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 |
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 |
model_macro_builder | EXPERIMENTAL: Turn a function into a model macro |
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. |
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