| ADbreak | NIMBLE language function to break tracking of derivatives |
| ADNimbleList | Data type for the return value of 'nimDerivs' |
| ADproxyModelClass-class | create an ADproxyModelClass object |
| any_na | Determine if any values in a vector are NA or NaN |
| as.carAdjacency | Convert CAR structural parameters to adjacency, weights, num... |
| as.carCM | Convert weights vector to parameters of 'dcar_proper'... |
| asRow | Turn a numeric vector into a single-row or single-column... |
| autoBlock | Automated parameter blocking procedure for efficient MCMC... |
| BUGSdeclClass-class | BUGSdeclClass contains the information extracted from one... |
| buildAGHQGrid | Build Adaptive Gauss-Hermite Quadrature Grid |
| buildAuxiliaryFilter | Placeholder for buildAuxiliaryFilter |
| buildBootstrapFilter | Placeholder for buildBootstrapFilter |
| buildEnsembleKF | Placeholder for buildEnsembleKF |
| buildIteratedFilter2 | Placeholder for buildIteratedFilter2 |
| buildLiuWestFilter | Placeholder for buildLiuWestFilter |
| buildMacro | EXPERIMENTAL: Turn a function into a model macro |
| buildMCEM | Builds an MCEM algorithm for a given NIMBLE model |
| buildMCMC | Create an MCMC object from a NIMBLE model, or an MCMC... |
| calculateWAIC | Calculating WAIC using an offline algorithm |
| carBounds | Calculate bounds for the autocorrelation parameter of the... |
| CAR_calcNumIslands | Calculate number of islands based on a CAR adjacency matrix. |
| carMaxBound | Calculate the upper bound for the autocorrelation parameter... |
| carMinBound | Calculate the lower bound for the autocorrelation parameter... |
| CAR-Normal | The CAR-Normal Distribution |
| CAR-Proper | The CAR-Proper Distribution |
| Categorical | The Categorical Distribution |
| checkInterrupt | Check for interrupt (e.g. Ctrl-C) during nimbleFunction... |
| ChineseRestaurantProcess | The Chinese Restaurant Process Distribution |
| clearCompiled | Clear compiled objects from a project and unload shared... |
| CmodelBaseClass-class | Class 'CmodelBaseClass' |
| CnimbleFunctionBase-class | Class 'CnimbleFunctionBase' |
| codeBlockClass-class | Class 'codeBlockClass' |
| compileNimble | compile NIMBLE models and nimbleFunctions |
| configureMCMC | Build the MCMCconf object for construction of an MCMC object |
| configureRJ | Configure Reversible Jump for Variable Selection |
| Constraint | Constraint calculations in NIMBLE |
| decide | Makes the Metropolis-Hastings acceptance decision, based upon... |
| decideAndJump | Creates a nimbleFunction for executing the... |
| declare | Explicitly declare a variable in run-time code of a... |
| deregisterDistributions | Remove user-supplied distributions from use in NIMBLE BUGS... |
| Dirichlet | The Dirichlet Distribution |
| distributionInfo | Get information about a distribution |
| Double-Exponential | The Double Exponential (Laplace) Distribution |
| eigenNimbleList | eigenNimbleList definition |
| Exponential | The Exponential Distribution |
| extractControlElement | Extract named elements from MCMC sampler control list |
| flat | The Improper Uniform Distribution |
| getBound | Get value of bound of a stochastic node in a model |
| getBUGSexampleDir | Get the directory path to one of the classic BUGS examples... |
| getConditionallyIndependentSets | Get a list of conditionally independent sets of nodes in a... |
| getDefinition | Get nimbleFunction definition |
| getMacroParameters | EXPERIMENTAL: Get list of parameter names generated by model... |
| getNimbleOption | Get NIMBLE Option |
| getParam | Get value of a parameter of a stochastic node in a model |
| getSamplesDPmeasure | Get posterior samples for a Dirichlet process measure |
| getsize | Returns number of rows of modelValues |
| identityMatrix | Create an Identity matrix (Deprecated) |
| initializeModel | Performs initialization of nimble model node values and log... |
| Interval | Interval calculations |
| Inverse-Gamma | The Inverse Gamma Distribution |
| Inverse-Wishart | The Inverse Wishart Distribution |
| is.nf | check if a nimbleFunction |
| is.nl | check if a nimbleList |
| laplace | Laplace approximation and adaptive Gauss-Hermite quadrature |
| LKJ | The LKJ Distribution for the Cholesky Factor of a Correlation... |
| makeBoundInfo | Make an object of information about a model-bound pairing for... |
| makeModelDerivsInfo | Information on model structure used for derivatives |
| makeParamInfo | Make an object of information about a model-parameter pairing... |
| MCMCconf-class | Class 'MCMCconf' |
| modelBaseClass-class | Class 'modelBaseClass' |
| modelDefClass-class | Class for NIMBLE model definition |
| modelInitialization | Information on initial values in a NIMBLE model |
| modelValues | Create a NIMBLE modelValues Object |
| modelValuesBaseClass-class | Class 'modelValuesBaseClass' |
| modelValuesConf | Create the confs for a custom NIMBLE modelValues object |
| Multinomial | The Multinomial Distribution |
| MultivariateNormal | The Multivariate Normal Distribution |
| Multivariate-t | The Multivariate t Distribution |
| nfMethod | access (call) a member function of a nimbleFunction |
| nfVar | Access or set a member variable of a nimbleFunction |
| nimbleCode | Turn BUGS model code into an object for use in 'nimbleModel'... |
| nimbleExternalCall | Create a nimbleFunction that wraps a call to external... |
| nimbleFunction | create a nimbleFunction |
| nimbleFunctionBase-class | Class 'nimbleFunctionBase' |
| nimbleFunctionList-class | Create a list of nimbleFunctions |
| nimbleFunctionVirtual | create a virtual nimbleFunction, a base class for other... |
| nimble-internal | Functions and Classes Internal to NIMBLE |
| nimbleList | create a nimbleList |
| nimble-math | Mathematical functions for BUGS and nimbleFunction... |
| nimbleMCMC | Executes one or more chains of NIMBLE's default MCMC... |
| nimbleModel | Create a NIMBLE model from BUGS code |
| nimbleOptions | NIMBLE Options Settings |
| nimble-package | nimble: MCMC, Particle Filtering, and Programmable... |
| nimbleRcall | Make an R function callable from compiled nimbleFunctions... |
| nimble-R-functions | NIMBLE language functions for R-like vector construction |
| nimbleType-class | create a nimbleType object |
| nimCat | cat function for use in nimbleFunctions |
| nimCopy | Copying function for NIMBLE |
| nimDerivs | Nimble Derivatives |
| nimDim | return sizes of an object whether it is a vector, matrix or... |
| nimEigen | Spectral Decomposition of a Matrix |
| nimIntegrate | Integration of One-Dimensional Functions |
| nimMatrix | Creates matrix or array objects for use in nimbleFunctions |
| nimNumeric | Creates numeric, integer or logical vectors for use in... |
| nimOptim | General-purpose Optimization |
| nimOptimDefaultControl | Creates a default 'control' argument for 'nimOptim'. |
| nimOptimMethod | Set or get an optimization function to be used by 'nimOptim' |
| nimPrint | print function for use in nimbleFunctions |
| nimStop | Halt execution of a nimbleFunction function method. Part of... |
| nimSvd | Singular Value Decomposition of a Matrix |
| nodeFunctions | calculate, calculateDiff, simulate, or get the current log... |
| optimControlNimbleList | Data type for the 'control' parameter of 'nimOptim' |
| optimDefaultControl | Creates a deafult 'control' argument for 'optim' (just an... |
| optimResultNimbleList | Data type for the return value of 'nimOptim' |
| parameterTransform | Automated transformations of model nodes to unconstrained... |
| pow_int | Power function for integer-valued exponent |
| printErrors | Print error messages after failed compilation |
| rankSample | Generates a weighted sample (with replacement) of ranks |
| readBUGSmodel | Create a NIMBLE BUGS model from a variety of input formats,... |
| registerDistributions | Add user-supplied distributions for use in NIMBLE BUGS models |
| resize | Resizes a modelValues object |
| Rmatrix2mvOneVar | Set values of one variable of a modelValues object from an R... |
| RmodelBaseClass-class | Class 'RmodelBaseClass' |
| runCrossValidate | Perform k-fold cross-validation on a NIMBLE model fit by MCMC |
| runLaplace | Combine steps of running Laplace or adaptive Gauss-Hermite... |
| runMCMC | Run one or more chains of an MCMC algorithm and return... |
| run.time | Time execution of NIMBLE code |
| samplers | MCMC Sampling Algorithms |
| setAndCalculate | Creates a nimbleFunction for setting the values of one or... |
| setAndCalculateOne | Creates a nimbleFunction for setting the value of a scalar... |
| setSize | set the size of a numeric variable in NIMBLE |
| setupMargNodes | Organize model nodes for marginalization |
| setupOutputs | Explicitly declare objects created in setup code to be... |
| simNodes | Basic nimbleFunctions for calculate, simulate, and getLogProb... |
| simNodesMV | Basic nimbleFunctions for using a NIMBLE model with sets of... |
| singleVarAccessClass-class | Class 'singleVarAccessClass' |
| StickBreakingFunction | The Stick Breaking Function |
| summaryLaplace | Summarize results from Laplace or adaptive Gauss-Hermite... |
| svdNimbleList | svdNimbleList definition |
| t | The t Distribution |
| testBUGSmodel | Tests BUGS examples in the NIMBLE system |
| valueInCompiledNimbleFunction | get or set value of member data from a compiled... |
| values | Access or set values for a set of nodes in a model |
| waic | Using WAIC |
| waicDetailsNimbleList | waicDetailsNimbleList definition |
| waicNimbleList | waicNimbleList definition |
| Wishart | The Wishart Distribution |
| withNimbleOptions | Temporarily set some NIMBLE options. |
