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

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.

Install the latest version of this package by entering the following in R:
install.packages("nimble")
AuthorPerry de Valpine, Christopher Paciorek, Daniel Turek, Cliff Anderson- Bergman, Duncan Temple Lang
Date of publication2016-12-14 23:15:44
MaintainerChristopher Paciorek <paciorek@stat.berkeley.edu>
LicenseBSD_3_clause + file LICENSE
Version0.6-3
http://r-nimble.org

View on CRAN

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

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

is.nf: check if a nimbleFunction

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

nimArray: Creates a array object of arbitrary dimension for use in...

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

nimble-math: Mathematical functions for BUGS and nimbleFunction...

nimbleModel: Create a NIMBLE model from BUGS code

nimbleOptions: NIMBLE Options Settings

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...

nimInteger: Creates an integer vector for use in NIMBLE DSL functions

nimMatrix: Creates a matrix object for use in NIMBLE DSL functions

nimNumeric: Creates a numeric vector for use in NIMBLE DSL functions

nimPrint: print function for use in nimbleFunctions

nimStop: Halt execution of a nimbleFunction function method. Part of...

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'

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

addMonitors Man page
addMonitors2 Man page
addSampler Man page
array Man page
asCol Man page
as.matrix.modelValuesBaseClass-Class Man page
asRow Man page
autoBlock Man page
autoBlockClass-Class Man page
BUGScontextClass-Class Man page
BUGSdeclClass Man page
BUGSdeclClass-class Man page
BUGSsingleContextClass-Class Man page
buildAuxiliaryFilter Man page
buildBootstrapFilter Man page
buildEnsembleKF Man page
buildLiuWestFilter Man page
buildMCEM Man page
buildMCMC Man page
calc_dmnormAltParams Man page
calc_dmnormConjugacyContributions Man page
calcNodes Man page
calcNodesMV Man page
calculate Man page
calculateDiff Man page
Categorical Man page
checkConjugacy Man page
checkInterrupt Man page
cloglog Man page
CmodelBaseClass Man page
CmodelBaseClass-class Man page
[<-,CmodelValues-method Man page
[,CmodelValues-method Man page
[[<-,CmodelValues-method 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
CmultiNimbleFunctionClass-Class Man page
CnimbleFunctionBase Man page
CnimbleFunctionBase-class Man page
[[<-,CNumericList-method Man page
[[,CNumericList-method Man page
codeBlockClass Man page
codeBlockClass-class Man page
combine_MCMC_comparison_results Man page
compareMCMCs Man page
compileNimble Man page
configureMCMC Man page
conjugacyClass-Class Man page
conjugacyRelationshipsClass-Class Man page
[[,conjugacyRelationshipsClass-method Man page
Constraint Man page
cppBUGSmodelClass-Class Man page
cppCodeFileClass-Class Man page
cppCPPfileClass-Class Man page
cppHfileClass-Class Man page
cppModelValuesClass-Class Man page
cppNamedObjectsClass-Class Man page
cppNimbleFunctionClass-Class Man page
cppProjectClass-Class Man page
cppVirtualNimbleFunctionClass-Class Man page
crossLevel Man page
cube Man page
dcat Man page
dconstraint Man page
ddirch Man page
decide Man page
decideAndJump Man page
declare Man page
dependentClass-Class Man page
deregisterDistributions Man page
dexp_nimble Man page
dinterval Man page
dirichlet Man page
Dirichlet Man page
distClass-Class Man page
distributionInfo Man page
distributionsClass-Class Man page
[,distributionsClass-method Man page
[[,distributionsClass-method Man page
dmnorm_chol Man page
dmulti Man page
dmvt_chol Man page
dt_nonstandard Man page
dwish_chol Man page
expit Man page
Exponential Man page
exprClass-Class Man page
exprTypeInfoClass-Class Man page
getBound Man page
getBUGSexampleDir Man page
getDefinition Man page
getDependencies Man page
getDimension Man page
getDistribution Man page
getDistributionInfo Man page
getLoadingNamespace Man page
getLogProb Man page
getLogProbNodes Man page
getLogProbNodesMV Man page
getMonitors Man page
getNimbleOption Man page
getNimbleProject Man page
getNodeFunctionIndexedInfo Man page
getNodeNames Man page
getParam Man page
getParamNames Man page
getSamplers Man page
getsize Man page
getType Man page
getVarNames Man page
icloglog Man page
identityMatrix Man page
ilogit Man page
indexedNodeInfoTableClass-Class Man page
initializeModel Man page
inprod Man page
integer Man page
Interval Man page
inverse Man page
iprobit Man page
isBinary Man page
isData Man page
isDeterm Man page
isDiscrete Man page
isEndNode Man page
is.nf Man page
isStoch Man page
isTruncated Man page
isUnivariate Man page
isUserDefined Man page
keywordInfoClass-Class Man page
logdet Man page
logfact Man page
loggam Man page
logit Man page
makeBoundInfo Man page
MakeCustomModelClass-Class Man page
makeCustomModelValuesClass-Class Man page
make_MCMC_comparison_pages Man page
makeParamInfo Man page
mapsClass-Class Man page
matrix Man page
MCMCconf Man page
MCMCconf-class Man page
MCMCsuite Man page
MCMCsuiteClass Man page
MCMCsuiteClass-class Man page
modelBaseClass Man page
modelBaseClass-class Man page
[[<-,modelBaseClass-method Man page
[[,modelBaseClass-method Man page
modelDefClass Man page
modelDefClass-class Man page
modelDefInfoClass-Class Man page
modelValues Man page
modelValuesBaseClass Man page
modelValuesBaseClass-class Man page
[<-,modelValuesBaseClass-method Man page
[,modelValuesBaseClass-method Man page
modelValuesConf Man page
multinomial Man page
Multinomial Man page
MultivariateNormal Man page
multivariate-t Man page
Multivariate-t Man page
mvInfoClass-Class Man page
mvt Man page
newModel Man page
nfCompilationInfoClass-Class Man page
nfMethod Man page
nfVar Man page
nfVar<- Man page
nimArray Man page
nimbleCode Man page
nimbleFunction Man page
nimbleFunctionBase Man page
nimbleFunctionBase-class Man page
nimbleFunctionList Man page
nimbleFunctionList-class Man page
[[<-,nimbleFunctionList-method Man page
nimbleFunctionVirtual Man page
nimbleGraphClass-Class Man page
nimbleInternalFunctions Man page
nimbleModel Man page
nimbleOptions Man page
nimbleProjectClass-Class Man page
nimbleUserNamespace Man page
nimCat Man page
nimCopy Man page
nimDim Man page
nimEquals Man page
nimInteger Man page
nimMatrix Man page
nimNumeric Man page
[[<-,nimPointerList-method Man page
[[,nimPointerList-method Man page
nimPrint Man page
nimStep Man page
nimStop Man page
nimSwitch Man page
nodeFunctions Man page
[<-,numberedModelValuesAccessors-method Man page
[,numberedModelValuesAccessors-method Man page
[<-,numberedObjects-method Man page
[,numberedObjects-method Man page
numeric Man page
pexp_nimble Man page
phi Man page
posteriorClass-Class Man page
posterior_predictive Man page
pow Man page
pqDefined Man page
printSamplers Man page
probit Man page
pt_nonstandard Man page
qexp_nimble Man page
qt_nonstandard Man page
rankSample Man page
rcat Man page
RCfunctionCompileClass-Class Man page
RCfunInfoClass-Class Man page
rconstraint Man page
rdirch Man page
readBUGSmodel Man page
registerDistributions Man page
removeSamplers Man page
rename_MCMC_comparison_method Man page
resetData Man page
resetMonitors Man page
reshape_comparison_results Man page
resize Man page
rexp_nimble Man page
rinterval Man page
RMakeCustomModelClass-Class Man page
Rmatrix2mvOneVar Man page
rmnorm_chol Man page
RmodelBaseClass Man page
RmodelBaseClass-class Man page
rmulti Man page
rmvt_chol Man page
[[<-,RNumericList-method Man page
[[,RNumericList-method Man page
rt_nonstandard Man page
runMCMC Man page
run.time Man page
RW Man page
RW_block Man page
rwish_chol Man page
RW_llFunction Man page
RW_llFunction_block Man page
RW_multinomial Man page
RW_PF Man page
RW_PF_block Man page
sampler Man page
sampler_BASE Man page
sampler_binary Man page
sampler_crossLevel Man page
sampler_ess Man page
sampler_posterior_predictive Man page
sampler_RW Man page
sampler_RW_block Man page
sampler_RW_llFunction Man page
sampler_RW_llFunction_block Man page
sampler_RW_multinomial Man page
sampler_RW_PF Man page
sampler_RW_PF_block Man page
samplers Man page
sampler_slice Man page
setAndCalculate Man page
setAndCalculateDiff Man page
setAndCalculateOne Man page
setData Man page
setInits Man page
setSamplers Man page
setSize Man page
setThin Man page
setThin2 Man page
setupCodeTemplateClass-Class Man page
setupOutputs Man page
simNodes Man page
simNodesMV Man page
simulate Man page
singleModelValuesAccess Man page
singleModelValuesAccessClass-Class Man page
singleVarAccessClass Man page
singleVarAccessClass-class Man page
slice Man page
t Man page
testBUGSmodel Man page
topologicallySortNodes Man page
updateMCMCcomparisonWithHighOrderESS Man page
valueInCompiledNimbleFunction Man page
values Man page
values<- Man page
varInfoClass-Class Man page
wishart Man page
Wishart Man page

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/RcppNimbleUtils.cpp
inst/CppCode/accessorClasses.cpp
inst/CppCode/dllFinalizer.cpp
inst/CppCode/Utils.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-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-checkDSL.R inst/tests/test-models.R inst/tests/test-distributions.R inst/tests/test-trunc.R inst/tests/test-user.R inst/tests/test-getDependencies.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/NEWS
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inst/classic-bugs/ReadMe
inst/classic-bugs/other
inst/classic-bugs/other/dipper
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inst/include/Eigen/src/Core/ForceAlignedAccess.h
inst/include/Eigen/src/Core/Assign.h
inst/include/Eigen/src/Core/CoreIterators.h
inst/include/Eigen/src/Core/IO.h
inst/include/Eigen/src/Eigen2Support
inst/include/Eigen/src/Eigen2Support/Cwise.h
inst/include/Eigen/src/Eigen2Support/Macros.h
inst/include/Eigen/src/Eigen2Support/Lazy.h
inst/include/Eigen/src/Eigen2Support/MathFunctions.h
inst/include/Eigen/src/Eigen2Support/CMakeLists.txt
inst/include/Eigen/src/Eigen2Support/Geometry
inst/include/Eigen/src/Eigen2Support/Geometry/Rotation2D.h
inst/include/Eigen/src/Eigen2Support/Geometry/Hyperplane.h
inst/include/Eigen/src/Eigen2Support/Geometry/Quaternion.h
inst/include/Eigen/src/Eigen2Support/Geometry/Scaling.h
inst/include/Eigen/src/Eigen2Support/Geometry/CMakeLists.txt
inst/include/Eigen/src/Eigen2Support/Geometry/ParametrizedLine.h
inst/include/Eigen/src/Eigen2Support/Geometry/All.h
inst/include/Eigen/src/Eigen2Support/Geometry/Translation.h
inst/include/Eigen/src/Eigen2Support/Geometry/RotationBase.h
inst/include/Eigen/src/Eigen2Support/Geometry/Transform.h
inst/include/Eigen/src/Eigen2Support/Geometry/AlignedBox.h
inst/include/Eigen/src/Eigen2Support/Geometry/AngleAxis.h
inst/include/Eigen/src/Eigen2Support/LeastSquares.h
inst/include/Eigen/src/Eigen2Support/VectorBlock.h
inst/include/Eigen/src/Eigen2Support/QR.h
inst/include/Eigen/src/Eigen2Support/Memory.h
inst/include/Eigen/src/Eigen2Support/CwiseOperators.h
inst/include/Eigen/src/Eigen2Support/Meta.h
inst/include/Eigen/src/Eigen2Support/Block.h
inst/include/Eigen/src/Eigen2Support/SVD.h
inst/include/Eigen/src/Eigen2Support/LU.h
inst/include/Eigen/src/Eigen2Support/Minor.h
inst/include/Eigen/src/Eigen2Support/TriangularSolver.h
inst/include/Eigen/src/SparseLU
inst/include/Eigen/src/SparseLU/SparseLU_column_bmod.h
inst/include/Eigen/src/SparseLU/SparseLU_gemm_kernel.h
inst/include/Eigen/src/SparseLU/SparseLU_panel_bmod.h
inst/include/Eigen/src/SparseLU/SparseLU_pivotL.h
inst/include/Eigen/src/SparseLU/CMakeLists.txt
inst/include/Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h
inst/include/Eigen/src/SparseLU/SparseLU_copy_to_ucol.h
inst/include/Eigen/src/SparseLU/SparseLU_pruneL.h
inst/include/Eigen/src/SparseLU/SparseLU_Utils.h
inst/include/Eigen/src/SparseLU/SparseLU_Structs.h
inst/include/Eigen/src/SparseLU/SparseLU_kernel_bmod.h
inst/include/Eigen/src/SparseLU/SparseLU_relax_snode.h
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_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/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/nimbleCode.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/getLoadingNamespace.Rd man/MultivariateNormal.Rd man/reshape_comparison_results.Rd man/Interval.Rd man/registerDistributions.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/setAndCalculate.Rd man/simNodes.Rd man/buildMCEM.Rd man/nimMatrix.Rd man/Multivariate-t.Rd man/nimNumeric.Rd man/nimInteger.Rd man/rename_MCMC_comparison_method.Rd man/modelValuesConf.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/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/nimArray.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

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