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

ADNimbleListEXPERIMENTAL Data type for the return value of 'nimDerivs'
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...
buildAuxiliaryFilterCreate an auxiliary particle filter algorithm to estimate...
buildBootstrapFilterCreate a bootstrap particle filter algorithm to estimate...
buildEnsembleKFCreate an Ensemble Kalman filter algorithm to sample from...
buildLiuWestFilterCreate a Liu and West particle filter algorithm.
buildMCEMBuilds an MCEM algorithm from a given NIMBLE model
buildMCMCCreate an MCMC function, from an MCMCconf object
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...
CmodelBaseClass-classClass 'CmodelBaseClass'
CnimbleFunctionBase-classClass 'CnimbleFunctionBase'
codeBlockClass-classClass 'codeBlockClass'
combine_MCMC_comparison_resultsCombine multiple objects returned by compareMCMCs
compareMCMCsRun multiple MCMCs (packages or NIMBLE cases) for multiple...
compileNimblecompile NIMBLE models and nimbleFunctions
configureMCMCBuild the MCMCconf object for construction of an MCMC object
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
eigenNimbleListeigenNimbleList definition
ExponentialThe Exponential Distribution
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...
getDefinitionGet nimbleFunction definition
getLoadingNamespacereturn the namespace in which a nimbleFunction is being...
getNimbleOptionGet NIMBLE Option
getParamGet value of a parameter of a stochastic node in a model
getsizeReturns number of rows of modelValues
identityMatrixCreate an Identity matrix
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
makeBoundInfoMake an object of information about a model-bound pairing for...
make_MCMC_comparison_pagesMake html pages summarizing results from compareMCMCs
makeParamInfoMake an object of information about a model-parameter pairing...
MCMCconf-classClass 'MCMCconf'
MCMCsuiteExecutes multiple MCMC algorithms and organizes results.
MCMCsuiteClass-classClass 'MCMCsuiteClass'
modelBaseClass-classClass 'modelBaseClass'
modelDefClass-classClass for NIMBLE model definition
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
ModifiedRmmParseKeywords2[[' = 'outputCppArrayIndex2',
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
nimblenimble
nimbleCodeTurn BUGS model code into an object for use in 'nimbleModel'...
nimbleExternalCallEXPERIMENTAL Create a nimbleFunction that wraps a call to...
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
nimbleRcallEXPERIMENTAL Make an R function callable from compiled...
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...
optimControlNimbleListEXPERIMENTAL Data type for the 'control' parameter of...
optimDefaultControlCreates a deafult 'control' argument for 'optim' (just an...
optimResultNimbleListEXPERIMENTAL Data type for the return value of 'nimOptim'
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
rename_MCMC_comparison_methodRename a method in an object returned by compareMCMCs
reshape_comparison_resultsConvert comparison results to a more general format
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
samplerAssignmentRules-classClass 'samplerAssignmentRules'
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
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'
svdNimbleListsvdNimbleList definition
tThe t Distribution
testBUGSmodelTests BUGS examples in the NIMBLE system
updateMCMCcomparisonWithHighOrderESSRe-estimate effective sample size from results of...
valueInCompiledNimbleFunctionget or set value of member data from a compiled...
valuesAccess or set values for a set of nodes in a model
WishartThe Wishart Distribution
withNimbleOptionsTemporarily set some NIMBLE options.
nimble documentation built on Nov. 22, 2017, 5:06 p.m.