nimble: Flexible BUGS-Compatible System for Hierarchical Statistical Modeling and Algorithm Development
Version 0.6-4

Flexible application of algorithms to models specified in the BUGS language. Algorithms can be written in the NIMBLE language and made available to any model.

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AuthorPerry de Valpine, Christopher Paciorek, Daniel Turek, Cliff Anderson- Bergman, Duncan Temple Lang
Date of publication2017-04-25 14:33:04 UTC
MaintainerChristopher Paciorek <paciorek@stat.berkeley.edu>
LicenseBSD_3_clause + file LICENSE
Version0.6-4
URL http://r-nimble.org
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("nimble")

Man pages

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...
buildAuxiliaryFilter: Create an auxiliary particle filter algorithm to estimate...
buildBootstrapFilter: Create a bootstrap particle filter algorithm to estimate...
buildEnsembleKF: Create an Ensemble Kalman filter algorithm to sample from...
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
Categorical: The Categorical Distribution
checkInterrupt: Check for interrupt (e.g. Ctrl-C) during nimbleFunction...
CmodelBaseClass-class: Class 'CmodelBaseClass'
CnimbleFunctionBase-class: Class 'CnimbleFunctionBase'
codeBlockClass-class: Class 'codeBlockClass'
combine_MCMC_comparison_results: Combine multiple objects returned by compareMCMCs
compareMCMCs: Run multiple MCMCs (packages or NIMBLE cases) for multiple...
compileNimble: compile NIMBLE models and nimbleFunctions
configureMCMC: Build the MCMCconf object for construction of an MCMC object
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
eigenNimbleList: eigenNimbleList definition
Exponential: The Exponential 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...
getDefinition: Get nimbleFunction definition
getLoadingNamespace: return the namespace in which a nimbleFunction is being...
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...
Interval: Interval calculations
Inverse-Gamma: The Inverse Gamma Distribution
is.nf: check if a nimbleFunction
is.nl: check if a nimbleList
makeBoundInfo: Make an object of information about a model-bound pairing for...
make_MCMC_comparison_pages: Make html pages summarizing results from compareMCMCs
makeParamInfo: Make an object of information about a model-parameter pairing...
MCMCconf-class: Class 'MCMCconf'
MCMCsuite: Executes multiple MCMC algorithms and organizes results.
MCMCsuiteClass-class: Class 'MCMCsuiteClass'
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
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'...
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...
nimbleModel: Create a NIMBLE model from BUGS code
nimbleOptions: NIMBLE Options Settings
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
nimDim: return sizes of an object whether it is a vector, matrix or...
nimEigen: Spectral Decomposition of a Matrix
nimMatrix: Creates matrix or array objects for use in nimbleFunctions
nimNumeric: Creates numeric, integer or logical vectors for use in...
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...
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
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
Rmatrix2mvOneVar: Set values of one variable of a modelValues object from an R...
RmodelBaseClass-class: Class 'RmodelBaseClass'
runMCMC: Run one or more chains of an MCMC algorithm and extract...
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
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'
svdNimbleList: svdNimbleList definition
t: The t Distribution
testBUGSmodel: Tests BUGS examples in the NIMBLE system
updateMCMCcomparisonWithHighOrderESS: Re-estimate effective sample size from results of...
valueInCompiledNimbleFunction: get or set value of member data from a compiled...
values: Access or set values for a set of nodes in a model
Wishart: The Wishart Distribution

Functions

AF_slice Man page
BUGScontextClass-Class Man page
BUGSdeclClass Man page
BUGSdeclClass-class Man page
BUGSdistToRdist Source code
BUGSmodel Source code
BUGSsingleContextClass-Class Man page
Categorical Man page
Cmatrix2mvOneVar Source code
CmodelBaseClass Man page
CmodelBaseClass-class Man page
CmultiNimbleFunctionClass-Class Man page
CmultiNimbleListClass-Class Man page
CmultiNimbleObjClass-Class Man page
CnimbleFunctionBase Man page
CnimbleFunctionBase-class Man page
Constraint Man page
Dirichlet Man page
EigenNewExpr Source code
Exponential Man page
Interval Man page
Inverse-Gamma Man page
MCMCconf Man page
MCMCconf-class Man page
MCMCefficiencyHO Source code
MCMCefficiencyHOlist Source code
MCMCsuite Man page Source code
MCMCsuiteClass Man page
MCMCsuiteClass-class Man page
MakeCustomModelClass Source code
MakeCustomModelClass-Class Man page
Multinomial Man page
Multivariate-t Man page
MultivariateNormal Man page
RCfunInfoClass-Class Man page
RCfunction Source code
RCfunctionCompileClass-Class Man page
RMakeCustomModelClass Source code
RMakeCustomModelClass-Class Man page
RW Man page
RW_PF Man page
RW_PF_block Man page
RW_block Man page
RW_llFunction Man page
RW_llFunction_block Man page
RW_multinomial Man page
Rmatrix2mvOneVar Man page Source code
RmodelBaseClass Man page
RmodelBaseClass-class Man page
Rname2CppName Source code
RparseTree2ExprClasses Source code
Wishart Man page
[,CmodelValues-method Man page
[,CmodelValues-method,ANY,ANY Man page
[,CmodelValues-method,character,missing Man page
[,CmodelValues-method,character,missing,ANY-method Man page
[,distributionsClass-method Man page
[,modelValuesBaseClass-method Man page
[,numberedModelValuesAccessors-method Man page
[,numberedObjects-method Man page
[<-,CmodelValues-method Man page
[<-,modelValuesBaseClass-method Man page
[<-,numberedModelValuesAccessors-method Man page
[<-,numberedObjects-method Man page
[[,CNumericList-method Man page
[[,CmodelValues-method Man page
[[,RNumericList-method Man page
[[,conjugacyRelationshipsClass-method Man page
[[,distributionsClass-method Man page
[[,modelBaseClass-method Man page
[[,nimPointerList-method Man page
[[<-,CNumericList-method Man page
[[<-,CmodelValues-method Man page
[[<-,RNumericList-method Man page
[[<-,modelBaseClass-method Man page
[[<-,nimPointerList-method Man page
[[<-,nimbleFunctionList-method Man page
addArg Source code
addBlockFromCppName Source code
addDIB Source code
addDistList2matchFunctions Source code
addIndentToList Source code
addMissingIndexingRecurse Source code
addModelDollarSign Source code
addMonitors Man page
addMonitors2 Man page
addNecessaryIndexingToNewNode Source code
addNecessarySetupCode Source code
addNewCode Source code
addSampler Man page
addSamplerToConf Source code
addSetupCodeNames Source code
addToTypeEnv Source code
addTransposeIfNeededForNonSeqBlock Source code
allParamEfficiencyComparisonComponent Source code
anyNonScalar Source code
areMVSymTabsEqual Source code
argInfo2PointerStaticCast Source code
argType2symbol Source code
argType2symbolInternal Source code
argTypeList2symbolTable Source code
arithmeticOutputType Source code
array Man page
as.matrix.CmodelValues Source code
as.matrix.modelValuesBaseClass Source code
as.matrix.modelValuesBaseClass-Class Man page
asCol Man page Source code
asRow Man page Source code
assignLogProbName Source code
assignNumberedObject Source code
assignmentTypeWarn Source code
autoBlock Man page Source code
autoBlockClass-Class Man page
autoBlockParamDefaults Source code
blockIndexInfo Source code
buildAuxiliaryFilter Man page
buildBootstrapFilter Man page
buildCopyLineFromSEXP Source code
buildCopyLineToSEXP Source code
buildEnsembleKF Man page
buildIntermNone Source code
buildLiuWestFilter Man page
buildMCEM Man page Source code
buildMCMC Man page
buildModelInterface Source code
buildNeededObjects Source code
buildNimbleListInterface Source code
buildNimbleObjInterface Source code
buildSimpleIntermCall Source code
buildSymbolTable Source code
c Man page
cGetNRow Source code
calcNodes Man page
calcNodesMV Man page
calc_dmnormAltParams Man page
calc_dmnormConjugacyContributions Man page
calculate Man page Source code
calculateDiff Man page Source code
callToPackVPtrs Source code
cat Man page
cc_checkLinearity Source code
cc_combineExprsAddition Source code
cc_combineExprsDivision Source code
cc_combineExprsMultiplication Source code
cc_combineExprsSubtraction Source code
cc_createStructureExpr Source code
cc_expandDetermNodesInExpr Source code
cc_getNodesInExpr Source code
cc_linkCheck Source code
cc_makeConjugateSamplerName Source code
cc_makeRDistributionName Source code
cc_makeSamplerTypeName Source code
cc_negateExpr Source code
cc_nodeInExpr Source code
cc_otherParamsCheck Source code
cc_vectorizedComponentCheck Source code
character2index Source code
checkConjugacy Man page
checkDistributionFunctions Source code
checkDistributionInput Source code
checkForDeterministicDorR Source code
checkForDuplicateNodeDeclaration Source code
checkInterrupt Man page Source code
checkNimbleFunctionListCpp Source code
checkNimbleOrRfunctionNames Source code
checkUserDefinedDistribution Source code
cleanWhite Source code
clearCompiled Source code
clearNeededObjects Source code
cloglog Man page Source code
code2Name_fromArgList Source code
codeBlockClass Man page
codeBlockClass-class Man page
codeProcessIfThenElse Source code
codeSubstitute Source code
collectEdges Source code
collectInferredVertexEdges Source code
combineIndices2Flat Source code
combine_MCMC_comparison_results Man page Source code
compareConjugacyLists Source code
compareMCMCs Man page Source code
compileBUGSmodel Source code
compileNimble Man page Source code
compileNimbleFunction Source code
compileRCfunction Source code
configureMCMC Man page Source code
conjugacyClass-Class Man page
conjugacyRelationshipsClass-Class Man page
copierVector Source code
copy Man page
copyFromRobject Source code
copyFromRobjectViaActiveBindings Source code
countDllObjects Source code
cppBUGSmodelClass-Class Man page
cppCPPfileClass-Class Man page
cppCodeFileClass-Class Man page
cppDouble Source code
cppEigenMap Source code
cppHfileClass-Class Man page
cppInt Source code
cppLiteral Source code
cppMinusOne Source code
cppModelValuesAccessorVector Source code
cppModelValuesClass-Class Man page
cppModelValuesMapAccessorVector Source code
cppModelVariableAccessorVector Source code
cppModelVariableMapAccessorVector Source code
cppNamedObjectsClass-Class Man page
cppNewNimbleList Source code
cppNimArr Source code
cppNimArrPtr Source code
cppNimbleClassClass-Class Man page
cppNimbleFunctionClass-Class Man page
cppNimbleListClass-Class Man page
cppNimbleListReturningOperator Source code
cppNodeFunctionVector Source code Source code
cppOptimObject Source code
cppOutputBinaryOrUnary Source code
cppOutputBlank Source code
cppOutputBracket Source code
cppOutputCall Source code
cppOutputCallAsIs Source code
cppOutputCallWithName Source code
cppOutputCast Source code
cppOutputChainedCall Source code
cppOutputColon Source code
cppOutputCout Source code
cppOutputCoutNoNewline Source code
cppOutputDereference Source code
cppOutputDoubleBracket Source code
cppOutputEigBlank Source code
cppOutputEigExternalUnaryFunction Source code
cppOutputEigMemberFunction Source code
cppOutputEigMemberFunctionNoTranslate Source code
cppOutputEigenCast Source code
cppOutputEigenMapAssign Source code
cppOutputFor Source code
cppOutputGetBound Source code
cppOutputGetNodeFunctionIndexedInfo Source code
cppOutputGetParam Source code
cppOutputIfWhile Source code
cppOutputLiteral Source code
cppOutputMakeFixedVector Source code
cppOutputMemberFunction Source code
cppOutputMemberFunctionDeref Source code
cppOutputMemberFunctionGeneric Source code
cppOutputMidOperator Source code
cppOutputNFmethod Source code
cppOutputNFvar Source code
cppOutputNimFunListAccess Source code
cppOutputNimSwitch Source code
cppOutputNonNativeEigen Source code
cppOutputNumList Source code
cppOutputParen Source code
cppOutputPointerDereference Source code
cppOutputPow Source code
cppOutputPtrType Source code
cppOutputReturn Source code
cppOutputSize Source code
cppOutputTemplate Source code
cppOutputVoidPtr Source code
cppProjectClass-Class Man page
cppSEXP Source code
cppStrideType Source code
cppVecNimArr Source code
cppVecNimArrPtr Source code
cppVecVoidPtr Source code
cppVirtualNimbleFunctionClass-Class Man page
cppVoid Source code
createDFfromABlist Source code
createDefault_isDataObj Source code
createDynamicConjugateSamplerName Source code
createNamedObjectsFromList Source code
crossLevel Man page
cube Man page Source code
dcat Man page Source code
dconstraint Man page Source code
ddirch Man page Source code
decide Man page Source code
decideAndJump Man page
declare Man page Source code
declareHandler Source code
deparse Source code
dependentClass-Class Man page
deregisterDistributions Man page Source code
determineContextSize Source code
determineNdimFromOneCase Source code
determineNdimsFromNfproc Source code
determineNodeIndexSizes Source code
dexp_nimble Man page Source code
diag Man page
dim Man page
dimOrLength Source code
dinterval Man page Source code
dinvgamma Man page Source code
dirichlet Man page
distClass-Class Man page
distributionInfo Man page
distributionsClass-Class Man page
dmFunHandler Source code
dmnorm_chol Man page Source code
dmulti Man page Source code
dmvt_chol Man page Source code
dropSingleSizes Source code
dt_nonstandard Man page Source code
dwish_chol Man page Source code
dynamicConjugateSamplerAdd Source code
dynamicConjugateSamplerExists Source code
dynamicConjugateSamplerGet Source code
dynamicConjugateSamplerWrite Source code
effectiveSizeHO Source code
effectiveSizeStan Source code
efficiencyDetailsComparisonComponent Source code
eigen Man page
eigenCast Source code
eigenNimbleList Man page
eigenizeArrayize Source code
eigenizeMatricize Source code
eigenizeName Source code
eigenizeNameStrided Source code
eigenize_alwaysMatrix Source code
eigenize_asRowOrCol Source code
eigenize_assign_before_recurse Source code
eigenize_cWiseAddSub Source code
eigenize_cWiseBinaryArray Source code
eigenize_cWiseBinaryArrayLogical Source code
eigenize_cWiseBinaryEitherMatch Source code
eigenize_cWiseBinaryMatrix Source code
eigenize_cWiseByScalarArray Source code
eigenize_cWiseMultDiv Source code
eigenize_cWiseUnaryArray Source code
eigenize_cWiseUnaryEither Source code
eigenize_cWiseUnaryMatrix Source code
eigenize_chainedCall Source code
eigenize_coeffSetter Source code
eigenize_doNotRecurse Source code
eigenize_eigenBlock Source code
eigenize_matrixOps Source code
eigenize_nfVar Source code
eigenize_nimbleNullaryClass Source code
eigenize_nimbleNullaryClass-Class Man page
eigenize_nonSeq Source code
eigenize_recyclingRuleFunction Source code
eigenize_reductionArray Source code
eigenize_reductionBinaryEither Source code
eigenize_reductionEither Source code
embedInRbracket Source code
embedListInRbracket Source code
emptyTypeInfo Source code
evalBracketArgs Source code
evalBracketArgsKnownBracket Source code
evalInDistsMatchCallEnv Source code
example_fillInMissingIndices Source code
example_getMissingDimensions Source code
existsFunctionEnvVar Source code
expandContextAndReplacements Source code
expandIndexSet4sapply Source code
expandMVNames Source code
expit Man page Source code
exprAsListDrop2 Source code
exprClass-Class Man page
exprClassProcessingErrorMsg Source code
exprClasses_addDebugMarks Source code
exprClasses_buildInterms Source code
exprClasses_eigenize Source code
exprClasses_initSizes Source code
exprClasses_insertAssertions Source code
exprClasses_labelForEigenization Source code
exprClasses_liftMaps Source code
exprClasses_processSpecificCalls Source code
exprClasses_setSizes Source code
exprName2Cpp Source code
exprTypeInfoClass-Class Man page
extractAnyVectorizedIndexExprs Source code
extractFlatIndices_wVarInfo Source code
funName2OptimFunName Source code
gd_allNeighbors Source code
gd_getDependencies_IDs Source code
genIndexVarValues_recurse Source code
genLocalMakevars Source code
genLogProbNodeExprAndReplacements Source code
genName2 Source code
genReplacementsAndCodeRecurse Source code
generalFunSizeHandler Source code
generateAll Source code
generateClassHeader Source code
generateConditionalLines Source code
generateFunctionHeader Source code
generateObjectDefs Source code
getAdditonalArgsListForOptim Source code
getAllDistributionsInfo Source code
getArgInfoFromNFSym Source code
getArgsFromOptimCallForTargetFun Source code
getArgumentType Source code
getBUGSexampleDir Man page Source code
getBoolValue Source code
getBound Man page Source code
getCallText Source code
getCharacterValue Source code
getCharacterVectorValue Source code
getDefinition Man page Source code
getDependencies Man page
getDependencyPaths Source code
getDimension Man page Source code
getDistribution Man page
getDistributionInfo Man page Source code
getDistributionList Source code
getDoubleValue Source code
getFunctionEnvVar Source code
getIntValue Source code
getLoadingNamespace Man page Source code
getLogProb Man page Source code
getLogProbNodes Man page
getLogProbNodesMV Man page
getMVName Source code
getMVptr Source code
getMaxDim Source code
getModelValuesConf Source code
getMonitors Man page
getMonitors2 Man page
getNamedObjected Source code
getNimValues Source code
getNimbleFunctionEnvironment Source code
getNimbleOption Man page Source code
getNimbleProject Man page Source code
getNimbleTypes Source code
getNodeFunctionIndexedInfo Man page Source code
getNodeNames Man page
getNumberedObject Source code
getParam Man page Source code
getParamID Source code
getParamNames Man page Source code
getSamplers Man page
getSetCharacterScalar Source code
getSetCharacterVector Source code
getSetDoubleScalar Source code
getSetIntegerScalar Source code
getSetLogicalScalar Source code
getSetModelValues Source code
getSetModelValuesPtr Source code
getSetModelVarPtr Source code
getSetNimPtrList Source code
getSetNimbleFunction Source code
getSetNimbleList Source code
getSetNumericVector Source code
getSize_NumberedObjects Source code
getSymObj_recurse Source code
getSymbolicParentNodes Source code
getSymbolicParentNodesRecurse Source code
getType Man page Source code
getValueDim Source code
getValues Source code
getValuesAccess Source code
getVarAndIndices Source code
getVarNames Man page
getsize Man page Source code
handleScaleAndRateForExpNimble Source code
handleScaleAndRateForGamma Source code
hasBracket Source code
icloglog Man page Source code
identityAssert Source code
identityMatrix Man page
ilogit Man page Source code
indexedNodeInfoTableClass Source code
indexedNodeInfoTableClass-Class Man page
initializeModel Man page
inner_populateNodeFxnVec Source code
inprod Man page Source code
insertEigenTranspose Source code
insertExprClassLayer Source code
insertIndexingBracket Source code
insertSingleIndexBrackets Source code
insertSubIndexExpr Source code
integer Man page
inverse Man page Source code
iprobit Man page Source code
is.Cnf Source code
is.blank Source code
is.indexed Source code
is.na.vec Source code
is.nan.vec Source code
is.nf Man page Source code
is.nfGenerator Source code
is.nl Man page Source code
is.nlGenerator Source code
is.rcf Source code
is.vectorized Source code
isBinary Man page
isCodeArgBlank Source code
isCodeScalar Source code
isData Man page
isDeterm Man page
isDiscrete Man page Source code
isEigScalar Source code
isEndNode Man page
isExprLiftable Source code
isIntegerEquivalent Source code
isModelValuesConf Source code
isNameInExpr Source code
isNameInExprList Source code
isRbracket Source code
isSetupCodeGenerated Source code
isStoch Man page
isSymbolType Source code
isTruncated Man page
isUnivariate Man page
isUserDefined Man page Source code
isValid Source code
keywordInfoClass-Class Man page
labelFunctionCreator Source code
length Man page
length.nimPointerList Source code
logdet Man page Source code
logfact Man page Source code
loggam Man page Source code
logical Man page
logit Man page Source code
makeBUGSactiveBindingDef Source code
makeBUGSclassFields Source code
makeBoundInfo Man page Source code
makeCallList Source code
makeCppNIMBLEfunction Source code
makeCustomModelValuesClass Source code
makeCustomModelValuesClass-Class Man page
makeDSLCallforVoidPtr_fromArgInfAndCall Source code
makeDeclareSizeField Source code
makeDefaultDirName Source code
makeEigenArgsMatch Source code
makeEigenBlockExprFromBrackets Source code
makeEigenName Source code
makeEigenTypeLabel Source code
makeEnvName Source code
makeFillValue Source code
makeFixedParameterCallCodeForOptim Source code
makeGetCodeFromAccessorVector Source code
makeIndexNamePieces Source code
makeIndexedVariable Source code
makeLogProbEnvName Source code
makeLogProbName Source code
makeMV_GID_Map Source code
makeMapAccessExpr Source code
makeMapExprFromBrackets Source code
makeMapInfoFromAccessorVector Source code
makeMapInfoFromAccessorVectorFaster Source code
makeMapSetupCodeNames Source code
makeModelBindingFields Source code
makeModelCppCopyTypes Source code
makeModelValuesClassFields Source code
makeNFBindingFields Source code
makeNameName Source code
makeNewConfFromOldConf Source code
makeNewNimListSEXPRESSIONFromC Source code
makeNewParsCharCopyLine Source code
makeNimbleFxnCppCopyTypes Source code
makeNimbleFxnInterfaceCallMethodCode Source code
makeNimbleListBindingFields Source code
makeOffsetRexpr Source code
makeOptimFunctionCallLine Source code
makeParamInfo Man page Source code
makeReturnVector Source code
makeRowName Source code
makeSetCodeFromAccessorVector Source code
makeSingleIndexAccessCodeNames Source code
makeSingleIndexAccessExpr Source code
makeSizeExpressions Source code
makeSpaces Source code
makeStaticCastingChunk Source code
makeStrideRexprs Source code
makeVecName Source code
makeVertexNamesFromIndexArray Source code
makeVertexNamesFromIndexArray2 Source code
makeVoidPointerName_fromObjName Source code
make_MCMC_comparison_pages Man page Source code
make_example_html Source code
make_main Source code
makefnScaleLine Source code
mapsClass-Class Man page
matchAndFill.call Source code
matchKeywordCode Source code
matchKeywordCodeMemberFun Source code
matchKeywords_recurse Source code
matrix Man page
matrix2mv Source code
mcmc_findControlListNamesInCode Source code
mcmc_generateControlListArgument Source code
mcmc_listContentsToStr Source code
mergeMultiLineStatements Source code
minMaxHandler Source code
minMeanAllComparisonComponent Source code
minMeanComparisonComponent Source code
modelBaseClass Man page
modelBaseClass-class Man page
modelDefClass Man page
modelDefClass-class Man page
modelDefInfoClass-Class Man page
modelValues Man page Source code
modelValuesAccessorVector Source code
modelValuesBaseClass Man page
modelValuesBaseClass-class Man page
modelValuesConf Man page Source code
modelValuesElement2Matrix Source code
modelVariableAccessorVector Source code
multiMaxSizeExprs Source code
multinomial Man page
multivariate-t Man page
mvAccessHandler Source code
mvInfoClass-Class Man page
mvt Man page
ndf_addModelDollarSignsToMethods Source code
ndf_createContains Source code
ndf_createMethodList Source code
ndf_createSetupFunction Source code
ndf_createSingleMethod Source code
ndf_createStochCalculate Source code
ndf_createStochCalculateTrunc Source code
ndf_createStochSimulate Source code
ndf_createStochSimulateTrunc Source code
ndf_createVirtualNodeFunctionDefinition Source code
ndf_createVirtualNodeFunctionDefinitionsList Source code
ndf_generateGetParamFunction Source code
ndf_generateGetParamSwitchFunction Source code
newAssignmentExpression Source code
newBracketExpr Source code
newModel Man page
newNumberedObjects Source code
newObjElementPtr Source code
newSpacesFunction Source code
nfBuildCInterface Source code
nfCompilationInfoClass-Class Man page
nfGetDefVar Source code
nfMethod Man page Source code
nfMethodErrorHandler Source code
nfVar Man page Source code
nfVar<- Man page
nfWriteCompileAndLoadSO Source code
nf_assignmentLHSvars Source code
nf_changeNimKeywords Source code
nf_changeNimKeywordsOne Source code
nf_checkDSLcode Source code
nf_createAList Source code
nf_createAllNamesFromMethodList Source code
nf_createGeneratorFunctionArgs Source code
nf_createGeneratorFunctionDef Source code
nf_createRefClassDef Source code
nf_createRefClassDef_fields Source code
nf_createSetupOutputNames Source code
nf_getArgOutputNames Source code
nf_getGeneratorFunction Source code
nf_getInstances Source code
nf_getMethodList Source code
nf_getNamesFromSetupOutputDeclaration Source code
nf_getRefClassObject Source code
nf_getReturnTypeOutputNames Source code
nf_getSetupOutputNames Source code
nf_getVarFromAssignmentLHScode Source code
nf_namesNotHidden Source code
nf_preProcessMemberDataObject Source code
nf_processSetupFunctionBody Source code
nf_substituteExceptFunctionsAndDollarSigns Source code
nimArrMapExpr Source code
nimArray Man page Source code
nimArrayGeneralHandler Source code
nimC Man page Source code
nimCat Man page Source code
nimCopy Man page Source code
nimDeparse Source code
nimDim Man page Source code
nimEigen Man page Source code
nimEquals Man page Source code
nimGenerateCpp Source code
nimInteger Man page Source code
nimLogical Man page Source code
nimMatrix Man page Source code
nimNumeric Man page Source code
nimPrint Man page Source code
nimRep Man page Source code
nimRound Man page
nimSeq Man page Source code
nimStep Man page Source code
nimStop Man page Source code
nimSvd Man page Source code
nimSwitch Man page Source code
nimble-R-functions Man page
nimbleCode Man page Source code
nimbleFinalize Source code
nimbleFunction Man page Source code
nimbleFunctionBase Man page
nimbleFunctionBase-class Man page
nimbleFunctionList Man page
nimbleFunctionList-class Man page
nimbleFunctionVirtual Man page Source code
nimbleGeneralParseDeparse Source code
nimbleGraphClass-Class Man page
nimbleIncludeFile Source code
nimbleInternalFunctions Man page
nimbleList Man page Source code
nimbleListDefClass-Class Man page
nimbleModel Man page Source code
nimbleOptions Man page Source code
nimbleProjectClass-Class Man page
nimbleType Man page
nimbleType-class Man page
nimbleUserNamespace Man page
nl.getDefinitionContent Source code
nl.getGenerator Source code
nl.getListDef Source code
nl.getNestedGens Source code
nlCompilationInfoClass-Class Man page
nl_addIndicesToVariables Source code
nl_aggregateConsecutiveBlocks Source code
nl_checkNodeNamesInModel Source code
nl_checkVarNamesInModel Source code
nl_createVarsAndFlatIndexRanges Source code
nl_determineFlatIndex Source code
nl_expandNodeIndex Source code
nl_expandNodeIndexExpr Source code
nl_expandNodeNames Source code
nl_getVarNameFromNodeName Source code
nl_nodeVectorReadyNodes Source code
nl_removeNodeNamesNotInSymbolTable Source code
nl_vectorizedExpandNodeIndex Source code
nl_vectorizedExpandNodeIndexExprs Source code
nm_seq_noDecrease Source code
nndf_addModelDollarSignsToMethods Source code
nndf_createMethodList Source code
nndf_createSetupFunction Source code
nndf_generateGetBoundSwitchFunction Source code
nndf_generateGetParamSwitchFunction Source code
nndf_makeNodeFunctionIndexAccessCall Source code
nndf_makeNodeFunctionIndexLabels Source code
nndf_replaceSetupOutputsWithIndexedNodeInfo Source code
nodeFunction Source code
nodeFunctionNew Source code
nodeFunctions Man page
numeric Man page
outputCppArrayIndex2 Source code
outputCppBinaryOperation2 Source code
outputCppCommentBlock2 Source code
outputCppCout2 Source code
outputCppDereference2 Source code
outputCppExit2 Source code
outputCppFor2 Source code
outputCppIfElse2 Source code
outputCppLiteral Source code
outputCppOpenBracket2 Source code
outputCppOpenBracketInvisible Source code
outputCppOpenParentheses2 Source code
outputCppParseTree2 Source code
outputCppReference2 Source code
outputCppScopeResolution2 Source code
outputCppTempArray2 Source code
outputCppWhile2 Source code
outputEigenOperation2 Source code
outputGeneralCppFunction2 Source code
outputTypeCast2 Source code
parseEvalCharacter Source code
parseEvalCharacterMany Source code
parseEvalNumeric Source code
parseEvalNumericMany Source code
parseEvalNumericManyFindErrors Source code
parseEvalNumericManyHandleError Source code
parseEvalNumericManyList Source code
parseTreeSubstitute Source code
pasteSemicolon Source code
pexp_nimble Man page Source code
phi Man page Source code
pinvgamma Man page Source code
plotABS Source code
plotMinMeanAll Source code
pointAt Source code
populateCopierVector Source code
populateIndexedNodeInfoTable Source code
populateManyModelValuesMapAccess Source code
populateManyModelVarMapAccess Source code
populateNodeFxnVec Source code
populateNodeFxnVecNew Source code
posteriorClass-Class Man page
posteriorSummaryComparisonComponent Source code
posterior_predictive Man page
pow Man page Source code
pqDefined Man page Source code
prepareDistributionInput Source code
print Man page
printMinTimeABS Source code
printMonitors Man page
printSamplers Man page
probit Man page Source code
processDistributionAliases Source code
processKeyword Source code
processKeywordCodeMemberFun Source code
processKeywords_recurse Source code
processModelFile Source code
processMonitorNames Source code
processNonParseableCode Source code
processVarBlock Source code
productSizeExprs Source code
promoteArgTypes Source code
promoteTypes Source code
pt_nonstandard Man page Source code
putCodeLinesInBrackets Source code
qexp_nimble Man page Source code
qinvgamma Man page Source code
qt_nonstandard Man page Source code
rCalcDiffNodes Source code
rCalcNodes Source code
rFunHandler Source code
rGetLogProbsNodes Source code
rSimNodes Source code
rankSample Man page Source code
rcat Man page Source code
rconstraint Man page Source code
rdirch Man page Source code
readBUGSmodel Man page Source code
recurseGetListST Source code
recurseSetSizes Source code
reduceDF Source code
registerDistributions Man page Source code
removeColonOperator Source code
removeExprClassLayer Source code
removeIndexing Source code
removeLayerHandler Source code
removeLogProbName Source code
removeNonScalarElementsFromList Source code
removeSamplers Man page
rename_MCMC_comparison_method Man page Source code
rep Man page
replaceAllCodeSuccessfully Source code
replaceConstantsRecurse Source code
replaceDistributionAliases Source code
replaceDistributionAliasesNameOnly Source code
replaceWhatWeCan Source code
replacementHandler Source code
reprioritizeColonOperator Source code
resetData Man page
resetMonitors Man page
reshape_comparison_results Man page Source code
resize Man page Source code
resize_NumberedObjects Source code
rexp_nimble Man page Source code
rinterval Man page Source code
rinvgamma Man page Source code
rmFunHandler Source code
rmnorm_chol Man page Source code
rmulti Man page Source code
rmvt_chol Man page Source code
rt_nonstandard Man page Source code
run.time Man page Source code
runMCMC Man page Source code
rwish_chol Man page Source code
sameDir Source code
sampler Man page
sampler_AF_slice Man page
sampler_BASE Man page
sampler_RW Man page
sampler_RW_PF Man page
sampler_RW_PF_block Man page
sampler_RW_block Man page
sampler_RW_dirichlet Man page
sampler_RW_llFunction Man page
sampler_RW_llFunction_block Man page
sampler_RW_multinomial Man page
sampler_binary Man page
sampler_crossLevel Man page
sampler_ess Man page
sampler_posterior_predictive Man page
sampler_slice Man page
samplers Man page
seq Man page
seqAlongHandler Source code
setAndCalculate Man page
setAndCalculateDiff Man page
setAndCalculateOne Man page
setArg Source code
setAsRowOrCol Source code
setBoolValue Source code
setCaller Source code
setCharacterValue Source code
setCharacterVectorValue Source code
setData Man page
setDoublePtrFromSinglePtr Source code
setDoubleValue Source code
setInits Man page
setIntValue Source code
setNimValues Source code
setNimbleOption Source code
setOnePtrVectorOfPtrs Source code
setPtrVectorOfPtrs Source code
setReturnType Source code
setSamplers Man page
setSize Man page Source code
setSmartPtrFromDoublePtr Source code
setSmartPtrFromSinglePtr Source code
setThin Man page
setThin2 Man page
setValues Source code
setValuesAccess Source code
setupCodeTemplateClass-Class Man page
setupOutputs Man page Source code
simNodes Man page
simNodesMV Man page
simulate Man page Source code
singleModelValuesAccess Man page Source code
singleModelValuesAccessClass-Class Man page
singleVarAccess Source code
singleVarAccessClass Man page
singleVarAccessClass-class Man page
sizeAsRowOrCol Source code
sizeAssign Source code
sizeAssignAfterRecursing Source code
sizeBinaryCwise Source code
sizeBinaryCwiseLogical Source code
sizeBinaryReduction Source code
sizeBinaryUnaryCwise Source code
sizeChainedCall Source code
sizeColonOperator Source code
sizeConcatenate Source code
sizeCppPointerDereference Source code
sizeDiagonal Source code
sizeDim Source code
sizeDoubleBracket Source code
sizeFor Source code
sizeGetBound Source code
sizeGetParam Source code
sizeIndexingBracket Source code
sizeInsertIntermediate Source code
sizeMatrixMult Source code
sizeMatrixSquareReduction Source code
sizeNFvar Source code
sizeNewNimbleList Source code
sizeNimArrayGeneral Source code
sizeNimbleFunction Source code
sizeNimbleListReturningFunction Source code
sizeOneEigenCommand Source code
sizeProxyForDebugging Source code
sizeRCfunction Source code
sizeRecyclingRule Source code
sizeRecyclingRuleRfunction Source code
sizeRep Source code
sizeResizeNoPtr Source code
sizeReturn Source code
sizeRmultivarFirstArg Source code
sizeRunTime Source code
sizeScalar Source code
sizeScalarModelOp Source code
sizeScalarRecurse Source code
sizeSeq Source code
sizeSetSize Source code
sizeSimulate Source code
sizeSolveOp Source code
sizeSwitch Source code
sizeTranspose Source code
sizeUnaryCwise Source code
sizeUnaryCwiseSquare Source code
sizeUnaryNonaryCwise Source code
sizeUnaryReduction Source code
sizeUndefined Source code
sizeValues Source code
sizeVoidPtr Source code
sizeWhich Source code
sizeasDoublePtr Source code
sizecallC Source code
sizeforceEigenize Source code
sizemap Source code
sizemvAccessBracket Source code
slice Man page
spectrum0.ar.big Source code
splitCompletionForOrigNodes Source code
splitVertexIDsToElementIDs Source code
splitVertices Source code
stop Man page
stripArgs Source code
stripPrefix Source code
svd Man page
svdNimbleList Man page
symTypeFromSymTab Source code
symbolDouble Source code
symbolInt Source code
symbolTable2cppVars Source code
t Man page
testBUGSmodel Man page Source code
timeComparisonComponent Source code
topologicallySortNodes Man page
updateMCMCcomparisonWithHighOrderESS Man page Source code
valueInCompiledNimbleFunction Man page Source code
values Man page Source code
values<- Man page
varAndIndices2flatIndex Source code
varAndIndices2mapParts Source code
varInfoClass-Class Man page
vectorIndex_2_flat Source code
which Man page
whyInvalid Source code
wishart Man page
wrapAsNumeric Source code
writeCode Source code

Files

inst
inst/make
inst/make/Makevars.win.in
inst/make/Makevars_lib.in
inst/make/Makevars.in
inst/CppCode
inst/CppCode/dists.cpp
inst/CppCode/Makevars
inst/CppCode/NamedObjects.cpp
inst/CppCode/ModelClassUtils.cpp
inst/CppCode/nimbleGraph.cpp
inst/CppCode/GNUmakefile
inst/CppCode/smartPtrs.cpp
inst/CppCode/RcppNimbleUtils.cpp
inst/CppCode/accessorClasses.cpp
inst/CppCode/dllFinalizer.cpp
inst/CppCode/Utils.cpp
inst/CppCode/EigenTypedefs.cpp
inst/CppCode/eigenUsingClasses.cpp
inst/CppCode/RcppUtils.cpp
inst/CppCode/nimDists.cpp
inst/tests
inst/tests/test-filtering.R
inst/tests/test_utils.R
inst/tests/test-Filtering2.R
inst/tests/test-Math2.R
inst/tests/test-modelValuesInterface.R
inst/tests/test-dsl_dists.R
inst/tests/test-Mcmc2.R
inst/tests/test-getDistributionInfo.R
inst/tests/test-mcmc.R
inst/tests/test-Mcmc3.R
inst/tests/test-getParam.R
inst/tests/test-nimbleFunctionInterfaces.R
inst/tests/test-numericTypes.R
inst/tests/test-checkDSL.R
inst/tests/test-models.R
inst/tests/test-nimbleList.R
inst/tests/test-distributions.R
inst/tests/test-trunc.R
inst/tests/test-types.R
inst/tests/test-user.R
inst/tests/test-getDependencies.R
inst/tests/test-coreR.R
inst/tests/test-copy.R
inst/tests/test-mcem.R
inst/tests/test-getBound.R
inst/tests/test-size.R
inst/tests/test-math.R
inst/tests/test-setData.R
inst/tests/test-compareMCMCs.R
inst/tests/test-declare.R
inst/tests/test-misc.R
inst/tests/test-allocation.R
inst/NEWS
inst/classic-bugs
inst/classic-bugs/vol1
inst/classic-bugs/vol1/kidney
inst/classic-bugs/vol1/kidney/kidney-data.R
inst/classic-bugs/vol1/kidney/ReadMe
inst/classic-bugs/vol1/kidney/kidney.bug
inst/classic-bugs/vol1/kidney/kidney-init.R
inst/classic-bugs/vol1/kidney/bench-test1.R
inst/classic-bugs/vol1/kidney/notest1.cmd
inst/classic-bugs/vol1/blocker
inst/classic-bugs/vol1/blocker/test1.R
inst/classic-bugs/vol1/blocker/blockert.bug
inst/classic-bugs/vol1/blocker/blocker-data.R
inst/classic-bugs/vol1/blocker/ReadMe
inst/classic-bugs/vol1/blocker/notest3.cmd
inst/classic-bugs/vol1/blocker/blockert-init.R
inst/classic-bugs/vol1/blocker/test1.cmd
inst/classic-bugs/vol1/blocker/blockht-data.R
inst/classic-bugs/vol1/blocker/notest2.cmd
inst/classic-bugs/vol1/blocker/blockht.bug
inst/classic-bugs/vol1/blocker/blocker-init.R
inst/classic-bugs/vol1/blocker/bench-test3.R
inst/classic-bugs/vol1/blocker/bench-test1.R
inst/classic-bugs/vol1/blocker/blocker.bug
inst/classic-bugs/vol1/blocker/bench-test2.R
inst/classic-bugs/vol1/epil
inst/classic-bugs/vol1/epil/epil3.bug
inst/classic-bugs/vol1/epil/epil-inits.R
inst/classic-bugs/vol1/epil/test1.R
inst/classic-bugs/vol1/epil/test2.cmd
inst/classic-bugs/vol1/epil/test1.cmd
inst/classic-bugs/vol1/epil/epil2.bug
inst/classic-bugs/vol1/epil/test2.R
inst/classic-bugs/vol1/epil/bench-test1.R
inst/classic-bugs/vol1/epil/epil-data.R
inst/classic-bugs/vol1/epil/bench-test2.R
inst/classic-bugs/vol1/salm
inst/classic-bugs/vol1/salm/salm-pareto.bug
inst/classic-bugs/vol1/salm/test1.R
inst/classic-bugs/vol1/salm/test2.cmd
inst/classic-bugs/vol1/salm/salm-init.R
inst/classic-bugs/vol1/salm/salm.bug
inst/classic-bugs/vol1/salm/test1.cmd
inst/classic-bugs/vol1/salm/test2.R
inst/classic-bugs/vol1/salm/bench-test1.R
inst/classic-bugs/vol1/salm/salm-data.R
inst/classic-bugs/vol1/salm/bench-test2.R
inst/classic-bugs/vol1/equiv
inst/classic-bugs/vol1/equiv/test1.R
inst/classic-bugs/vol1/equiv/test2.cmd
inst/classic-bugs/vol1/equiv/ReadMe
inst/classic-bugs/vol1/equiv/equivmiss-data.R
inst/classic-bugs/vol1/equiv/equiv-data.R
inst/classic-bugs/vol1/equiv/test1.cmd
inst/classic-bugs/vol1/equiv/equiv.bug
inst/classic-bugs/vol1/equiv/equiv-init.R
inst/classic-bugs/vol1/equiv/bench-test1.R
inst/classic-bugs/vol1/equiv/bench-test2.R
inst/classic-bugs/vol1/litters
inst/classic-bugs/vol1/litters/litters.bug
inst/classic-bugs/vol1/litters/test1.R
inst/classic-bugs/vol1/litters/ReadMe
inst/classic-bugs/vol1/litters/litters-data.R
inst/classic-bugs/vol1/litters/test1.cmd
inst/classic-bugs/vol1/litters/litters-init.R
inst/classic-bugs/vol1/litters/bench-test1.R
inst/classic-bugs/vol1/lsat
inst/classic-bugs/vol1/lsat/test1.R
inst/classic-bugs/vol1/lsat/test2.cmd
inst/classic-bugs/vol1/lsat/lsat.dat
inst/classic-bugs/vol1/lsat/lsat-init.R
inst/classic-bugs/vol1/lsat/lsat.bug
inst/classic-bugs/vol1/lsat/lsat2-init.R
inst/classic-bugs/vol1/lsat/test1.cmd
inst/classic-bugs/vol1/lsat/lsat-data.R
inst/classic-bugs/vol1/lsat/test2.R
inst/classic-bugs/vol1/lsat/bench-test1.R
inst/classic-bugs/vol1/lsat/lsat2.bug
inst/classic-bugs/vol1/lsat/bench-test2.R
inst/classic-bugs/vol1/leuk
inst/classic-bugs/vol1/leuk/test1.R
inst/classic-bugs/vol1/leuk/leukfr.bug
inst/classic-bugs/vol1/leuk/leuk-data.R
inst/classic-bugs/vol1/leuk/leukfr.in
inst/classic-bugs/vol1/leuk/leuk-poisson.bug
inst/classic-bugs/vol1/leuk/leukfr-s.dat
inst/classic-bugs/vol1/leuk/test1.cmd
inst/classic-bugs/vol1/leuk/leuk.bug
inst/classic-bugs/vol1/leuk/leuk.in
inst/classic-bugs/vol1/leuk/leuk-init.R
inst/classic-bugs/vol1/leuk/leukfr.dat
inst/classic-bugs/vol1/leuk/bench-test1.R
inst/classic-bugs/vol1/leuk/leuk-s.dat
inst/classic-bugs/vol1/seeds
inst/classic-bugs/vol1/seeds/seeds-init.R
inst/classic-bugs/vol1/seeds/test1.R
inst/classic-bugs/vol1/seeds/test4.cmd
inst/classic-bugs/vol1/seeds/seeds-data.R
inst/classic-bugs/vol1/seeds/test2.cmd
inst/classic-bugs/vol1/seeds/test5.R
inst/classic-bugs/vol1/seeds/seedsuni.bug
inst/classic-bugs/vol1/seeds/seedssig.bug
inst/classic-bugs/vol1/seeds/test4.R
inst/classic-bugs/vol1/seeds/seeds.bug
inst/classic-bugs/vol1/seeds/seedspar.bug
inst/classic-bugs/vol1/seeds/bench-test5.R
inst/classic-bugs/vol1/seeds/test1.cmd
inst/classic-bugs/vol1/seeds/bench-test4.R
inst/classic-bugs/vol1/seeds/test3.R
inst/classic-bugs/vol1/seeds/test5.cmd
inst/classic-bugs/vol1/seeds/seedszro.bug
inst/classic-bugs/vol1/seeds/test2.R
inst/classic-bugs/vol1/seeds/bench-test3.R
inst/classic-bugs/vol1/seeds/bench-test1.R
inst/classic-bugs/vol1/seeds/test3.cmd
inst/classic-bugs/vol1/seeds/bench-test2.R
inst/classic-bugs/vol1/dyes
inst/classic-bugs/vol1/dyes/dyes-init.R
inst/classic-bugs/vol1/dyes/test1.R
inst/classic-bugs/vol1/dyes/dyes.bug
inst/classic-bugs/vol1/dyes/test1.cmd
inst/classic-bugs/vol1/dyes/dyes-data.R
inst/classic-bugs/vol1/dyes/bench-test1.R
inst/classic-bugs/vol1/oxford
inst/classic-bugs/vol1/oxford/test1.R
inst/classic-bugs/vol1/oxford/ReadMe
inst/classic-bugs/vol1/oxford/oxford-init.R
inst/classic-bugs/vol1/oxford/test1.cmd
inst/classic-bugs/vol1/oxford/oxford.dat
inst/classic-bugs/vol1/oxford/bench-test1.R
inst/classic-bugs/vol1/oxford/oxford-data.R
inst/classic-bugs/vol1/oxford/oxford.bug
inst/classic-bugs/vol1/rats
inst/classic-bugs/vol1/rats/test1.R
inst/classic-bugs/vol1/rats/ratsmiss-data.R
inst/classic-bugs/vol1/rats/test2.cmd
inst/classic-bugs/vol1/rats/rats.bug
inst/classic-bugs/vol1/rats/rats-init.R
inst/classic-bugs/vol1/rats/test1.cmd
inst/classic-bugs/vol1/rats/rats-data.R
inst/classic-bugs/vol1/rats/bench-test1.R
inst/classic-bugs/vol1/rats/bench-test2.R
inst/classic-bugs/vol1/pump
inst/classic-bugs/vol1/pump/test1.R
inst/classic-bugs/vol1/pump/test1.cmd
inst/classic-bugs/vol1/pump/pump-init.R
inst/classic-bugs/vol1/pump/pump.bug
inst/classic-bugs/vol1/pump/bench-test1.R
inst/classic-bugs/vol1/pump/pump-data.R
inst/classic-bugs/vol1/bones
inst/classic-bugs/vol1/bones/test1.R
inst/classic-bugs/vol1/bones/bones-init.R
inst/classic-bugs/vol1/bones/bones-data.R
inst/classic-bugs/vol1/bones/test1.cmd
inst/classic-bugs/vol1/bones/bones.bug
inst/classic-bugs/vol1/bones/bench-test1.R
inst/classic-bugs/vol1/mice
inst/classic-bugs/vol1/mice/mice.bug
inst/classic-bugs/vol1/mice/test1.R
inst/classic-bugs/vol1/mice/mice-data.R
inst/classic-bugs/vol1/mice/mice-init.R
inst/classic-bugs/vol1/mice/test1.cmd
inst/classic-bugs/vol1/mice/bench-test1.R
inst/classic-bugs/vol1/inhaler
inst/classic-bugs/vol1/inhaler/test1.R
inst/classic-bugs/vol1/inhaler/inhaler.bug
inst/classic-bugs/vol1/inhaler/inhaler-inits.R
inst/classic-bugs/vol1/inhaler/test1.cmd
inst/classic-bugs/vol1/inhaler/bench-test1.R
inst/classic-bugs/vol1/inhaler/inhaler-data.R
inst/classic-bugs/vol1/inhaler/inhaler.cmd
inst/classic-bugs/vol1/line
inst/classic-bugs/vol1/line/test1.R
inst/classic-bugs/vol1/line/line-data.R
inst/classic-bugs/vol1/line/line.bug
inst/classic-bugs/vol1/line/line-inits.R
inst/classic-bugs/vol1/line/test1.cmd
inst/classic-bugs/vol1/line/bench-test1.R
inst/classic-bugs/ReadMe
inst/classic-bugs/other
inst/classic-bugs/other/dipper
inst/classic-bugs/other/dipper/dipper-data.R
inst/classic-bugs/other/dipper/dipper.bug
inst/classic-bugs/R
inst/classic-bugs/R/check.R
inst/classic-bugs/R/Rcheck.R
inst/classic-bugs/R/bench.R
inst/classic-bugs/LICENSE
inst/classic-bugs/vol2
inst/classic-bugs/vol2/ice
inst/classic-bugs/vol2/ice/icear.bug
inst/classic-bugs/vol2/ice/ice-inits.R
inst/classic-bugs/vol2/ice/ReadMe
inst/classic-bugs/vol2/ice/test1.cmd
inst/classic-bugs/vol2/ice/bench.R
inst/classic-bugs/vol2/ice/ice-data.R
inst/classic-bugs/vol2/ice/bench-test1.R
inst/classic-bugs/vol2/dugongs
inst/classic-bugs/vol2/dugongs/test1.R
inst/classic-bugs/vol2/dugongs/dugongs-inits.R
inst/classic-bugs/vol2/dugongs/dugongs.bug
inst/classic-bugs/vol2/dugongs/dugongs-data.R
inst/classic-bugs/vol2/dugongs/test1.cmd
inst/classic-bugs/vol2/dugongs/bench-test1.R
inst/classic-bugs/vol2/air
inst/classic-bugs/vol2/air/air-data.R
inst/classic-bugs/vol2/air/ReadMe
inst/classic-bugs/vol2/air/bench.R
inst/classic-bugs/vol2/air/air.bug
inst/classic-bugs/vol2/air/bench-test1.R
inst/classic-bugs/vol2/air/notest1.cmd
inst/classic-bugs/vol2/air/air-inits.R
inst/classic-bugs/vol2/jaw
inst/classic-bugs/vol2/jaw/test1.R
inst/classic-bugs/vol2/jaw/test2.cmd
inst/classic-bugs/vol2/jaw/jaw-linear.bug
inst/classic-bugs/vol2/jaw/jaw-data.R
inst/classic-bugs/vol2/jaw/ReadMe
inst/classic-bugs/vol2/jaw/jaw-inits.R
inst/classic-bugs/vol2/jaw/test1.cmd
inst/classic-bugs/vol2/jaw/test3.R
inst/classic-bugs/vol2/jaw/test2.R
inst/classic-bugs/vol2/jaw/jaw-quadratic.bug
inst/classic-bugs/vol2/jaw/bench-test3.R
inst/classic-bugs/vol2/jaw/jaw-constant.bug
inst/classic-bugs/vol2/jaw/bench-test1.R
inst/classic-bugs/vol2/jaw/test3.cmd
inst/classic-bugs/vol2/jaw/bench-test2.R
inst/classic-bugs/vol2/asia
inst/classic-bugs/vol2/asia/test1.R
inst/classic-bugs/vol2/asia/test2.cmd
inst/classic-bugs/vol2/asia/asia2.bug
inst/classic-bugs/vol2/asia/asia.bug
inst/classic-bugs/vol2/asia/test1.cmd
inst/classic-bugs/vol2/asia/asia-data.R
inst/classic-bugs/vol2/asia/test2.R
inst/classic-bugs/vol2/asia/asia2-data.R
inst/classic-bugs/vol2/asia/bench-test1.R
inst/classic-bugs/vol2/asia/bench-test2.R
inst/classic-bugs/vol2/stagnant
inst/classic-bugs/vol2/stagnant/test1.R
inst/classic-bugs/vol2/stagnant/test2.cmd
inst/classic-bugs/vol2/stagnant/notest4.cmd
inst/classic-bugs/vol2/stagnant/ReadMe
inst/classic-bugs/vol2/stagnant/stagnant-data.R
inst/classic-bugs/vol2/stagnant/notest3.cmd
inst/classic-bugs/vol2/stagnant/stagnant-inits3.R
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inst/include/Eigen/src/SparseLU/SparseLU_panel_dfs.h
inst/include/Eigen/src/SparseLU/SparseLU_column_dfs.h
inst/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h
inst/include/Eigen/src/SparseLU/SparseLU_Memory.h
inst/include/Eigen/src/SparseLU/SparseLU.h
inst/include/Eigen/src/SparseLU/SparseLUImpl.h
inst/include/Eigen/src/Jacobi
inst/include/Eigen/src/Jacobi/CMakeLists.txt
inst/include/Eigen/src/Jacobi/Jacobi.h
inst/include/Eigen/src/UmfPackSupport
inst/include/Eigen/src/UmfPackSupport/UmfPackSupport.h
inst/include/Eigen/src/UmfPackSupport/CMakeLists.txt
inst/include/Eigen/src/PardisoSupport
inst/include/Eigen/src/PardisoSupport/CMakeLists.txt
inst/include/Eigen/src/PardisoSupport/PardisoSupport.h
inst/include/Eigen/src/SuperLUSupport
inst/include/Eigen/src/SuperLUSupport/CMakeLists.txt
inst/include/Eigen/src/SuperLUSupport/SuperLUSupport.h
inst/include/Eigen/src/QR
inst/include/Eigen/src/QR/ColPivHouseholderQR_MKL.h
inst/include/Eigen/src/QR/CMakeLists.txt
inst/include/Eigen/src/QR/HouseholderQR.h
inst/include/Eigen/src/QR/ColPivHouseholderQR.h
inst/include/Eigen/src/QR/HouseholderQR_MKL.h
inst/include/Eigen/src/QR/FullPivHouseholderQR.h
inst/include/Eigen/src/IterativeLinearSolvers
inst/include/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h
inst/include/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h
inst/include/Eigen/src/IterativeLinearSolvers/CMakeLists.txt
inst/include/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h
inst/include/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h
inst/include/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h
inst/include/Eigen/src/SVD
inst/include/Eigen/src/SVD/JacobiSVD_MKL.h
inst/include/Eigen/src/SVD/CMakeLists.txt
inst/include/Eigen/src/SVD/JacobiSVD.h
inst/include/Eigen/src/SVD/UpperBidiagonalization.h
inst/include/Eigen/src/CholmodSupport
inst/include/Eigen/src/CholmodSupport/CholmodSupport.h
inst/include/Eigen/src/CholmodSupport/CMakeLists.txt
inst/include/Eigen/src/OrderingMethods
inst/include/Eigen/src/OrderingMethods/Amd.h
inst/include/Eigen/src/OrderingMethods/CMakeLists.txt
inst/include/Eigen/src/OrderingMethods/Ordering.h
inst/include/Eigen/src/OrderingMethods/Eigen_Colamd.h
inst/include/Eigen/src/SPQRSupport
inst/include/Eigen/src/SPQRSupport/CMakeLists.txt
inst/include/Eigen/src/SPQRSupport/SuiteSparseQRSupport.h
inst/include/Eigen/SparseCore
inst/include/Eigen/Cholesky
inst/include/Eigen/MetisSupport
inst/include/Eigen/CMakeLists.txt
inst/include/Eigen/Dense
inst/include/Eigen/SparseCholesky
inst/include/Eigen/Geometry
inst/include/Eigen/LU
inst/include/Eigen/PaStiXSupport
inst/include/Eigen/Array
inst/include/Eigen/Householder
inst/include/Eigen/Core
inst/include/Eigen/Eigen2Support
inst/include/Eigen/QtAlignedMalloc
inst/include/Eigen/SparseLU
inst/include/Eigen/Jacobi
inst/include/Eigen/UmfPackSupport
inst/include/Eigen/PardisoSupport
inst/include/Eigen/Sparse
inst/include/Eigen/LeastSquares
inst/include/Eigen/Eigen_License.MPL2
inst/include/Eigen/SuperLUSupport
inst/include/Eigen/QR
inst/include/Eigen/IterativeLinearSolvers
inst/include/Eigen/StdList
inst/include/Eigen/SVD
inst/include/Eigen/StdDeque
inst/include/Eigen/CholmodSupport
inst/include/Eigen/OrderingMethods
inst/include/Eigen/Eigen
inst/include/Eigen/SPQRSupport
configure.ac
src
src/DO_NOT_PUT_CODE_HERE_DO_IN_INST_CPPCODE
src/Makevars.in
src/Makevars.win
src/nimble.cpp
NAMESPACE
INSTALL
NEWS
R
R/cppDefs_nimbleList.R
R/cppDefs_BUGSmodel.R
R/BUGS_modelDef.R
R/genCpp_eigenization.R
R/genCpp_addDebugMarks.R
R/all_utils.R
R/RCfunction_compile.R
R/types_numericLists.R
R/nimbleFunction_util.R
R/cppInterfaces_modelValues.R
R/types_nodeFxnVector.R
R/nimbleFunction_nodeFunction.R
R/genCpp_initSizes.R
R/BUGS_readBUGS.R
R/genCpp_sizeProcessing.R
R/distributions_processInputList.R
R/cppDefs_RCfunction.R
R/BUGS_getDependencies.R
R/cppDefs_variables.R
R/nimbleProject.R
R/MCMC_samplers.R
R/BUGS_BUGSdecl.R
R/cppDefs_namedObjects.R
R/NF_utils.R
R/BUGS_testBUGS.R
R/genCpp_liftMaps.R
R/genCpp_processSpecificCalls.R
R/cppDefs_modelValues.R
R/MCMC_comparisons.R
R/nimbleList_core.R
R/cppDefs_outputCppFromRparseTree.R
R/genCpp_insertAssertions.R
R/cppDefs_cppProject.R
R/types_util.R
R/BUGS_contexts.R
R/nimbleFunction_keywordProcessing.R
R/cppInterfaces_utils.R
R/genCpp_operatorLists.R
R/MCMC_run.R
R/nimbleFunction_nodeFunctionNew.R
R/MCMC_build.R
R/MCMC_configuration.R
R/cppInterfaces_otherTypes.R
R/filtering_liuwest.R
R/MCEM_build.R
R/types_modelVariableAccessor.R
R/setNimbleInternalFunctions.R
R/cppInterfaces_models.R
R/genCpp_buildIntermediates.R
R/options.R
R/BUGS_model.R
R/MCMC_utils.R
R/initializeModel.R
R/filtering_enkf.R
R/types_nimbleFunctionList.R
R/genCpp_generateCpp.R
R/cppDefs_core.R
R/optimTools.R
R/config.R
R/BUGS_mathCompatibility.R
R/MCMC_suite.R
R/nimbleFunction_Rexecution.R
R/registration.R
R/RCfunction_core.R
R/genCpp_RparseTree2exprClasses.R
R/config.R.in
R/types_symbolTable.R
R/cppDefs_nimbleFunction.R
R/types_modelValues.R
R/filtering_bootstrap.R
R/types_modelValuesAccessor.R
R/cppInterfaces_nimbleFunctions.R
R/distributions_implementations.R
R/cppDefs_utils.R
R/MCMC_conjugacy.R
R/BUGS_graphNodeMaps.R
R/genCpp_maps.R
R/MCMC_autoBlock.R
R/distributions_inputList.R
R/genCpp_exprClass.R
R/nimbleFunction_core.R
R/nimble-package.r
R/miscFunctions.R
R/zzz.R
R/makevars.R
R/BUGS_utils.R
R/nimbleFunction_compile.R
R/BUGS_nimbleGraph.R
R/filtering_auxiliary.R
README.md
MD5
DESCRIPTION
configure
man
man/nimbleList.Rd
man/nimbleCode.Rd
man/nimSvd.Rd
man/MCMCconf-class.Rd
man/buildAuxiliaryFilter.Rd
man/getBUGSexampleDir.Rd
man/nimbleFunction.Rd
man/decideAndJump.Rd
man/setupOutputs.Rd
man/nimPrint.Rd
man/codeBlockClass-class.Rd
man/nimbleFunctionVirtual.Rd
man/autoBlock.Rd
man/initializeModel.Rd
man/Inverse-Gamma.Rd
man/getLoadingNamespace.Rd
man/MultivariateNormal.Rd
man/reshape_comparison_results.Rd
man/Interval.Rd
man/registerDistributions.Rd
man/eigenNimbleList.Rd
man/nodeFunctions.Rd
man/checkInterrupt.Rd
man/nimbleOptions.Rd
man/configureMCMC.Rd
man/buildEnsembleKF.Rd
man/values.Rd
man/identityMatrix.Rd
man/getDefinition.Rd
man/Categorical.Rd
man/nimble-R-functions.Rd
man/setAndCalculate.Rd
man/simNodes.Rd
man/buildMCEM.Rd
man/is.nl.Rd
man/nimMatrix.Rd
man/Multivariate-t.Rd
man/nimNumeric.Rd
man/rename_MCMC_comparison_method.Rd
man/modelValuesConf.Rd
man/nimbleType-class.Rd
man/runMCMC.Rd
man/Wishart.Rd
man/nimble-internal.Rd
man/Exponential.Rd
man/buildBootstrapFilter.Rd
man/makeParamInfo.Rd
man/getBound.Rd
man/setAndCalculateOne.Rd
man/buildMCMC.Rd
man/compileNimble.Rd
man/modelValues.Rd
man/getParam.Rd
man/svdNimbleList.Rd
man/RmodelBaseClass-class.Rd
man/getsize.Rd
man/CmodelBaseClass-class.Rd
man/nimbleFunctionBase-class.Rd
man/setSize.Rd
man/is.nf.Rd
man/nfVar.Rd
man/nimStop.Rd
man/declare.Rd
man/t.Rd
man/Rmatrix2mvOneVar.Rd
man/rankSample.Rd
man/nfMethod.Rd
man/nimble-math.Rd
man/asRow.Rd
man/makeBoundInfo.Rd
man/getNimbleOption.Rd
man/modelDefClass-class.Rd
man/readBUGSmodel.Rd
man/simNodesMV.Rd
man/BUGSdeclClass-class.Rd
man/Dirichlet.Rd
man/valueInCompiledNimbleFunction.Rd
man/modelBaseClass-class.Rd
man/buildLiuWestFilter.Rd
man/deregisterDistributions.Rd
man/CnimbleFunctionBase-class.Rd
man/singleVarAccessClass-class.Rd
man/resize.Rd
man/modelValuesBaseClass-class.Rd
man/nimEigen.Rd
man/run.time.Rd
man/Multinomial.Rd
man/MCMCsuite.Rd
man/testBUGSmodel.Rd
man/nimbleFunctionList-class.Rd
man/nimbleModel.Rd
man/nimDim.Rd
man/updateMCMCcomparisonWithHighOrderESS.Rd
man/compareMCMCs.Rd
man/combine_MCMC_comparison_results.Rd
man/distributionInfo.Rd
man/MCMCsuiteClass-class.Rd
man/nimCopy.Rd
man/make_MCMC_comparison_pages.Rd
man/decide.Rd
man/Constraint.Rd
man/nimCat.Rd
man/samplers.Rd
configure.win
cleanup
LICENSE
cleanup.win
nimble documentation built on May 19, 2017, 7:48 p.m.