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...
buildAGHQGridBuild Adaptive Gauss-Hermite Quadrature Grid
buildAuxiliaryFilterPlaceholder for buildAuxiliaryFilter
buildBootstrapFilterPlaceholder for buildBootstrapFilter
buildEnsembleKFPlaceholder for buildEnsembleKF
buildIteratedFilter2Placeholder for buildIteratedFilter2
buildLiuWestFilterPlaceholder for buildLiuWestFilter
buildMCEMBuilds an MCEM algorithm for 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'
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
getMacroParametersEXPERIMENTAL: Get list of parameter names generated by model...
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 and adaptive Gauss-Hermite quadrature
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'
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
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
nimble-packagenimble: MCMC, Particle Filtering, and Programmable...
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
nimIntegrateIntegration of One-Dimensional Functions
nimMatrixCreates matrix or array objects for use in nimbleFunctions
nimNumericCreates numeric, integer or logical vectors for use in...
nimOptimGeneral-purpose Optimization
nimOptimDefaultControlCreates a default 'control' argument for 'nimOptim'.
nimOptimMethodSet or get an optimization function to be used by '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
runLaplaceCombine steps of running Laplace or adaptive Gauss-Hermite...
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 or adaptive Gauss-Hermite...
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 Sept. 11, 2024, 7:10 p.m.