| NIMBLE language function to break tracking of derivatives | ADbreak |
| Data type for the return value of 'nimDerivs' | ADNimbleList |
| create an ADproxyModelClass object | ADproxyModelClass ADproxyModelClass-class |
| Determine if any values in a vector are NA or NaN | any_na any_nan |
| Convert CAR structural parameters to adjacency, weights, num format | as.carAdjacency |
| Convert weights vector to parameters of 'dcar_proper' distributio | as.carCM |
| Turn a numeric vector into a single-row or single-column matrix | asCol asRow |
| Automated parameter blocking procedure for efficient MCMC sampling | autoBlock |
| BUGSdeclClass contains the information extracted from one BUGS declaration | BUGSdeclClass BUGSdeclClass-class |
| Build Adaptive Gauss-Hermite Quadrature Grid | buildAGHQGrid |
| Placeholder for buildAuxiliaryFilter | buildAuxiliaryFilter |
| Placeholder for buildBootstrapFilter | buildBootstrapFilter |
| Placeholder for buildEnsembleKF | buildEnsembleKF |
| Placeholder for buildIteratedFilter2 | buildIteratedFilter2 |
| Laplace approximation and adaptive Gauss-Hermite quadrature | AGHQ AGHQuad buildAGHQ buildLaplace Laplace laplace |
| Placeholder for buildLiuWestFilter | buildLiuWestFilter |
| EXPERIMENTAL: Turn a function into a model macro | buildMacro |
| Builds an MCEM algorithm for a given NIMBLE model | buildMCEM |
| Create an MCMC object from a NIMBLE model, or an MCMC configuration object | buildMCMC |
| Calculating WAIC using an offline algorithm | calculateWAIC |
| Calculate number of islands based on a CAR adjacency matrix. | CAR_calcNumIslands |
| The CAR-Normal Distribution | CAR-Normal dcar_normal rcar_normal |
| The CAR-Proper Distribution | CAR-Proper dcar_proper rcar_proper |
| Calculate bounds for the autocorrelation parameter of the 'dcar_proper' distribution | carBounds |
| Calculate the upper bound for the autocorrelation parameter of the 'dcar_proper' distribution | carMaxBound |
| Calculate the lower bound for the autocorrelation parameter of the 'dcar_proper' distribution | carMinBound |
| The Categorical Distribution | Categorical dcat rcat |
| Check for interrupt (e.g. Ctrl-C) during nimbleFunction execution. Part of the NIMBLE language. | checkInterrupt |
| The Chinese Restaurant Process Distribution | ChineseRestaurantProcess dCRP rCRP |
| Clear compiled objects from a project and unload shared library | clearCompiled |
| Class 'CmodelBaseClass' | CmodelBaseClass CmodelBaseClass-class |
| Class 'CnimbleFunctionBase' | CnimbleFunctionBase CnimbleFunctionBase-class |
| Class 'codeBlockClass' | codeBlockClass codeBlockClass-class |
| compile NIMBLE models and nimbleFunctions | compileNimble |
| Build the MCMCconf object for construction of an MCMC object | configureMCMC |
| Configure Reversible Jump for Variable Selection | configureRJ |
| Constraint calculations in NIMBLE | Constraint dconstraint rconstraint |
| Makes the Metropolis-Hastings acceptance decision, based upon the input (log) Metropolis-Hastings ratio | decide |
| Creates a nimbleFunction for executing the Metropolis-Hastings jumping decision, and updating values in the model, or in a carbon copy modelValues object, accordingly. | decideAndJump |
| Explicitly declare a variable in run-time code of a nimbleFunction | declare |
| Remove user-supplied distributions from use in NIMBLE BUGS models | deregisterDistributions |
| The Dirichlet Distribution | ddirch Dirichlet dirichlet rdirch |
| Get information about a distribution | distributionInfo getDistributionInfo getParamNames getType isUserDefined pqDefined |
| The Double Exponential (Laplace) Distribution | ddexp Double-Exponential pdexp qdexp rdexp |
| eigenNimbleList definition | eigenNimbleList |
| The Exponential Distribution | dexp_nimble Exponential pexp_nimble qexp_nimble rexp_nimble |
| Extract named elements from MCMC sampler control list | extractControlElement |
| The Improper Uniform Distribution | dflat dhalfflat flat halfflat rflat rhalfflat |
| Get value of bound of a stochastic node in a model | getBound |
| Get the directory path to one of the classic BUGS examples installed with NIMBLE package | getBUGSexampleDir |
| Get a list of conditionally independent sets of nodes in a nimble model | getConditionallyIndependentSets |
| Get nimbleFunction definition | getDefinition |
| EXPERIMENTAL: Get list of parameter names generated by model macros | getMacroParameters |
| Get NIMBLE Option | getNimbleOption |
| Get value of a parameter of a stochastic node in a model | getParam |
| Get posterior samples for a Dirichlet process measure | getSamplesDPmeasure |
| Returns number of rows of modelValues | getsize |
| Create an Identity matrix (Deprecated) | identityMatrix |
| Performs initialization of nimble model node values and log probabilities | initializeModel |
| Interval calculations | dinterval Interval rinterval |
| The Inverse Gamma Distribution | dinvgamma Inverse-Gamma pinvgamma qinvgamma rinvgamma |
| The Inverse Wishart Distribution | dinvwish_chol Inverse-Wishart inverse-wishart rinvwish_chol |
| check if a nimbleFunction | is.nf |
| check if a nimbleList | is.nl |
| The LKJ Distribution for the Cholesky Factor of a Correlation Matrix | dlkj dlkj_corr_cholesky LKJ lkj lkj_corr lkj_corr_cholesky rlkj rlkj_corr_cholesky |
| Make an object of information about a model-bound pairing for getBound. Used internally | makeBoundInfo |
| Information on model structure used for derivatives | makeModelDerivsInfo |
| Make an object of information about a model-parameter pairing for getParam. Used internally | makeParamInfo |
| Class 'MCMCconf' | addMonitors addMonitors2 addSampler getMonitors getMonitors2 getSamplerExecutionOrder getSamplers MCMCconf MCMCconf-class printMonitors printSamplers removeSamplers resetMonitors setMonitors setMonitors2 setSamplerExecutionOrder setSamplers setThin setThin2 |
| Class 'modelBaseClass' | 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 |
| Class for NIMBLE model definition | modelDefClass modelDefClass-class |
| Information on initial values in a NIMBLE model | modelInitialization |
| Create a NIMBLE modelValues Object | modelValues |
| Class 'modelValuesBaseClass' | 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 |
| Create the confs for a custom NIMBLE modelValues object | modelValuesConf |
| The Multinomial Distribution | dmulti Multinomial multinomial rmulti |
| The Multivariate t Distribution | dmvt_chol Multivariate-t multivariate-t mvt rmvt_chol |
| The Multivariate Normal Distribution | dmnorm_chol MultivariateNormal rmnorm_chol |
| access (call) a member function of a nimbleFunction | nfMethod |
| Access or set a member variable of a nimbleFunction | nfVar nfVar<- |
| Functions and Classes Internal to NIMBLE | 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_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 exprClass-Class exprTypeInfoClass-Class findMethodsInExprClass-Class getNimbleProject getNodeFunctionIndexedInfo 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 mvInfoClass-Class nfCompilationInfoClass-Class nf_preProcessMemberDataObject nimbleGraphClass-Class nimbleInternalFunctions nimbleListDefClass-Class nimbleProjectClass-Class nimbleUserNamespace nimDerivsInfoClass-Class nlCompilationInfoClass-Class posteriorClass-Class RCfunctionCompileClass-Class RCfunInfoClass-Class RMakeCustomModelClass-Class rsqrtinvgamma samplesSummary setupCodeTemplateClass-Class singleModelValuesAccess singleModelValuesAccessClass-Class 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 |
| Mathematical functions for BUGS and nimbleFunction programming | besselK cloglog cube expit icloglog ilogit inprod inverse iprobit logdet logfact loggam logit nimEquals nimRound nimStep nimSwitch phi pow probit |
| NIMBLE language functions for R-like vector construction | all any c diag is.na is.nan length nimble-R-functions nimC nimRep nimSeq rep seq seq_along which |
| Turn BUGS model code into an object for use in 'nimbleModel' or 'readBUGSmodel' | nimbleCode |
| Create a nimbleFunction that wraps a call to external compiled code | nimbleExternalCall |
| create a nimbleFunction | nimbleFunction |
| Class 'nimbleFunctionBase' | nimbleFunctionBase nimbleFunctionBase-class |
| Create a list of nimbleFunctions | nimbleFunctionList nimbleFunctionList-class |
| create a virtual nimbleFunction, a base class for other nimbleFunctions | nimbleFunctionVirtual |
| create a nimbleList | nimbleList |
| Executes one or more chains of NIMBLE's default MCMC algorithm, for a model specified using BUGS code | nimbleMCMC |
| Create a NIMBLE model from BUGS code | nimbleModel |
| NIMBLE Options Settings | nimbleOptions |
| Make an R function callable from compiled nimbleFunctions (including nimbleModels). | nimbleRcall |
| create a nimbleType object | nimbleType nimbleType-class |
| cat function for use in nimbleFunctions | cat nimCat |
| Copying function for NIMBLE | copy nimCopy |
| Nimble Derivatives | AD derivs nimDerivs |
| return sizes of an object whether it is a vector, matrix or array | dim nimDim |
| Spectral Decomposition of a Matrix | eigen nimEigen |
| Integration of One-Dimensional Functions | integrate nimIntegrate |
| Creates matrix or array objects for use in nimbleFunctions | array matrix nimArray nimMatrix |
| Creates numeric, integer or logical vectors for use in nimbleFunctions | integer logical nimInteger nimLogical nimNumeric numeric |
| General-purpose Optimization | nimOptim |
| Creates a default 'control' argument for 'nimOptim'. | nimOptimDefaultControl |
| Set or get an optimization function to be used by 'nimOptim' | nimOptimMethod |
| print function for use in nimbleFunctions | nimPrint print |
| Halt execution of a nimbleFunction function method. Part of the NIMBLE language | nimStop stop |
| Singular Value Decomposition of a Matrix | nimSvd svd |
| calculate, calculateDiff, simulate, or get the current log probabilities (densities) a set of nodes in a NIMBLE model | calculate calculateDiff getLogProb nodeFunctions simulate |
| Data type for the 'control' parameter of 'nimOptim' | optimControlNimbleList |
| Creates a deafult 'control' argument for 'optim' (just an empty list). | optimDefaultControl |
| Data type for the return value of 'nimOptim' | optimResultNimbleList |
| Automated transformations of model nodes to unconstrained scales | parameterTransform |
| Power function for integer-valued exponent | pow_int |
| Print error messages after failed compilation | printErrors |
| Generates a weighted sample (with replacement) of ranks | rankSample |
| Create a NIMBLE BUGS model from a variety of input formats, including BUGS model files | readBUGSmodel |
| Add user-supplied distributions for use in NIMBLE BUGS models | registerDistributions |
| Resizes a modelValues object | resize |
| Set values of one variable of a modelValues object from an R matrix | Rmatrix2mvOneVar |
| Class 'RmodelBaseClass' | RmodelBaseClass RmodelBaseClass-class |
| Time execution of NIMBLE code | run.time |
| Perform k-fold cross-validation on a NIMBLE model fit by MCMC | runCrossValidate |
| Combine steps of running Laplace or adaptive Gauss-Hermite quadrature approximation | runAGHQ runLaplace |
| Run one or more chains of an MCMC algorithm and return samples, summary and/or WAIC | runMCMC |
| MCMC Sampling Algorithms | AF_slice barker binary categorical crossLevel CRP CRP_concentration DPmeasure 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_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 |
| 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. | setAndCalculate setAndCalculateDiff |
| 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. | setAndCalculateOne |
| set the size of a numeric variable in NIMBLE | setSize |
| Organize model nodes for marginalization | setupMargNodes |
| Explicitly declare objects created in setup code to be preserved and compiled as member data | setupOutputs |
| Basic nimbleFunctions for calculate, simulate, and getLogProb with a set of nodes | calcNodes getLogProbNodes simNodes |
| Basic nimbleFunctions for using a NIMBLE model with sets of stored values | calcNodesMV getLogProbNodesMV simNodesMV |
| Class 'singleVarAccessClass' | singleVarAccessClass singleVarAccessClass-class |
| The Stick Breaking Function | stickbreaking StickBreakingFunction stick_breaking |
| Summarize results from Laplace or adaptive Gauss-Hermite quadrature approximation | summaryAGHQ summaryLaplace |
| svdNimbleList definition | svdNimbleList |
| The t Distribution | dt_nonstandard pt_nonstandard qt_nonstandard rt_nonstandard t |
| Tests BUGS examples in the NIMBLE system | testBUGSmodel |
| get or set value of member data from a compiled nimbleFunction using a multi-interface | valueInCompiledNimbleFunction |
| Access or set values for a set of nodes in a model | values values<- |
| Using WAIC | buildWAIC enableWAIC getWAIC getWAICdetails WAIC waic |
| waicDetailsNimbleList definition | waicDetailsNimbleList |
| waicNimbleList definition | waicNimbleList |
| The Wishart Distribution | dwish_chol rwish_chol Wishart wishart |
| Temporarily set some NIMBLE options. | withNimbleOptions |
