ADNimbleList            Data type for the return value of 'nimDerivs'
ADbreak                 NIMBLE language function to break tracking of
                        derivatives
ADproxyModelClass-class
                        create an ADproxyModelClass object
BUGSdeclClass-class     BUGSdeclClass contains the information
                        extracted from one BUGS declaration
CAR-Normal              The CAR-Normal Distribution
CAR-Proper              The CAR-Proper Distribution
CAR_calcNumIslands      Calculate number of islands based on a CAR
                        adjacency matrix.
Categorical             The Categorical Distribution
ChineseRestaurantProcess
                        The Chinese Restaurant Process Distribution
CmodelBaseClass-class   Class 'CmodelBaseClass'
CnimbleFunctionBase-class
                        Class 'CnimbleFunctionBase'
Constraint              Constraint calculations in NIMBLE
Dirichlet               The Dirichlet Distribution
Double-Exponential      The Double Exponential (Laplace) Distribution
Exponential             The Exponential Distribution
Interval                Interval calculations
Inverse-Gamma           The Inverse Gamma Distribution
Inverse-Wishart         The Inverse Wishart Distribution
LKJ                     The LKJ Distribution for the Cholesky Factor of
                        a Correlation Matrix
MCMCconf-class          Class 'MCMCconf'
Multinomial             The Multinomial Distribution
Multivariate-t          The Multivariate t Distribution
MultivariateNormal      The Multivariate Normal Distribution
Rmatrix2mvOneVar        Set values of one variable of a modelValues
                        object from an R matrix
RmodelBaseClass-class   Class 'RmodelBaseClass'
StickBreakingFunction   The Stick Breaking Function
Wishart                 The Wishart Distribution
any_na                  Determine if any values in a vector are NA or
                        NaN
as.carAdjacency         Convert CAR structural parameters to adjacency,
                        weights, num format
as.carCM                Convert weights vector to parameters of
                        'dcar_proper' distributio
as.list.modelValuesBaseClass-Class
                        Functions and Classes Internal to NIMBLE
asRow                   Turn a numeric vector into a single-row or
                        single-column matrix
autoBlock               Automated parameter blocking procedure for
                        efficient MCMC sampling
besselK                 Mathematical functions for BUGS and
                        nimbleFunction programming
buildAGHQ               Placeholder for buildAGHQ
buildAuxiliaryFilter    Placeholder for buildAuxiliaryFilter
buildBootstrapFilter    Placeholder for buildBootstrapFilter
buildEnsembleKF         Placeholder for buildEnsembleKF
buildIteratedFilter2    Placeholder for buildIteratedFilter2
buildLaplace            Placeholder for buildLaplace
buildLiuWestFilter      Placeholder for buildLiuWestFilter
buildMCEM               Builds an MCEM algorithm for a given NIMBLE
                        model
buildMCMC               Create an MCMC object from a NIMBLE model, or
                        an MCMC configuration object
buildMacro              EXPERIMENTAL: Turn a function into a model
                        macro
calculateWAIC           Calculating WAIC using an offline algorithm
carBounds               Calculate bounds for the autocorrelation
                        parameter of the 'dcar_proper' distribution
carMaxBound             Calculate the upper bound for the
                        autocorrelation parameter of the 'dcar_proper'
                        distribution
carMinBound             Calculate the lower bound for the
                        autocorrelation parameter of the 'dcar_proper'
                        distribution
checkInterrupt          Check for interrupt (e.g. Ctrl-C) during
                        nimbleFunction execution. Part of the NIMBLE
                        language.
clearCompiled           Clear compiled objects from a project and
                        unload shared library
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
decide                  Makes the Metropolis-Hastings acceptance
                        decision, based upon the input (log)
                        Metropolis-Hastings ratio
decideAndJump           Creates a nimbleFunction for executing the
                        Metropolis-Hastings jumping decision, and
                        updating values in the model, or in a carbon
                        copy modelValues object, accordingly.
declare                 Explicitly declare a variable in run-time code
                        of a nimbleFunction
deregisterDistributions
                        Remove user-supplied distributions from use in
                        NIMBLE BUGS models
derived_BASE            MCMC Derived Quantities
distributionInfo        Get information about a distribution
eigenNimbleList         eigenNimbleList definition
expAv                   Matrix Exponential times a vector
expm                    Matrix Exponential
extractControlElement   Extract named elements from MCMC sampler
                        control list
flat                    The Improper Uniform Distribution
getBUGSexampleDir       Get the directory path to one of the classic
                        BUGS examples installed with NIMBLE package
getBound                Get value of bound of a stochastic node in a
                        model
getConditionallyIndependentSets
                        Get a list of conditionally independent sets of
                        nodes in a nimble model
getDefinition           Get nimbleFunction definition
getMacroParameters      EXPERIMENTAL: Get list of parameter names
                        generated by model macros
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
                        distribution (measure)
getsize                 Returns number of rows of modelValues
identityMatrix          Create an Identity matrix (Deprecated)
initializeModel         Performs initialization of nimble model node
                        values and log probabilities
is.nf                   check if a nimbleFunction
is.nl                   check if a nimbleList
makeBoundInfo           Make an object of information about a
                        model-bound pairing for getBound. Used
                        internally
makeModelDerivsInfo     Information on model structure used for
                        derivatives
makeParamInfo           Make an object of information about a
                        model-parameter pairing for getParam.  Used
                        internally
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
nfMethod                access (call) a member function of a
                        nimbleFunction
nfVar                   Access or set a member variable of a
                        nimbleFunction
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 array
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 nimbleFunctions
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 the NIMBLE language
nimSvd                  Singular Value Decomposition of a Matrix
nimble-R-functions      NIMBLE language functions for R-like vector
                        construction
nimbleCode              Turn BUGS model code into an object for use in
                        'nimbleModel' or 'readBUGSmodel'
nimbleExternalCall      Create a nimbleFunction that wraps a call to
                        external compiled code
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 nimbleFunctions
nimbleList              create a nimbleList
nimbleMCMC              Executes one or more chains of NIMBLE's default
                        MCMC algorithm, for a model specified using
                        BUGS code
nimbleModel             Create a NIMBLE model from model code
nimbleOptions           NIMBLE Options Settings
nimbleRcall             Make an R function callable from compiled
                        nimbleFunctions (including nimbleModels).
nimbleType-class        create a nimbleType object
nodeFunctions           calculate, calculateDiff, simulate, or get the
                        current log probabilities (densities) a set of
                        nodes in a NIMBLE model
optimControlNimbleList
                        Data type for the 'control' parameter of
                        'nimOptim'
optimDefaultControl     Creates a deafult 'control' argument for
                        'optim' (just an empty list).
optimResultNimbleList   Data type for the return value of 'nimOptim'
parameterTransform      Automated transformations of model nodes to
                        unconstrained scales
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, including BUGS model files
registerDistributions   Add user-supplied distributions for use in
                        NIMBLE BUGS models
resize                  Resizes a modelValues object
run.time                Time execution of NIMBLE code
runAGHQ                 Placeholder for runAGHQ
runCrossValidate        Perform k-fold cross-validation on a NIMBLE
                        model fit by MCMC
runLaplace              Placeholder for runLaplace
runMCMC                 Run one or more chains of an MCMC algorithm and
                        return samples, summary and/or WAIC
sampler_BASE            MCMC Sampling Algorithms
setAndCalculate         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.
setAndCalculateOne      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.
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 preserved and compiled as member
                        data
simNodes                Basic nimbleFunctions for calculate, simulate,
                        and getLogProb with a set of nodes
simNodesMV              Basic nimbleFunctions for using a NIMBLE model
                        with sets of stored values
singleVarAccessClass-class
                        Class 'singleVarAccessClass'
summaryAGHQ             Placeholder for summaryAGHQ
summaryLaplace          Placeholder for summaryLaplace
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
                        nimbleFunction using a multi-interface
values                  Access or set values for a set of nodes in a
                        model
waic                    Using WAIC
waicDetailsNimbleList   waicDetailsNimbleList definition
waicNimbleList          waicNimbleList definition
withNimbleOptions       Temporarily set some NIMBLE options.
