Man pages for nimble
MCMC, Particle Filtering, and Programmable Hierarchical Modeling

ADbreakNIMBLE language function to break tracking of derivatives
ADNimbleListData type for the return value of 'nimDerivs'
ADproxyModelClass-classcreate an ADproxyModelClass object
any_naDetermine if any values in a vector are NA or NaN
as.carAdjacencyConvert CAR structural parameters to adjacency, weights, num...
as.carCMConvert weights vector to parameters of 'dcar_proper'...
asRowTurn a numeric vector into a single-row or single-column...
autoBlockAutomated parameter blocking procedure for efficient MCMC...
BUGSdeclClass-classBUGSdeclClass contains the information extracted from one...
buildAuxiliaryFilterPlaceholder for buildAuxiliaryFilter
buildBootstrapFilterPlaceholder for buildBootstrapFilter
buildEnsembleKFPlaceholder for buildEnsembleKF
buildIteratedFilter2Placeholder for buildIteratedFilter2
buildLiuWestFilterPlaceholder for buildLiuWestFilter
buildMCEMBuilds an MCEM algorithm from a given NIMBLE model
buildMCMCCreate an MCMC object from a NIMBLE model, or an MCMC...
calculateWAICCalculating WAIC using an offline algorithm
carBoundsCalculate bounds for the autocorrelation parameter of the...
CAR_calcNumIslandsCalculate number of islands based on a CAR adjacency matrix.
carMaxBoundCalculate the upper bound for the autocorrelation parameter...
carMinBoundCalculate the lower bound for the autocorrelation parameter...
CAR-NormalThe CAR-Normal Distribution
CAR-ProperThe CAR-Proper Distribution
CategoricalThe Categorical Distribution
checkInterruptCheck for interrupt (e.g. Ctrl-C) during nimbleFunction...
ChineseRestaurantProcessThe Chinese Restaurant Process Distribution
clearCompiledClear compiled objects from a project and unload shared...
CmodelBaseClass-classClass 'CmodelBaseClass'
CnimbleFunctionBase-classClass 'CnimbleFunctionBase'
codeBlockClass-classClass 'codeBlockClass'
compareMCMCsPlaceholder for compareMCMCs
compileNimblecompile NIMBLE models and nimbleFunctions
configureMCMCBuild the MCMCconf object for construction of an MCMC object
configureRJConfigure Reversible Jump for Variable Selection
ConstraintConstraint calculations in NIMBLE
decideMakes the Metropolis-Hastings acceptance decision, based upon...
decideAndJumpCreates a nimbleFunction for executing the...
declareExplicitly declare a variable in run-time code of a...
deregisterDistributionsRemove user-supplied distributions from use in NIMBLE BUGS...
DirichletThe Dirichlet Distribution
distributionInfoGet information about a distribution
Double-ExponentialThe Double Exponential (Laplace) Distribution
eigenNimbleListeigenNimbleList definition
ExponentialThe Exponential Distribution
extractControlElementExtract named elements from MCMC sampler control list
flatThe Improper Uniform Distribution
getBoundGet value of bound of a stochastic node in a model
getBUGSexampleDirGet the directory path to one of the classic BUGS examples...
getConditionallyIndependentSetsGet a list of conditionally independent sets of nodes in a...
getDefinitionGet nimbleFunction definition
getNimbleOptionGet NIMBLE Option
getParamGet value of a parameter of a stochastic node in a model
getSamplesDPmeasureGet posterior samples for a Dirichlet process measure
getsizeReturns number of rows of modelValues
identityMatrixCreate an Identity matrix (Deprecated)
initializeModelPerforms initialization of nimble model node values and log...
IntervalInterval calculations
Inverse-GammaThe Inverse Gamma Distribution
Inverse-WishartThe Inverse Wishart Distribution
is.nfcheck if a nimbleFunction
is.nlcheck if a nimbleList
laplaceLaplace approximation
LKJThe LKJ Distribution for the Cholesky Factor of a Correlation...
makeBoundInfoMake an object of information about a model-bound pairing for...
makeModelDerivsInfoInformation on model structure used for derivatives
makeParamInfoMake an object of information about a model-parameter pairing...
MCMCconf-classClass 'MCMCconf'
MCMCsuitePlaceholder for MCMCsuite
modelBaseClass-classClass 'modelBaseClass'
modelDefClass-classClass for NIMBLE model definition
modelInitializationInformation on initial values in a NIMBLE model
model_macro_builderEXPERIMENTAL: Turn a function into a model macro builder A...
modelValuesCreate a NIMBLE modelValues Object
modelValuesBaseClass-classClass 'modelValuesBaseClass'
modelValuesConfCreate the confs for a custom NIMBLE modelValues object
MultinomialThe Multinomial Distribution
MultivariateNormalThe Multivariate Normal Distribution
Multivariate-tThe Multivariate t Distribution
nfMethodaccess (call) a member function of a nimbleFunction
nfVarAccess or set a member variable of a nimbleFunction
nimbleCodeTurn BUGS model code into an object for use in 'nimbleModel'...
nimbleExternalCallCreate a nimbleFunction that wraps a call to external...
nimbleFunctioncreate a nimbleFunction
nimbleFunctionBase-classClass 'nimbleFunctionBase'
nimbleFunctionList-classCreate a list of nimbleFunctions
nimbleFunctionVirtualcreate a virtual nimbleFunction, a base class for other...
nimble-internalFunctions and Classes Internal to NIMBLE
nimbleListcreate a nimbleList
nimble-mathMathematical functions for BUGS and nimbleFunction...
nimbleMCMCExecutes one or more chains of NIMBLE's default MCMC...
nimbleModelCreate a NIMBLE model from BUGS code
nimbleOptionsNIMBLE Options Settings
nimbleRcallMake an R function callable from compiled nimbleFunctions...
nimble-R-functionsNIMBLE language functions for R-like vector construction
nimbleType-classcreate a nimbleType object
nimCatcat function for use in nimbleFunctions
nimCopyCopying function for NIMBLE
nimDerivsNimble Derivatives
nimDimreturn sizes of an object whether it is a vector, matrix or...
nimEigenSpectral Decomposition of a Matrix
nimMatrixCreates matrix or array objects for use in nimbleFunctions
nimNumericCreates numeric, integer or logical vectors for use in...
nimOptimNimble wrapper around R's builtin 'optim'.
nimOptimDefaultControlCreates a deafult 'control' argument for 'nimOptim'.
nimPrintprint function for use in nimbleFunctions
nimStopHalt execution of a nimbleFunction function method. Part of...
nimSvdSingular Value Decomposition of a Matrix
nodeFunctionscalculate, calculateDiff, simulate, or get the current log...
optimControlNimbleListData type for the 'control' parameter of 'nimOptim'
optimDefaultControlCreates a deafult 'control' argument for 'optim' (just an...
optimResultNimbleListData type for the return value of 'nimOptim'
parameterTransformAutomated transformations of model nodes to unconstrained...
pow_intPower function for integer-valued exponent
printErrorsPrint error messages after failed compilation
rankSampleGenerates a weighted sample (with replacement) of ranks
readBUGSmodelCreate a NIMBLE BUGS model from a variety of input formats,...
registerDistributionsAdd user-supplied distributions for use in NIMBLE BUGS models
resizeResizes a modelValues object
Rmatrix2mvOneVarSet values of one variable of a modelValues object from an R...
RmodelBaseClass-classClass 'RmodelBaseClass'
runCrossValidatePerform k-fold cross-validation on a NIMBLE model fit by MCMC
runMCMCRun one or more chains of an MCMC algorithm and return...
run.timeTime execution of NIMBLE code
samplersMCMC Sampling Algorithms
setAndCalculateCreates a nimbleFunction for setting the values of one or...
setAndCalculateOneCreates a nimbleFunction for setting the value of a scalar...
setSizeset the size of a numeric variable in NIMBLE
setupMargNodesOrganize model nodes for marginalization
setupOutputsExplicitly declare objects created in setup code to be...
simNodesBasic nimbleFunctions for calculate, simulate, and getLogProb...
simNodesMVBasic nimbleFunctions for using a NIMBLE model with sets of...
singleVarAccessClass-classClass 'singleVarAccessClass'
StickBreakingFunctionThe Stick Breaking Function
summaryLaplaceSummarize results from Laplace approximation
svdNimbleListsvdNimbleList definition
tThe t Distribution
testBUGSmodelTests BUGS examples in the NIMBLE system
valueInCompiledNimbleFunctionget or set value of member data from a compiled...
valuesAccess or set values for a set of nodes in a model
waicUsing WAIC
waicDetailsNimbleListwaicDetailsNimbleList definition
waicNimbleListwaicNimbleList definition
WishartThe Wishart Distribution
withNimbleOptionsTemporarily set some NIMBLE options.
nimble documentation built on July 9, 2023, 5:24 p.m.