RW_block", "RW_block_lkj_corr_cholesky", "RW_dirichlet", "RW_lkj_corr_cholesky", "RW_llFunction", "RW_llFunction_block", "RW_multinomial", "RW_PF", "RW_PF_block", "RW_wishart", "sampler", "samplers", "sampler_AF_slice", "sampler_barker", "sampler_BASE", "sampler_binary", "sampler_CAR_normal", "sampler_CAR_proper", "sampler_categorical", "sampler_crossLevel", "sampler_CRP", "sampler_CRP_concentration", "sampler_ess", "sampler_noncentered", "sampler_partial_mvn", "sampler_polyagamma", "sampler_posterior_predictive", "sampler_prior_samples", "sampler_RJ_fixed_prior", "sampler_RJ_indicator", "sampler_RJ_toggled", "sampler_RW", "sampler_RW_block", "sampler_RW_block_lkj_corr_cholesky", "sampler_RW_dirichlet", "sampler_RW_lkj_corr_cholesky", "sampler_RW_llFunction", "sampler_RW_llFunction_block", "sampler_RW_multinomial", "sampler_RW_wishart", "sampler_slice", "sampler_slice_CRP_base_param", "slice" ] }, { "page": "setAndCalculate", "title": "Creates a nimbleFunction for setting the values of one or more model nodes, calculating the associated deterministic dependents and logProb values, and returning the total sum log-probability.", "topics": [ "setAndCalculate", "setAndCalculateDiff" ] }, { "page": "setAndCalculateOne", "title": "Creates a nimbleFunction for setting the value of a scalar model node, calculating the associated deterministic dependents and logProb values, and returning the total sum log-probability.", "topics": [ "setAndCalculateOne" ] }, { "page": "setSize", "title": "set the size of a numeric variable in NIMBLE", "topics": [ "setSize" ] }, { "page": "setupMargNodes", "title": "Organize model nodes for marginalization", "topics": [ "setupMargNodes" ] }, { "page": "setupOutputs", "title": "Explicitly declare objects created in setup code to be preserved and compiled as member data", "topics": [ "setupOutputs" ] }, { "page": "simNodes", "title": "Basic nimbleFunctions for calculate, simulate, and getLogProb with a set of nodes", "topics": [ "calcNodes", "getLogProbNodes", "simNodes" ] }, { "page": "simNodesMV", "title": "Basic nimbleFunctions for using a NIMBLE model with sets of stored values", "topics": [ "calcNodesMV", "getLogProbNodesMV", "simNodesMV" ] }, { "page": "singleVarAccessClass-class", "title": "Class 'singleVarAccessClass'", "topics": [ "singleVarAccessClass", "singleVarAccessClass-class" ] }, { "page": "StickBreakingFunction", "title": "The Stick Breaking Function", "topics": [ "stickbreaking", "StickBreakingFunction", "stick_breaking" ] }, { "page": "summaryLaplace", "title": "Placeholder for summaryLaplace", "topics": [ "summaryLaplace" ] }, { "page": "svdNimbleList", "title": "svdNimbleList definition", "topics": [ "svdNimbleList" ] }, { "page": "t", "title": "The t Distribution", "topics": [ "dt_nonstandard", "pt_nonstandard", "qt_nonstandard", "rt_nonstandard", "t" ] }, { "page": "testBUGSmodel", "title": "Tests BUGS examples in the NIMBLE system", "topics": [ "testBUGSmodel" ] }, { "page": "valueInCompiledNimbleFunction", "title": "get or set value of member data from a compiled nimbleFunction using a multi-interface", "topics": [ "valueInCompiledNimbleFunction" ] }, { "page": "values", "title": 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