BUGSdeclClass-class     BUGSdeclClass contains the information
                        extracted from one BUGS declaration
Categorical             The Categorical Distribution
CmodelBaseClass-class   Class 'CmodelBaseClass'
CnimbleFunctionBase-class
                        Class 'CnimbleFunctionBase'
Constraint              Constraint calculations in NIMBLE
Dirichlet               The Dirichlet Distribution
Exponential             The Exponential Distribution
Interval                Interval calculations
MCMCconf-class          Class 'MCMCconf'
MCMCsuite               Executes multiple MCMC algorithms and organizes
                        results.
MCMCsuiteClass-class    Class 'MCMCsuiteClass'
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'
Wishart                 The Wishart Distribution
as.matrix.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
buildAuxiliaryFilter    Create an auxiliary particle filter algorithm
                        to estimate log-likelihood.
buildBootstrapFilter    Create a bootstrap particle filter algorithm to
                        estimate log-likelihood.
buildEnsembleKF         Create an Ensemble Kalman filter algorithm to
                        sample from latent states.
buildLiuWestFilter      Create a Liu and West particle filter
                        algorithm.
buildMCEM               Builds an MCEM algorithm from a given NIMBLE
                        model
buildMCMC               Create an MCMC function, from an MCMCconf
                        object
checkInterrupt          Check for interrupt (e.g. Ctrl-C) during
                        nimbleFunction execution. Part of the NIMBLE
                        language.
cloglog                 Mathematical functions for BUGS and
                        nimbleFunction programming
codeBlockClass-class    Class 'codeBlockClass'
combine_MCMC_comparison_results
                        Combine multiple objects returned by
                        compareMCMCs
compareMCMCs            Run multiple MCMCs (packages or NIMBLE cases)
                        for multiple models and return summary results
compileNimble           compile NIMBLE models and nimbleFunctions
configureMCMC           Build the MCMCconf object for construction of
                        an MCMC object
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
distributionInfo        Get information about a 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
getDefinition           Get nimbleFunction definition
getLoadingNamespace     return the namespace in which a nimbleFunction
                        is being loaded
getNimbleOption         Get NIMBLE Option
getParam                Get value of a parameter of a stochastic node
                        in a model
getsize                 Returns number of rows of modelValues
identityMatrix          Create an Identity matrix
initializeModel         Performs initialization of nimble model node
                        values and log probabilities
is.nf                   check if a nimbleFunction
makeBoundInfo           Make an object of information about a
                        model-bound pairing for getBound. Used
                        internally
makeParamInfo           Make an object of information about a
                        model-parameter pairing for getParam.  Used
                        internally
make_MCMC_comparison_pages
                        Make html pages summarizing results from
                        compareMCMCs
modelBaseClass-class    Class 'modelBaseClass'
modelDefClass-class     Class for NIMBLE model definition
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
nimArray                Creates a array object of arbitrary dimension
                        for use in NIMBLE DSL functions
nimCat                  cat function for use in nimbleFunctions
nimCopy                 Copying function for NIMBLE
nimDim                  return sizes of an object whether it is a
                        vector, matrix or array
nimInteger              Creates an integer vector for use in NIMBLE DSL
                        functions
nimMatrix               Creates a matrix object for use in NIMBLE DSL
                        functions
nimNumeric              Creates a numeric vector for use in NIMBLE DSL
                        functions
nimPrint                print function for use in nimbleFunctions
nimStop                 Halt execution of a nimbleFunction function
                        method.  Part of the NIMBLE language
nimbleCode              Turn BUGS model code into an object for use in
                        'nimbleModel' or 'readBUGSmodel'
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
nimbleModel             Create a NIMBLE model from BUGS code
nimbleOptions           NIMBLE Options Settings
nodeFunctions           calculate, calculateDiff, simulate, or get the
                        current log probabilities (densities) a set of
                        nodes in a NIMBLE model
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
rename_MCMC_comparison_method
                        Rename a method in an object returned by
                        compareMCMCs
reshape_comparison_results
                        Convert comparison results to a more general
                        format
resize                  Resizes a modelValues object
run.time                Time execution of NIMBLE code
runMCMC                 Run one or more chains of an MCMC algorithm and
                        extract samples
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
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'
t                       The t Distribution
testBUGSmodel           Tests BUGS examples in the NIMBLE system
updateMCMCcomparisonWithHighOrderESS
                        Re-estimate effective sample size from results
                        of compareMCMCs
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
