├── .Rbuildignore ├── .github ├── .gitignore └── workflows │ └── ci.yaml ├── .gitignore ├── .zenodo.json ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── ISSUES ├── LICENSE ├── README.md ├── UserManual ├── .gitignore ├── NimbleUserManual.pdf ├── NimbleUserManual_files │ └── figure-html │ │ ├── linearRegressionGraph-1.png │ │ ├── mcmcPump-1.png │ │ ├── mcmcPump-2.png │ │ ├── mcmcPump2-1.png │ │ ├── mcmcPump2-2.png │ │ └── plotPump-1.png ├── README ├── cha-AD.html ├── cha-RCfunctions.html ├── cha-algos-provided.html ├── cha-bnp.html ├── cha-building-models.html ├── cha-data-structures.html ├── cha-installing-nimble.html ├── cha-lightning-intro.html ├── cha-mcmc.html ├── cha-more-introduction.html ├── cha-progr-with-models.html ├── cha-spatial.html ├── cha-user-defined.html ├── cha-using-models.html ├── cha-welcome-nimble.html ├── cha-writing-models.html ├── nimble-icon.png ├── overview.html ├── references.html ├── search_index.json └── src │ ├── .auctex-auto │ └── UserManualRefs.el │ ├── ADreferences.bib │ ├── Makefile │ ├── UserManualRefs.bib │ ├── _bookdown.yml │ ├── _output.yml │ ├── chapter_AD.Rmd │ ├── chapter_BNP.Rmd │ ├── chapter_BuildingModels.Rmd │ ├── chapter_DataStructures.Rmd │ ├── chapter_InstallingNimble.Rmd │ ├── chapter_Laplace.Rmd │ ├── chapter_LightningIntroduction.Rmd │ ├── chapter_MCMC.Rmd │ ├── chapter_MoreIntroduction.Rmd │ ├── chapter_OtherAlgorithms.Rmd │ ├── chapter_ProgrammingOverview.Rmd │ ├── chapter_RCfunctions.Rmd │ ├── chapter_Spatial.Rmd │ ├── chapter_UserDefined.Rmd │ ├── chapter_UsingModels.Rmd │ ├── chapter_WelcomeToNimble.Rmd │ ├── chapter_WritingModels.Rmd │ ├── chapter_WritingNimbleFunctions.Rmd │ ├── chunks │ ├── introExample_chunks.R │ ├── programmingWithModels_chunks.R │ ├── usingBugsModels_chunks.R │ └── writingModels_chunks.R │ ├── index.Rmd │ ├── latex2Rmd.R │ ├── refs.Rmd │ ├── tables │ ├── BNPconjugacyTable.md │ ├── BNPconjugacyTable2.md │ ├── conjugacyTable.md │ ├── coreRtableLong.md │ ├── densityAliasesTable.md │ ├── densityTableLong.md │ ├── eigenSvdTableMatrixAsNimList.md │ ├── eigenSvdTableMatrixElements.md │ ├── functionTableLong.md │ ├── functionTableMatrixLong.md │ ├── linksTable.md │ └── parameterizationTableLong.md │ └── title.tex ├── appveyor.yml ├── install_requirements.R ├── install_revDeps.R ├── notes ├── ModelsAndSamplers.tex ├── bnp_ModelsAndSamplers.pdf └── bnp_ModelsAndSamplers.tex ├── packages ├── .clang-format ├── .gitignore ├── AD-full-tests │ ├── test-ADdists-full.R │ └── test-ADmodels-full.R ├── GPL_header.txt ├── Laplace-examples │ ├── glmm-Pois-NB │ │ └── glmmPoisNB.R │ ├── glmm-binom │ │ └── glmmbiom.R │ ├── lmm │ │ ├── lmm.cpp │ │ ├── lmmNimble.R │ │ └── lmmTMB.R │ ├── pump │ │ ├── pumpNimble.R │ │ ├── pumpTMB.R │ │ └── pumpTMB.cpp │ ├── spatial │ │ ├── spatial.cpp │ │ ├── spatialNimble.R │ │ ├── spatialTMB.R │ │ └── spatial_data.R │ └── state-space │ │ ├── thetalog.cpp │ │ ├── thetalog.dat │ │ ├── thetalogNimble.R │ │ └── thetalogTMB.R ├── Makefile ├── MyMakevars_template ├── RELEASE_INSTRUCTIONS ├── TOFIX ├── benchmark.R ├── generateStaticCode.R ├── nimble │ ├── .Rbuildignore │ ├── DESCRIPTION │ ├── INSTALL │ ├── LICENSE │ ├── NAMESPACE │ ├── NOT_IN_TARBALL │ ├── R │ │ ├── .gitignore │ │ ├── BNP_distributions.R │ │ ├── BNP_samplers.R │ │ ├── BUGS_BUGSdecl.R │ │ ├── BUGS_contexts.R │ │ ├── BUGS_getDependencies.R │ │ ├── BUGS_graphNodeMaps.R │ │ ├── BUGS_macros.R │ │ ├── BUGS_mathCompatibility.R │ │ ├── BUGS_model.R │ │ ├── BUGS_modelDef.R │ │ ├── BUGS_nimbleGraph.R │ │ ├── BUGS_readBUGS.R │ │ ├── BUGS_testBUGS.R │ │ ├── BUGS_utils.R │ │ ├── CAR.R │ │ ├── MCEM_build.R │ │ ├── MCMC_RJ.R │ │ ├── MCMC_WAIC.R │ │ ├── MCMC_autoBlock.R │ │ ├── MCMC_build.R │ │ ├── MCMC_configuration.R │ │ ├── MCMC_conjugacy.R │ │ ├── MCMC_derived.R │ │ ├── MCMC_run.R │ │ ├── MCMC_samplers.R │ │ ├── MCMC_utils.R │ │ ├── NF_utils.R │ │ ├── RCfunction_compile.R │ │ ├── RCfunction_core.R │ │ ├── all_utils.R │ │ ├── config.R.in │ │ ├── cppDefs_ADtools.R │ │ ├── cppDefs_BUGSmodel.R │ │ ├── cppDefs_RCfunction.R │ │ ├── cppDefs_core.R │ │ ├── cppDefs_cppProject.R │ │ ├── cppDefs_modelValues.R │ │ ├── cppDefs_namedObjects.R │ │ ├── cppDefs_nimbleFunction.R │ │ ├── cppDefs_nimbleList.R │ │ ├── cppDefs_outputCppFromRparseTree.R │ │ ├── cppDefs_utils.R │ │ ├── cppDefs_variables.R │ │ ├── cppInterfaces_modelValues.R │ │ ├── cppInterfaces_models.R │ │ ├── cppInterfaces_nimbleFunctions.R │ │ ├── cppInterfaces_otherTypes.R │ │ ├── cppInterfaces_utils.R │ │ ├── crossValidation.R │ │ ├── distributions_implementations.R │ │ ├── distributions_inputList.R │ │ ├── distributions_processInputList.R │ │ ├── externalCalls.R │ │ ├── genCpp_RparseTree2exprClasses.R │ │ ├── genCpp_addDebugMarks.R │ │ ├── genCpp_buildIntermediates.R │ │ ├── genCpp_eigenization.R │ │ ├── genCpp_exprClass.R │ │ ├── genCpp_generateCpp.R │ │ ├── genCpp_initSizes.R │ │ ├── genCpp_insertAssertions.R │ │ ├── genCpp_liftMaps.R │ │ ├── genCpp_maps.R │ │ ├── genCpp_operatorLists.R │ │ ├── genCpp_processSpecificCalls.R │ │ ├── genCpp_sizeProcessing.R │ │ ├── genCpp_toEigenize.R │ │ ├── initializeModel.R │ │ ├── makevars.R │ │ ├── miscAlgorithms.R │ │ ├── miscFunctions.R │ │ ├── nimble-package.r │ │ ├── nimbleFunction_Rderivs.R │ │ ├── nimbleFunction_Rexecution.R │ │ ├── nimbleFunction_compile.R │ │ ├── nimbleFunction_core.R │ │ ├── nimbleFunction_keywordProcessing.R │ │ ├── nimbleFunction_nodeFunction.R │ │ ├── nimbleFunction_nodeFunctionNew.R │ │ ├── nimbleFunction_util.R │ │ ├── nimbleList_core.R │ │ ├── nimbleProject.R │ │ ├── normTooling.R │ │ ├── options.R │ │ ├── parameterTransform.R │ │ ├── registration.R │ │ ├── setNimbleInternalFunctions.R │ │ ├── setupMargNodes.R │ │ ├── types_modelValues.R │ │ ├── types_modelValuesAccessor.R │ │ ├── types_modelVariableAccessor.R │ │ ├── types_nimbleFunctionList.R │ │ ├── types_nodeFxnVector.R │ │ ├── types_numericLists.R │ │ ├── types_symbolTable.R │ │ ├── types_util.R │ │ └── zzz.R │ ├── README.md │ ├── cleanup │ ├── cleanup.win │ ├── configure │ ├── configure.ac │ ├── configure.win │ ├── inst │ │ ├── CITATION │ │ ├── COPYRIGHTS │ │ ├── CppCode │ │ │ ├── .gitignore │ │ │ ├── EigenTypedefs.cpp │ │ │ ├── GNUmakefile │ │ │ ├── GNUmakefile_customizeMakeconf │ │ │ ├── Makevars.in │ │ │ ├── ModelClassUtils.cpp │ │ │ ├── NamedObjects.cpp │ │ │ ├── RcppNimbleUtils.cpp │ │ │ ├── RcppUtils.cpp │ │ │ ├── Utils.cpp │ │ │ ├── accessorClasses.cpp │ │ │ ├── customizeMakeconf.R │ │ │ ├── dists.cpp │ │ │ ├── dllFinalizer.cpp │ │ │ ├── eigenUsingClasses.cpp │ │ │ ├── nimDerivs_atomic_PDinverse_logdet.cpp │ │ │ ├── nimDerivs_atomic_backsolve.cpp │ │ │ ├── nimDerivs_atomic_cache.cpp │ │ │ ├── nimDerivs_atomic_cholesky.cpp │ │ │ ├── nimDerivs_atomic_classes.cpp │ │ │ ├── nimDerivs_atomic_classes_temp.cpp │ │ │ ├── nimDerivs_atomic_dyn_ind.cpp │ │ │ ├── nimDerivs_atomic_forwardsolve.cpp │ │ │ ├── nimDerivs_atomic_log_pow_int.cpp │ │ │ ├── nimDerivs_atomic_matinverse.cpp │ │ │ ├── nimDerivs_atomic_matmult.cpp │ │ │ ├── nimDerivs_atomic_pow_int.cpp │ │ │ ├── nimDerivs_atomic_probit.cpp │ │ │ ├── nimDerivs_atomic_solve_base.cpp │ │ │ ├── nimDerivs_atomic_solve_generic.cpp │ │ │ ├── nimDerivs_atomic_zround.cpp │ │ │ ├── nimDists.cpp │ │ │ ├── nimIntegrate.cpp │ │ │ ├── nimOptim.cpp │ │ │ ├── nimbleCppAD.cpp │ │ │ ├── nimbleGraph.cpp │ │ │ ├── nodeFun.cpp │ │ │ ├── predefinedNimbleLists.cpp │ │ │ ├── removeCustomizedMakeconf.R │ │ │ └── smartPtrs.cpp │ │ ├── NEWS.md │ │ ├── classic-bugs │ │ │ ├── LICENSE │ │ │ ├── R │ │ │ │ ├── Rcheck.R │ │ │ │ ├── bench.R │ │ │ │ └── check.R │ │ │ ├── ReadMe │ │ │ ├── other │ │ │ │ └── dipper │ │ │ │ │ ├── dipper-data.R │ │ │ │ │ └── dipper.bug │ │ │ ├── vol1 │ │ │ │ ├── blocker │ │ │ │ │ ├── ReadMe │ │ │ │ │ ├── bench-test1.R │ │ │ │ │ ├── bench-test2.R │ │ │ │ │ ├── bench-test3.R │ │ │ │ │ ├── blocker-data.R │ │ │ │ │ ├── blocker-init.R │ │ │ │ │ ├── blocker.bug │ │ │ │ │ ├── blockert-init.R │ │ │ │ │ ├── blockert.bug │ │ │ │ │ ├── blockht-data.R │ │ │ │ │ ├── blockht.bug │ │ │ │ │ ├── notest2.cmd │ │ │ │ │ ├── notest3.cmd │ │ │ │ │ ├── test1.R │ │ │ │ │ └── test1.cmd │ │ │ │ ├── bones │ │ │ │ │ ├── bench-test1.R │ │ │ │ │ ├── bones-data.R │ │ │ │ │ ├── bones-init.R │ │ │ │ │ ├── bones.bug │ │ │ │ │ ├── test1.R │ │ │ │ │ └── test1.cmd │ │ │ │ ├── dyes │ │ │ │ │ ├── bench-test1.R │ │ │ │ │ ├── dyes-data.R │ │ │ │ │ ├── dyes-init.R │ │ │ │ │ ├── dyes.bug │ │ │ │ │ ├── test1.R │ │ │ │ │ └── test1.cmd │ │ │ │ ├── epil │ │ │ │ │ ├── bench-test1.R │ │ │ │ │ ├── bench-test2.R │ │ │ │ │ ├── epil-data.R │ │ │ │ │ ├── epil-inits.R │ │ │ │ │ ├── epil2.bug │ │ │ │ │ ├── epil3.bug │ │ │ │ │ ├── test1.R │ │ │ │ │ ├── test1.cmd │ │ │ │ │ ├── test2.R │ │ │ │ │ └── test2.cmd │ │ │ │ ├── equiv │ │ │ │ │ ├── ReadMe │ │ │ │ │ ├── bench-test1.R │ │ │ │ │ ├── bench-test2.R │ │ │ │ │ ├── equiv-data.R │ │ │ │ │ ├── equiv-init.R │ │ │ │ │ ├── equiv.bug │ │ │ │ │ ├── equivmiss-data.R │ │ │ │ │ ├── test1.R │ │ │ │ │ ├── test1.cmd │ │ │ │ │ └── test2.cmd │ │ │ │ ├── inhaler │ │ │ │ │ ├── bench-test1.R │ │ │ │ │ ├── inhaler-data.R │ │ │ │ │ ├── inhaler-inits.R │ │ │ │ │ ├── inhaler.bug │ │ │ │ │ ├── inhaler.cmd │ │ │ │ │ ├── test1.R │ │ │ │ │ └── test1.cmd │ │ │ │ ├── kidney │ │ │ │ │ ├── ReadMe │ │ │ │ │ ├── bench-test1.R │ │ │ │ │ ├── kidney-data.R │ │ │ │ │ ├── kidney-init.R │ │ │ │ │ ├── kidney.bug │ │ │ │ │ └── notest1.cmd │ │ │ │ ├── leuk │ │ │ │ │ ├── bench-test1.R │ │ │ │ │ ├── leuk-data.R │ │ │ │ │ ├── leuk-init.R │ │ │ │ │ ├── leuk-poisson.bug │ │ │ │ │ ├── leuk-s.dat │ │ │ │ │ ├── leuk.bug │ │ │ │ │ ├── leuk.in │ │ │ │ │ ├── leukfr-s.dat │ │ │ │ │ ├── leukfr.bug │ │ │ │ │ ├── leukfr.dat │ │ │ │ │ ├── leukfr.in │ │ │ │ │ ├── test1.R │ │ │ │ │ └── test1.cmd │ │ │ │ ├── line │ │ │ │ │ ├── bench-test1.R │ │ │ │ │ ├── line-data.R │ │ │ │ │ ├── line-inits.R │ │ │ │ │ ├── line.bug │ │ │ │ │ ├── test1.R │ │ │ │ │ └── test1.cmd │ │ │ │ ├── litters │ │ │ │ │ ├── ReadMe │ │ │ │ │ ├── bench-test1.R │ │ │ │ │ ├── litters-data.R │ │ │ │ │ ├── litters-init.R │ │ │ │ │ ├── litters.bug │ │ │ │ │ ├── test1.R │ │ │ │ │ └── test1.cmd │ │ │ │ ├── lsat │ │ │ │ │ ├── bench-test1.R │ │ │ │ │ ├── bench-test2.R │ │ │ │ │ ├── lsat-data.R │ │ │ │ │ ├── lsat-init.R │ │ │ │ │ ├── lsat.bug │ │ │ │ │ ├── lsat.dat │ │ │ │ │ ├── lsat2-init.R │ │ │ │ │ ├── lsat2.bug │ │ │ │ │ ├── test1.R │ │ │ │ │ ├── test1.cmd │ │ │ │ │ ├── test2.R │ │ │ │ │ └── test2.cmd │ │ │ │ ├── mice │ │ │ │ │ ├── bench-test1.R │ │ │ │ │ ├── mice-data.R │ │ │ │ │ ├── mice-init.R │ │ │ │ │ ├── mice.bug │ │ │ │ │ ├── test1.R │ │ │ │ │ └── test1.cmd │ │ │ │ ├── oxford │ │ │ │ │ ├── ReadMe │ │ │ │ │ ├── bench-test1.R │ │ │ │ │ ├── oxford-data.R │ │ │ │ │ ├── oxford-init.R │ │ │ │ │ ├── oxford.bug │ │ │ │ │ ├── oxford.dat │ │ │ │ │ ├── test1.R │ │ │ │ │ └── test1.cmd │ │ │ │ ├── pump │ │ │ │ │ ├── bench-test1.R │ │ │ │ │ ├── pump-data.R │ │ │ │ │ ├── pump-init.R │ │ │ │ │ ├── pump.bug │ │ │ │ │ ├── test1.R │ │ │ │ │ └── test1.cmd │ │ │ │ ├── rats │ │ │ │ │ ├── bench-test1.R │ │ │ │ │ ├── bench-test2.R │ │ │ │ │ ├── rats-data.R │ │ │ │ │ ├── rats-init.R │ │ │ │ │ ├── rats.bug │ │ │ │ │ ├── ratsmiss-data.R │ │ │ │ │ ├── test1.R │ │ │ │ │ ├── test1.cmd │ │ │ │ │ └── test2.cmd │ │ │ │ ├── salm │ │ │ │ │ ├── bench-test1.R │ │ │ │ │ ├── bench-test2.R │ │ │ │ │ ├── salm-data.R │ │ │ │ │ ├── salm-init.R │ │ │ │ │ ├── salm-pareto.bug │ │ │ │ │ ├── salm.bug │ │ │ │ │ ├── test1.R │ │ │ │ │ ├── test1.cmd │ │ │ │ │ ├── test2.R │ │ │ │ │ └── test2.cmd │ │ │ │ └── seeds │ │ │ │ │ ├── bench-test1.R │ │ │ │ │ ├── bench-test2.R │ │ │ │ │ ├── bench-test3.R │ │ │ │ │ ├── bench-test4.R │ │ │ │ │ ├── bench-test5.R │ │ │ │ │ ├── seeds-data.R │ │ │ │ │ ├── seeds-init.R │ │ │ │ │ ├── seeds.bug │ │ │ │ │ ├── seedspar.bug │ │ │ │ │ ├── seedssig.bug │ │ │ │ │ ├── seedsuni.bug │ │ │ │ │ ├── seedszro.bug │ │ │ │ │ ├── test1.R │ │ │ │ │ ├── test1.cmd │ │ │ │ │ ├── test2.R │ │ │ │ │ ├── test2.cmd │ │ │ │ │ ├── test3.R │ │ │ │ │ ├── test3.cmd │ │ │ │ │ ├── test4.R │ │ │ │ │ ├── test4.cmd │ │ │ │ │ ├── test5.R │ │ │ │ │ └── test5.cmd │ │ │ └── vol2 │ │ │ │ ├── air │ │ │ │ ├── ReadMe │ │ │ │ ├── air-data.R │ │ │ │ ├── air-inits.R │ │ │ │ ├── air.bug │ │ │ │ ├── bench-test1.R │ │ │ │ ├── bench.R │ │ │ │ └── notest1.cmd │ │ │ │ ├── alli │ │ │ │ ├── alli-data.R │ │ │ │ ├── alli-inits.R │ │ │ │ ├── alli.bug │ │ │ │ ├── bench-test1.R │ │ │ │ ├── test1.R │ │ │ │ └── test1.cmd │ │ │ │ ├── asia │ │ │ │ ├── asia-data.R │ │ │ │ ├── asia.bug │ │ │ │ ├── asia2-data.R │ │ │ │ ├── asia2.bug │ │ │ │ ├── bench-test1.R │ │ │ │ ├── bench-test2.R │ │ │ │ ├── test1.R │ │ │ │ ├── test1.cmd │ │ │ │ ├── test2.R │ │ │ │ └── test2.cmd │ │ │ │ ├── beetles │ │ │ │ ├── beetles-cloglog.bug │ │ │ │ ├── beetles-data.R │ │ │ │ ├── beetles-inits.R │ │ │ │ ├── beetles-logit.bug │ │ │ │ ├── beetles-probit.bug │ │ │ │ ├── bench-test1.R │ │ │ │ ├── bench-test2.R │ │ │ │ ├── bench-test3.R │ │ │ │ ├── test1.R │ │ │ │ ├── test1.cmd │ │ │ │ ├── test2.R │ │ │ │ ├── test2.cmd │ │ │ │ ├── test3.R │ │ │ │ └── test3.cmd │ │ │ │ ├── biops │ │ │ │ ├── ReadMe │ │ │ │ ├── bench-test1.R │ │ │ │ ├── biops-data.R │ │ │ │ ├── biops-inits.R │ │ │ │ ├── biops.bug │ │ │ │ ├── test1.R │ │ │ │ └── test1.cmd │ │ │ │ ├── birats │ │ │ │ ├── bench-test1.R │ │ │ │ ├── bench-test2.R │ │ │ │ ├── bench-test3.R │ │ │ │ ├── bench-test4.R │ │ │ │ ├── birats-data.R │ │ │ │ ├── birats-inits.R │ │ │ │ ├── birats1.bug │ │ │ │ ├── birats2.bug │ │ │ │ ├── birats3.bug │ │ │ │ ├── birats4.bug │ │ │ │ ├── test1.R │ │ │ │ ├── test1.cmd │ │ │ │ ├── test2.R │ │ │ │ ├── test2.cmd │ │ │ │ ├── test3.R │ │ │ │ ├── test3.cmd │ │ │ │ ├── test4.R │ │ │ │ └── test4.cmd │ │ │ │ ├── cervix │ │ │ │ ├── ReadMe │ │ │ │ ├── cervix-data.R │ │ │ │ ├── cervix-inits.R │ │ │ │ ├── cervix.bug │ │ │ │ ├── test1.R │ │ │ │ └── test1.cmd │ │ │ │ ├── dugongs │ │ │ │ ├── bench-test1.R │ │ │ │ ├── dugongs-data.R │ │ │ │ ├── dugongs-inits.R │ │ │ │ ├── dugongs.bug │ │ │ │ ├── test1.R │ │ │ │ └── test1.cmd │ │ │ │ ├── eyes │ │ │ │ ├── ReadMe │ │ │ │ ├── bench-test1.R │ │ │ │ ├── eyes-data.R │ │ │ │ ├── eyes-inits.R │ │ │ │ ├── eyes.bug │ │ │ │ ├── eyes.dat │ │ │ │ ├── eyes2.bug │ │ │ │ ├── notest2.cmd │ │ │ │ ├── test1.R │ │ │ │ └── test1.cmd │ │ │ │ ├── hearts │ │ │ │ ├── bench-test1.R │ │ │ │ ├── hearts-data.R │ │ │ │ ├── hearts-inits.R │ │ │ │ ├── hearts.bug │ │ │ │ ├── hearts.dat │ │ │ │ ├── test1.R │ │ │ │ └── test1.cmd │ │ │ │ ├── ice │ │ │ │ ├── ReadMe │ │ │ │ ├── bench-test1.R │ │ │ │ ├── bench.R │ │ │ │ ├── ice-data.R │ │ │ │ ├── ice-inits.R │ │ │ │ ├── icear.bug │ │ │ │ └── test1.cmd │ │ │ │ ├── jaw │ │ │ │ ├── ReadMe │ │ │ │ ├── bench-test1.R │ │ │ │ ├── bench-test2.R │ │ │ │ ├── bench-test3.R │ │ │ │ ├── jaw-constant.bug │ │ │ │ ├── jaw-data.R │ │ │ │ ├── jaw-inits.R │ │ │ │ ├── jaw-linear.bug │ │ │ │ ├── jaw-quadratic.bug │ │ │ │ ├── test1.R │ │ │ │ ├── test1.cmd │ │ │ │ ├── test2.R │ │ │ │ ├── test2.cmd │ │ │ │ ├── test3.R │ │ │ │ └── test3.cmd │ │ │ │ ├── orange │ │ │ │ ├── bench-test1.R │ │ │ │ ├── bench-test2.R │ │ │ │ ├── mvotree-data.R │ │ │ │ ├── mvotree-inits.R │ │ │ │ ├── mvotree.bug │ │ │ │ ├── orange-data.R │ │ │ │ ├── orange-inits.R │ │ │ │ ├── otree.bug │ │ │ │ ├── otree.dat │ │ │ │ ├── otree.in │ │ │ │ ├── test1.R │ │ │ │ ├── test1.cmd │ │ │ │ ├── test2.R │ │ │ │ └── test2.cmd │ │ │ │ ├── pigs │ │ │ │ ├── bench-test1.R │ │ │ │ ├── pigs-data.R │ │ │ │ ├── pigs-inits.R │ │ │ │ ├── pigs.bug │ │ │ │ ├── test1.R │ │ │ │ └── test1.cmd │ │ │ │ ├── schools │ │ │ │ ├── bench-test1.R │ │ │ │ ├── schools-data.R │ │ │ │ ├── schools-inits.R │ │ │ │ ├── schools.bug │ │ │ │ ├── schools.dat │ │ │ │ ├── test.bug │ │ │ │ ├── test1.R │ │ │ │ └── test1.cmd │ │ │ │ └── stagnant │ │ │ │ ├── ReadMe │ │ │ │ ├── bench-test1.R │ │ │ │ ├── bench-test2.R │ │ │ │ ├── notest3.cmd │ │ │ │ ├── notest4.cmd │ │ │ │ ├── stagnant-data.R │ │ │ │ ├── stagnant-inits1.R │ │ │ │ ├── stagnant-inits2.R │ │ │ │ ├── stagnant-inits3.R │ │ │ │ ├── stagnant-inits4.R │ │ │ │ ├── stagnant.bug │ │ │ │ ├── stagnant2.bug │ │ │ │ ├── test1.R │ │ │ │ ├── test1.cmd │ │ │ │ ├── test2.R │ │ │ │ └── test2.cmd │ │ ├── include │ │ │ ├── Eigen │ │ │ │ ├── Cholesky │ │ │ │ ├── CholmodSupport │ │ │ │ ├── Core │ │ │ │ ├── Dense │ │ │ │ ├── Eigen │ │ │ │ ├── Eigenvalues │ │ │ │ ├── Geometry │ │ │ │ ├── Householder │ │ │ │ ├── IterativeLinearSolvers │ │ │ │ ├── Jacobi │ │ │ │ ├── KLUSupport │ │ │ │ ├── LU │ │ │ │ ├── MetisSupport │ │ │ │ ├── OrderingMethods │ │ │ │ ├── PaStiXSupport │ │ │ │ ├── PardisoSupport │ │ │ │ ├── QR │ │ │ │ ├── QtAlignedMalloc │ │ │ │ ├── SPQRSupport │ │ │ │ ├── SVD │ │ │ │ ├── Sparse │ │ │ │ ├── SparseCholesky │ │ │ │ ├── SparseCore │ │ │ │ ├── SparseLU │ │ │ │ ├── SparseQR │ │ │ │ ├── StdDeque │ │ │ │ ├── StdList │ │ │ │ ├── StdVector │ │ │ │ ├── SuperLUSupport │ │ │ │ ├── UmfPackSupport │ │ │ │ └── src │ │ │ │ │ ├── Cholesky │ │ │ │ │ ├── LDLT.h │ │ │ │ │ ├── LLT.h │ │ │ │ │ └── LLT_LAPACKE.h │ │ │ │ │ ├── CholmodSupport │ │ │ │ │ └── CholmodSupport.h │ │ │ │ │ ├── Core │ │ │ │ │ ├── ArithmeticSequence.h │ │ │ │ │ ├── Array.h │ │ │ │ │ ├── ArrayBase.h │ │ │ │ │ ├── ArrayWrapper.h │ │ │ │ │ ├── Assign.h │ │ │ │ │ ├── AssignEvaluator.h │ │ │ │ │ ├── Assign_MKL.h │ │ │ │ │ ├── BandMatrix.h │ │ │ │ │ ├── Block.h │ │ │ │ │ ├── BooleanRedux.h │ │ │ │ │ ├── CommaInitializer.h │ │ │ │ │ ├── ConditionEstimator.h │ │ │ │ │ ├── CoreEvaluators.h │ │ │ │ │ ├── CoreIterators.h │ │ │ │ │ ├── CwiseBinaryOp.h │ │ │ │ │ ├── CwiseNullaryOp.h │ │ │ │ │ ├── CwiseTernaryOp.h │ │ │ │ │ ├── CwiseUnaryOp.h │ │ │ │ │ ├── CwiseUnaryView.h │ │ │ │ │ ├── DenseBase.h │ │ │ │ │ ├── DenseCoeffsBase.h │ │ │ │ │ ├── DenseStorage.h │ │ │ │ │ ├── Diagonal.h │ │ │ │ │ ├── DiagonalMatrix.h │ │ │ │ │ ├── DiagonalProduct.h │ │ │ │ │ ├── Dot.h │ │ │ │ │ ├── EigenBase.h │ │ │ │ │ ├── ForceAlignedAccess.h │ │ │ │ │ ├── Fuzzy.h │ │ │ │ │ ├── GeneralProduct.h │ │ │ │ │ ├── GenericPacketMath.h │ │ │ │ │ ├── GlobalFunctions.h │ │ │ │ │ ├── IO.h │ │ │ │ │ ├── IndexedView.h │ │ │ │ │ ├── Inverse.h │ │ │ │ │ ├── Map.h │ │ │ │ │ ├── MapBase.h │ │ │ │ │ ├── MathFunctions.h │ │ │ │ │ ├── MathFunctionsImpl.h │ │ │ │ │ ├── Matrix.h │ │ │ │ │ ├── MatrixBase.h │ │ │ │ │ ├── NestByValue.h │ │ │ │ │ ├── NoAlias.h │ │ │ │ │ ├── NumTraits.h │ │ │ │ │ ├── PartialReduxEvaluator.h │ │ │ │ │ ├── PermutationMatrix.h │ │ │ │ │ ├── PlainObjectBase.h │ │ │ │ │ ├── Product.h │ │ │ │ │ ├── ProductEvaluators.h │ │ │ │ │ ├── Random.h │ │ │ │ │ ├── Redux.h │ │ │ │ │ ├── Ref.h │ │ │ │ │ ├── Replicate.h │ │ │ │ │ ├── Reshaped.h │ │ │ │ │ ├── ReturnByValue.h │ │ │ │ │ ├── Reverse.h │ │ │ │ │ ├── Select.h │ │ │ │ │ ├── SelfAdjointView.h │ │ │ │ │ ├── SelfCwiseBinaryOp.h │ │ │ │ │ ├── Solve.h │ │ │ │ │ ├── SolveTriangular.h │ │ │ │ │ ├── SolverBase.h │ │ │ │ │ ├── StableNorm.h │ │ │ │ │ ├── StlIterators.h │ │ │ │ │ ├── Stride.h │ │ │ │ │ ├── Swap.h │ │ │ │ │ ├── Transpose.h │ │ │ │ │ ├── Transpositions.h │ │ │ │ │ ├── TriangularMatrix.h │ │ │ │ │ ├── VectorBlock.h │ │ │ │ │ ├── VectorwiseOp.h │ │ │ │ │ ├── Visitor.h │ │ │ │ │ ├── arch │ │ │ │ │ │ ├── AVX │ │ │ │ │ │ │ ├── Complex.h │ │ │ │ │ │ │ ├── MathFunctions.h │ │ │ │ │ │ │ ├── PacketMath.h │ │ │ │ │ │ │ └── TypeCasting.h │ │ │ │ │ │ ├── AVX512 │ │ │ │ │ │ │ ├── Complex.h │ │ │ │ │ │ │ ├── MathFunctions.h │ │ │ │ │ │ │ ├── PacketMath.h │ │ │ │ │ │ │ └── TypeCasting.h │ │ │ │ │ │ ├── AltiVec │ │ │ │ │ │ │ ├── Complex.h │ │ │ │ │ │ │ ├── MathFunctions.h │ │ │ │ │ │ │ ├── MatrixProduct.h │ │ │ │ │ │ │ ├── MatrixProductCommon.h │ │ │ │ │ │ │ ├── MatrixProductMMA.h │ │ │ │ │ │ │ └── PacketMath.h │ │ │ │ │ │ ├── CUDA │ │ │ │ │ │ │ └── Complex.h │ │ │ │ │ │ ├── Default │ │ │ │ │ │ │ ├── BFloat16.h │ │ │ │ │ │ │ ├── ConjHelper.h │ │ │ │ │ │ │ ├── GenericPacketMathFunctions.h │ │ │ │ │ │ │ ├── GenericPacketMathFunctionsFwd.h │ │ │ │ │ │ │ ├── Half.h │ │ │ │ │ │ │ ├── Settings.h │ │ │ │ │ │ │ └── TypeCasting.h │ │ │ │ │ │ ├── GPU │ │ │ │ │ │ │ ├── MathFunctions.h │ │ │ │ │ │ │ ├── PacketMath.h │ │ │ │ │ │ │ └── TypeCasting.h │ │ │ │ │ │ ├── HIP │ │ │ │ │ │ │ └── hcc │ │ │ │ │ │ │ │ └── math_constants.h │ │ │ │ │ │ ├── MSA │ │ │ │ │ │ │ ├── Complex.h │ │ │ │ │ │ │ ├── MathFunctions.h │ │ │ │ │ │ │ └── PacketMath.h │ │ │ │ │ │ ├── NEON │ │ │ │ │ │ │ ├── Complex.h │ │ │ │ │ │ │ ├── GeneralBlockPanelKernel.h │ │ │ │ │ │ │ ├── MathFunctions.h │ │ │ │ │ │ │ ├── PacketMath.h │ │ │ │ │ │ │ └── TypeCasting.h │ │ │ │ │ │ ├── SSE │ │ │ │ │ │ │ ├── Complex.h │ │ │ │ │ │ │ ├── MathFunctions.h │ │ │ │ │ │ │ ├── PacketMath.h │ │ │ │ │ │ │ └── TypeCasting.h │ │ │ │ │ │ ├── SVE │ │ │ │ │ │ │ ├── MathFunctions.h │ │ │ │ │ │ │ ├── PacketMath.h │ │ │ │ │ │ │ └── TypeCasting.h │ │ │ │ │ │ ├── SYCL │ │ │ │ │ │ │ ├── InteropHeaders.h │ │ │ │ │ │ │ ├── MathFunctions.h │ │ │ │ │ │ │ ├── PacketMath.h │ │ │ │ │ │ │ ├── SyclMemoryModel.h │ │ │ │ │ │ │ └── TypeCasting.h │ │ │ │ │ │ └── ZVector │ │ │ │ │ │ │ ├── Complex.h │ │ │ │ │ │ │ ├── MathFunctions.h │ │ │ │ │ │ │ └── PacketMath.h │ │ │ │ │ ├── functors │ │ │ │ │ │ ├── AssignmentFunctors.h │ │ │ │ │ │ ├── BinaryFunctors.h │ │ │ │ │ │ ├── NullaryFunctors.h │ │ │ │ │ │ ├── StlFunctors.h │ │ │ │ │ │ ├── TernaryFunctors.h │ │ │ │ │ │ └── UnaryFunctors.h │ │ │ │ │ ├── products │ │ │ │ │ │ ├── GeneralBlockPanelKernel.h │ │ │ │ │ │ ├── GeneralMatrixMatrix.h │ │ │ │ │ │ ├── GeneralMatrixMatrixTriangular.h │ │ │ │ │ │ ├── GeneralMatrixMatrixTriangular_BLAS.h │ │ │ │ │ │ ├── GeneralMatrixMatrix_BLAS.h │ │ │ │ │ │ ├── GeneralMatrixVector.h │ │ │ │ │ │ ├── GeneralMatrixVector_BLAS.h │ │ │ │ │ │ ├── Parallelizer.h │ │ │ │ │ │ ├── SelfadjointMatrixMatrix.h │ │ │ │ │ │ ├── SelfadjointMatrixMatrix_BLAS.h │ │ │ │ │ │ ├── SelfadjointMatrixVector.h │ │ │ │ │ │ ├── SelfadjointMatrixVector_BLAS.h │ │ │ │ │ │ ├── SelfadjointProduct.h │ │ │ │ │ │ ├── SelfadjointRank2Update.h │ │ │ │ │ │ ├── TriangularMatrixMatrix.h │ │ │ │ │ │ ├── TriangularMatrixMatrix_BLAS.h │ │ │ │ │ │ ├── TriangularMatrixVector.h │ │ │ │ │ │ ├── TriangularMatrixVector_BLAS.h │ │ │ │ │ │ ├── TriangularSolverMatrix.h │ │ │ │ │ │ ├── TriangularSolverMatrix_BLAS.h │ │ │ │ │ │ └── TriangularSolverVector.h │ │ │ │ │ └── util │ │ │ │ │ │ ├── BlasUtil.h │ │ │ │ │ │ ├── ConfigureVectorization.h │ │ │ │ │ │ ├── Constants.h │ │ │ │ │ │ ├── DisableStupidWarnings.h │ │ │ │ │ │ ├── ForwardDeclarations.h │ │ │ │ │ │ ├── IndexedViewHelper.h │ │ │ │ │ │ ├── IntegralConstant.h │ │ │ │ │ │ ├── MKL_support.h │ │ │ │ │ │ ├── Macros.h │ │ │ │ │ │ ├── Memory.h │ │ │ │ │ │ ├── Meta.h │ │ │ │ │ │ ├── NonMPL2.h │ │ │ │ │ │ ├── ReenableStupidWarnings.h │ │ │ │ │ │ ├── ReshapedHelper.h │ │ │ │ │ │ ├── StaticAssert.h │ │ │ │ │ │ ├── SymbolicIndex.h │ │ │ │ │ │ └── XprHelper.h │ │ │ │ │ ├── Eigenvalues │ │ │ │ │ ├── ComplexEigenSolver.h │ │ │ │ │ ├── ComplexSchur.h │ │ │ │ │ ├── ComplexSchur_LAPACKE.h │ │ │ │ │ ├── EigenSolver.h │ │ │ │ │ ├── GeneralizedEigenSolver.h │ │ │ │ │ ├── GeneralizedSelfAdjointEigenSolver.h │ │ │ │ │ ├── HessenbergDecomposition.h │ │ │ │ │ ├── MatrixBaseEigenvalues.h │ │ │ │ │ ├── RealQZ.h │ │ │ │ │ ├── RealSchur.h │ │ │ │ │ ├── RealSchur_LAPACKE.h │ │ │ │ │ ├── SelfAdjointEigenSolver.h │ │ │ │ │ ├── SelfAdjointEigenSolver_LAPACKE.h │ │ │ │ │ └── Tridiagonalization.h │ │ │ │ │ ├── Geometry │ │ │ │ │ ├── AlignedBox.h │ │ │ │ │ ├── AngleAxis.h │ │ │ │ │ ├── EulerAngles.h │ │ │ │ │ ├── Homogeneous.h │ │ │ │ │ ├── Hyperplane.h │ │ │ │ │ ├── OrthoMethods.h │ │ │ │ │ ├── ParametrizedLine.h │ │ │ │ │ ├── Quaternion.h │ │ │ │ │ ├── Rotation2D.h │ │ │ │ │ ├── RotationBase.h │ │ │ │ │ ├── Scaling.h │ │ │ │ │ ├── Transform.h │ │ │ │ │ ├── Translation.h │ │ │ │ │ ├── Umeyama.h │ │ │ │ │ └── arch │ │ │ │ │ │ └── Geometry_SIMD.h │ │ │ │ │ ├── Householder │ │ │ │ │ ├── BlockHouseholder.h │ │ │ │ │ ├── Householder.h │ │ │ │ │ └── HouseholderSequence.h │ │ │ │ │ ├── IterativeLinearSolvers │ │ │ │ │ ├── BasicPreconditioners.h │ │ │ │ │ ├── BiCGSTAB.h │ │ │ │ │ ├── ConjugateGradient.h │ │ │ │ │ ├── IncompleteCholesky.h │ │ │ │ │ ├── IncompleteLUT.h │ │ │ │ │ ├── IterativeSolverBase.h │ │ │ │ │ ├── LeastSquareConjugateGradient.h │ │ │ │ │ └── SolveWithGuess.h │ │ │ │ │ ├── Jacobi │ │ │ │ │ └── Jacobi.h │ │ │ │ │ ├── KLUSupport │ │ │ │ │ └── KLUSupport.h │ │ │ │ │ ├── LU │ │ │ │ │ ├── Determinant.h │ │ │ │ │ ├── FullPivLU.h │ │ │ │ │ ├── InverseImpl.h │ │ │ │ │ ├── PartialPivLU.h │ │ │ │ │ ├── PartialPivLU_LAPACKE.h │ │ │ │ │ └── arch │ │ │ │ │ │ └── InverseSize4.h │ │ │ │ │ ├── MetisSupport │ │ │ │ │ └── MetisSupport.h │ │ │ │ │ ├── OrderingMethods │ │ │ │ │ ├── Amd.h │ │ │ │ │ ├── Eigen_Colamd.h │ │ │ │ │ └── Ordering.h │ │ │ │ │ ├── PaStiXSupport │ │ │ │ │ └── PaStiXSupport.h │ │ │ │ │ ├── PardisoSupport │ │ │ │ │ └── PardisoSupport.h │ │ │ │ │ ├── QR │ │ │ │ │ ├── ColPivHouseholderQR.h │ │ │ │ │ ├── ColPivHouseholderQR_LAPACKE.h │ │ │ │ │ ├── CompleteOrthogonalDecomposition.h │ │ │ │ │ ├── FullPivHouseholderQR.h │ │ │ │ │ ├── HouseholderQR.h │ │ │ │ │ └── HouseholderQR_LAPACKE.h │ │ │ │ │ ├── SPQRSupport │ │ │ │ │ └── SuiteSparseQRSupport.h │ │ │ │ │ ├── SVD │ │ │ │ │ ├── BDCSVD.h │ │ │ │ │ ├── JacobiSVD.h │ │ │ │ │ ├── JacobiSVD_LAPACKE.h │ │ │ │ │ ├── SVDBase.h │ │ │ │ │ └── UpperBidiagonalization.h │ │ │ │ │ ├── SparseCholesky │ │ │ │ │ ├── SimplicialCholesky.h │ │ │ │ │ └── SimplicialCholesky_impl.h │ │ │ │ │ ├── SparseCore │ │ │ │ │ ├── AmbiVector.h │ │ │ │ │ ├── CompressedStorage.h │ │ │ │ │ ├── ConservativeSparseSparseProduct.h │ │ │ │ │ ├── MappedSparseMatrix.h │ │ │ │ │ ├── SparseAssign.h │ │ │ │ │ ├── SparseBlock.h │ │ │ │ │ ├── SparseColEtree.h │ │ │ │ │ ├── SparseCompressedBase.h │ │ │ │ │ ├── SparseCwiseBinaryOp.h │ │ │ │ │ ├── SparseCwiseUnaryOp.h │ │ │ │ │ ├── SparseDenseProduct.h │ │ │ │ │ ├── SparseDiagonalProduct.h │ │ │ │ │ ├── SparseDot.h │ │ │ │ │ ├── SparseFuzzy.h │ │ │ │ │ ├── SparseMap.h │ │ │ │ │ ├── SparseMatrix.h │ │ │ │ │ ├── SparseMatrixBase.h │ │ │ │ │ ├── SparsePermutation.h │ │ │ │ │ ├── SparseProduct.h │ │ │ │ │ ├── SparseRedux.h │ │ │ │ │ ├── SparseRef.h │ │ │ │ │ ├── SparseSelfAdjointView.h │ │ │ │ │ ├── SparseSolverBase.h │ │ │ │ │ ├── SparseSparseProductWithPruning.h │ │ │ │ │ ├── SparseTranspose.h │ │ │ │ │ ├── SparseTriangularView.h │ │ │ │ │ ├── SparseUtil.h │ │ │ │ │ ├── SparseVector.h │ │ │ │ │ ├── SparseView.h │ │ │ │ │ └── TriangularSolver.h │ │ │ │ │ ├── SparseLU │ │ │ │ │ ├── SparseLU.h │ │ │ │ │ ├── SparseLUImpl.h │ │ │ │ │ ├── SparseLU_Memory.h │ │ │ │ │ ├── SparseLU_Structs.h │ │ │ │ │ ├── SparseLU_SupernodalMatrix.h │ │ │ │ │ ├── SparseLU_Utils.h │ │ │ │ │ ├── SparseLU_column_bmod.h │ │ │ │ │ ├── SparseLU_column_dfs.h │ │ │ │ │ ├── SparseLU_copy_to_ucol.h │ │ │ │ │ ├── SparseLU_gemm_kernel.h │ │ │ │ │ ├── SparseLU_heap_relax_snode.h │ │ │ │ │ ├── SparseLU_kernel_bmod.h │ │ │ │ │ ├── SparseLU_panel_bmod.h │ │ │ │ │ ├── SparseLU_panel_dfs.h │ │ │ │ │ ├── SparseLU_pivotL.h │ │ │ │ │ ├── SparseLU_pruneL.h │ │ │ │ │ └── SparseLU_relax_snode.h │ │ │ │ │ ├── SparseQR │ │ │ │ │ └── SparseQR.h │ │ │ │ │ ├── StlSupport │ │ │ │ │ ├── StdDeque.h │ │ │ │ │ ├── StdList.h │ │ │ │ │ ├── StdVector.h │ │ │ │ │ └── details.h │ │ │ │ │ ├── SuperLUSupport │ │ │ │ │ └── SuperLUSupport.h │ │ │ │ │ ├── UmfPackSupport │ │ │ │ │ └── UmfPackSupport.h │ │ │ │ │ ├── misc │ │ │ │ │ ├── Image.h │ │ │ │ │ ├── Kernel.h │ │ │ │ │ ├── RealSvd2x2.h │ │ │ │ │ ├── blas.h │ │ │ │ │ ├── lapack.h │ │ │ │ │ ├── lapacke.h │ │ │ │ │ └── lapacke_mangling.h │ │ │ │ │ └── plugins │ │ │ │ │ ├── ArrayCwiseBinaryOps.h │ │ │ │ │ ├── ArrayCwiseUnaryOps.h │ │ │ │ │ ├── BlockMethods.h │ │ │ │ │ ├── CommonCwiseBinaryOps.h │ │ │ │ │ ├── CommonCwiseUnaryOps.h │ │ │ │ │ ├── IndexedViewMethods.h │ │ │ │ │ ├── MatrixCwiseBinaryOps.h │ │ │ │ │ ├── MatrixCwiseUnaryOps.h │ │ │ │ │ └── ReshapedMethods.h │ │ │ ├── ad.hpp │ │ │ ├── atomic_index.hpp │ │ │ ├── cppad │ │ │ │ ├── COPYING │ │ │ │ ├── base_require.hpp │ │ │ │ ├── configure.hpp │ │ │ │ ├── core │ │ │ │ │ ├── abort_recording.hpp │ │ │ │ │ ├── abs.hpp │ │ │ │ │ ├── abs_normal_fun.hpp │ │ │ │ │ ├── ad.hpp │ │ │ │ │ ├── ad_assign.hpp │ │ │ │ │ ├── ad_binary.hpp │ │ │ │ │ ├── ad_ctor.hpp │ │ │ │ │ ├── ad_fun.hpp │ │ │ │ │ ├── ad_fun.omh │ │ │ │ │ ├── ad_io.hpp │ │ │ │ │ ├── ad_to_string.hpp │ │ │ │ │ ├── ad_type.hpp │ │ │ │ │ ├── ad_valued.hpp │ │ │ │ │ ├── add.hpp │ │ │ │ │ ├── add_eq.hpp │ │ │ │ │ ├── arithmetic.hpp │ │ │ │ │ ├── atan2.hpp │ │ │ │ │ ├── atomic │ │ │ │ │ │ ├── atomic.omh │ │ │ │ │ │ ├── four │ │ │ │ │ │ │ ├── atomic.hpp │ │ │ │ │ │ │ ├── atomic.omh │ │ │ │ │ │ │ ├── call.hpp │ │ │ │ │ │ │ ├── ctor.hpp │ │ │ │ │ │ │ ├── devel │ │ │ │ │ │ │ │ ├── devel.omh │ │ │ │ │ │ │ │ ├── hes_sparsity.hpp │ │ │ │ │ │ │ │ └── jac_sparsity.hpp │ │ │ │ │ │ │ ├── for_type.hpp │ │ │ │ │ │ │ ├── forward.hpp │ │ │ │ │ │ │ ├── hes_sparsity.hpp │ │ │ │ │ │ │ ├── jac_sparsity.hpp │ │ │ │ │ │ │ ├── rev_depend.hpp │ │ │ │ │ │ │ └── reverse.hpp │ │ │ │ │ │ ├── one │ │ │ │ │ │ │ └── atomic.hpp │ │ │ │ │ │ ├── three │ │ │ │ │ │ │ ├── afun.hpp │ │ │ │ │ │ │ ├── atomic.hpp │ │ │ │ │ │ │ ├── atomic.omh │ │ │ │ │ │ │ ├── ctor.hpp │ │ │ │ │ │ │ ├── for_type.hpp │ │ │ │ │ │ │ ├── forward.hpp │ │ │ │ │ │ │ ├── hes_sparsity.hpp │ │ │ │ │ │ │ ├── jac_sparsity.hpp │ │ │ │ │ │ │ ├── rev_depend.hpp │ │ │ │ │ │ │ └── reverse.hpp │ │ │ │ │ │ └── two │ │ │ │ │ │ │ ├── afun.hpp │ │ │ │ │ │ │ ├── atomic.hpp │ │ │ │ │ │ │ ├── clear.hpp │ │ │ │ │ │ │ ├── ctor.hpp │ │ │ │ │ │ │ ├── for_sparse_hes.hpp │ │ │ │ │ │ │ ├── for_sparse_jac.hpp │ │ │ │ │ │ │ ├── forward.hpp │ │ │ │ │ │ │ ├── option.hpp │ │ │ │ │ │ │ ├── rev_depend.hpp │ │ │ │ │ │ │ ├── rev_sparse_hes.hpp │ │ │ │ │ │ │ ├── rev_sparse_jac.hpp │ │ │ │ │ │ │ └── reverse.hpp │ │ │ │ │ ├── azmul.hpp │ │ │ │ │ ├── base2ad.hpp │ │ │ │ │ ├── base_complex.hpp │ │ │ │ │ ├── base_cond_exp.hpp │ │ │ │ │ ├── base_double.hpp │ │ │ │ │ ├── base_float.hpp │ │ │ │ │ ├── base_hash.hpp │ │ │ │ │ ├── base_limits.hpp │ │ │ │ │ ├── base_std_math.hpp │ │ │ │ │ ├── base_to_string.hpp │ │ │ │ │ ├── bender_quad.hpp │ │ │ │ │ ├── bool_fun.hpp │ │ │ │ │ ├── bool_valued.hpp │ │ │ │ │ ├── capacity_order.hpp │ │ │ │ │ ├── check_for_nan.hpp │ │ │ │ │ ├── chkpoint_one │ │ │ │ │ │ ├── chkpoint_one.hpp │ │ │ │ │ │ ├── ctor.hpp │ │ │ │ │ │ ├── for_sparse_jac.hpp │ │ │ │ │ │ ├── forward.hpp │ │ │ │ │ │ ├── rev_sparse_hes.hpp │ │ │ │ │ │ ├── rev_sparse_jac.hpp │ │ │ │ │ │ ├── reverse.hpp │ │ │ │ │ │ ├── set_hes_sparse_bool.hpp │ │ │ │ │ │ ├── set_hes_sparse_set.hpp │ │ │ │ │ │ ├── set_jac_sparse_bool.hpp │ │ │ │ │ │ └── set_jac_sparse_set.hpp │ │ │ │ │ ├── chkpoint_two │ │ │ │ │ │ ├── chk_fun.omh │ │ │ │ │ │ ├── chkpoint_two.hpp │ │ │ │ │ │ ├── ctor.hpp │ │ │ │ │ │ ├── dynamic.hpp │ │ │ │ │ │ ├── for_type.hpp │ │ │ │ │ │ ├── forward.hpp │ │ │ │ │ │ ├── hes_sparsity.hpp │ │ │ │ │ │ ├── jac_sparsity.hpp │ │ │ │ │ │ ├── rev_depend.hpp │ │ │ │ │ │ └── reverse.hpp │ │ │ │ │ ├── compare.hpp │ │ │ │ │ ├── compound_assign.hpp │ │ │ │ │ ├── con_dyn_var.hpp │ │ │ │ │ ├── cond_exp.hpp │ │ │ │ │ ├── convert.hpp │ │ │ │ │ ├── cppad_assert.hpp │ │ │ │ │ ├── dependent.hpp │ │ │ │ │ ├── discrete │ │ │ │ │ │ ├── devel.omh │ │ │ │ │ │ ├── discrete.hpp │ │ │ │ │ │ └── user.omh │ │ │ │ │ ├── div.hpp │ │ │ │ │ ├── div_eq.hpp │ │ │ │ │ ├── drivers.hpp │ │ │ │ │ ├── epsilon.hpp │ │ │ │ │ ├── equal_op_seq.hpp │ │ │ │ │ ├── for_hes_sparsity.hpp │ │ │ │ │ ├── for_jac_sparsity.hpp │ │ │ │ │ ├── for_one.hpp │ │ │ │ │ ├── for_sparse_hes.hpp │ │ │ │ │ ├── for_sparse_jac.hpp │ │ │ │ │ ├── for_two.hpp │ │ │ │ │ ├── forward │ │ │ │ │ │ ├── compare_change.omh │ │ │ │ │ │ ├── devel.omh │ │ │ │ │ │ ├── forward.hpp │ │ │ │ │ │ ├── forward.omh │ │ │ │ │ │ ├── forward_dir.omh │ │ │ │ │ │ ├── forward_one.omh │ │ │ │ │ │ ├── forward_order.omh │ │ │ │ │ │ ├── forward_two.omh │ │ │ │ │ │ ├── forward_zero.omh │ │ │ │ │ │ └── size_order.omh │ │ │ │ │ ├── fun_check.hpp │ │ │ │ │ ├── fun_construct.hpp │ │ │ │ │ ├── fun_eval.hpp │ │ │ │ │ ├── fun_property.omh │ │ │ │ │ ├── function_name.omh │ │ │ │ │ ├── graph │ │ │ │ │ │ ├── cpp_ad_graph.omh │ │ │ │ │ │ ├── cpp_graph.hpp │ │ │ │ │ │ ├── cpp_graph.omh │ │ │ │ │ │ ├── from_graph.hpp │ │ │ │ │ │ ├── from_json.hpp │ │ │ │ │ │ ├── graph_op_enum.hpp │ │ │ │ │ │ ├── json_ad_graph.omh │ │ │ │ │ │ ├── json_graph_op.omh │ │ │ │ │ │ ├── to_graph.hpp │ │ │ │ │ │ └── to_json.hpp │ │ │ │ │ ├── hash_code.hpp │ │ │ │ │ ├── hessian.hpp │ │ │ │ │ ├── identical.hpp │ │ │ │ │ ├── independent │ │ │ │ │ │ ├── devel.omh │ │ │ │ │ │ ├── independent.hpp │ │ │ │ │ │ └── user.omh │ │ │ │ │ ├── integer.hpp │ │ │ │ │ ├── jacobian.hpp │ │ │ │ │ ├── lu_ratio.hpp │ │ │ │ │ ├── mul.hpp │ │ │ │ │ ├── mul_eq.hpp │ │ │ │ │ ├── near_equal_ext.hpp │ │ │ │ │ ├── new_dynamic.hpp │ │ │ │ │ ├── nimble_ADbase_extensions.hpp │ │ │ │ │ ├── nimble_ADbase_tape_link_extensions.hpp │ │ │ │ │ ├── num_skip.hpp │ │ │ │ │ ├── numeric_limits.hpp │ │ │ │ │ ├── omp_max_thread.hpp │ │ │ │ │ ├── opt_val_hes.hpp │ │ │ │ │ ├── optimize.hpp │ │ │ │ │ ├── ordered.hpp │ │ │ │ │ ├── parallel_ad.hpp │ │ │ │ │ ├── pow.hpp │ │ │ │ │ ├── print_for.hpp │ │ │ │ │ ├── rev_hes_sparsity.hpp │ │ │ │ │ ├── rev_jac_sparsity.hpp │ │ │ │ │ ├── rev_one.hpp │ │ │ │ │ ├── rev_sparse_hes.hpp │ │ │ │ │ ├── rev_sparse_jac.hpp │ │ │ │ │ ├── rev_two.hpp │ │ │ │ │ ├── reverse.hpp │ │ │ │ │ ├── sign.hpp │ │ │ │ │ ├── sparse.hpp │ │ │ │ │ ├── sparse_hes.hpp │ │ │ │ │ ├── sparse_hessian.hpp │ │ │ │ │ ├── sparse_jac.hpp │ │ │ │ │ ├── sparse_jacobian.hpp │ │ │ │ │ ├── standard_math.hpp │ │ │ │ │ ├── std_math_11.hpp │ │ │ │ │ ├── sub.hpp │ │ │ │ │ ├── sub_eq.hpp │ │ │ │ │ ├── subgraph_jac_rev.hpp │ │ │ │ │ ├── subgraph_reverse.hpp │ │ │ │ │ ├── subgraph_sparsity.hpp │ │ │ │ │ ├── tape_link.hpp │ │ │ │ │ ├── test_vector.hpp │ │ │ │ │ ├── testvector.hpp │ │ │ │ │ ├── unary_minus.hpp │ │ │ │ │ ├── unary_plus.hpp │ │ │ │ │ ├── undef.hpp │ │ │ │ │ ├── user_ad.hpp │ │ │ │ │ ├── value.hpp │ │ │ │ │ ├── var2par.hpp │ │ │ │ │ ├── vec_ad │ │ │ │ │ │ ├── user.omh │ │ │ │ │ │ └── vec_ad.hpp │ │ │ │ │ └── zdouble.hpp │ │ │ │ ├── cppad.hpp │ │ │ │ ├── epl-2.0.txt │ │ │ │ ├── example │ │ │ │ │ ├── atomic_four │ │ │ │ │ │ ├── lin_ode │ │ │ │ │ │ │ ├── base_lin_ode.hpp │ │ │ │ │ │ │ ├── for_type.hpp │ │ │ │ │ │ │ ├── forward.hpp │ │ │ │ │ │ │ ├── get.hpp │ │ │ │ │ │ │ ├── hes_sparsity.hpp │ │ │ │ │ │ │ ├── implement.omh │ │ │ │ │ │ │ ├── jac_sparsity.hpp │ │ │ │ │ │ │ ├── lin_ode.hpp │ │ │ │ │ │ │ ├── lin_ode.omh │ │ │ │ │ │ │ ├── reverse.hpp │ │ │ │ │ │ │ └── set.hpp │ │ │ │ │ │ ├── mat_mul │ │ │ │ │ │ │ ├── base_mat_mul.hpp │ │ │ │ │ │ │ ├── for_type.hpp │ │ │ │ │ │ │ ├── forward.hpp │ │ │ │ │ │ │ ├── get.hpp │ │ │ │ │ │ │ ├── hes_sparsity.hpp │ │ │ │ │ │ │ ├── implement.omh │ │ │ │ │ │ │ ├── jac_sparsity.hpp │ │ │ │ │ │ │ ├── mat_mul.hpp │ │ │ │ │ │ │ ├── mat_mul.omh │ │ │ │ │ │ │ ├── rev_depend.hpp │ │ │ │ │ │ │ ├── reverse.hpp │ │ │ │ │ │ │ └── set.hpp │ │ │ │ │ │ └── vector │ │ │ │ │ │ │ ├── add_op.hpp │ │ │ │ │ │ │ ├── div_op.hpp │ │ │ │ │ │ │ ├── for_type.hpp │ │ │ │ │ │ │ ├── forward_op.hpp │ │ │ │ │ │ │ ├── hes_sparsity.hpp │ │ │ │ │ │ │ ├── implement.omh │ │ │ │ │ │ │ ├── jac_sparsity.hpp │ │ │ │ │ │ │ ├── mul_op.hpp │ │ │ │ │ │ │ ├── neg_op.hpp │ │ │ │ │ │ │ ├── rev_depend.hpp │ │ │ │ │ │ │ ├── reverse_op.hpp │ │ │ │ │ │ │ ├── sub_op.hpp │ │ │ │ │ │ │ ├── vector.hpp │ │ │ │ │ │ │ └── vector.omh │ │ │ │ │ ├── atomic_three │ │ │ │ │ │ └── mat_mul.hpp │ │ │ │ │ ├── atomic_two │ │ │ │ │ │ ├── eigen_cholesky.hpp │ │ │ │ │ │ ├── eigen_mat_inv.hpp │ │ │ │ │ │ └── eigen_mat_mul.hpp │ │ │ │ │ ├── base_adolc.hpp │ │ │ │ │ ├── code_gen_fun.hpp │ │ │ │ │ ├── cppad_eigen.hpp │ │ │ │ │ └── eigen_plugin.hpp │ │ │ │ ├── ipopt │ │ │ │ │ ├── solve.hpp │ │ │ │ │ ├── solve_callback.hpp │ │ │ │ │ └── solve_result.hpp │ │ │ │ ├── local │ │ │ │ │ ├── ad_tape.hpp │ │ │ │ │ ├── atom_state.hpp │ │ │ │ │ ├── atomic_index.hpp │ │ │ │ │ ├── color_general.hpp │ │ │ │ │ ├── color_symmetric.hpp │ │ │ │ │ ├── cppad_colpack.hpp │ │ │ │ │ ├── declare_ad.hpp │ │ │ │ │ ├── define.hpp │ │ │ │ │ ├── graph │ │ │ │ │ │ ├── cpp_graph_itr.hpp │ │ │ │ │ │ ├── cpp_graph_itr.omh │ │ │ │ │ │ ├── cpp_graph_op.hpp │ │ │ │ │ │ ├── dev_graph.omh │ │ │ │ │ │ ├── json_lexer.hpp │ │ │ │ │ │ ├── json_lexer.omh │ │ │ │ │ │ ├── json_parser.hpp │ │ │ │ │ │ └── json_writer.hpp │ │ │ │ │ ├── hash_code.hpp │ │ │ │ │ ├── independent.hpp │ │ │ │ │ ├── is_pod.hpp │ │ │ │ │ ├── is_pod.hpp.in │ │ │ │ │ ├── nimble_atomic_index.hpp │ │ │ │ │ ├── op.hpp │ │ │ │ │ ├── op │ │ │ │ │ │ ├── abs_op.hpp │ │ │ │ │ │ ├── acos_op.hpp │ │ │ │ │ │ ├── acosh_op.hpp │ │ │ │ │ │ ├── add_op.hpp │ │ │ │ │ │ ├── asin_op.hpp │ │ │ │ │ │ ├── asinh_op.hpp │ │ │ │ │ │ ├── atan_op.hpp │ │ │ │ │ │ ├── atanh_op.hpp │ │ │ │ │ │ ├── binary_op.omh │ │ │ │ │ │ ├── comp_op.hpp │ │ │ │ │ │ ├── cond_op.hpp │ │ │ │ │ │ ├── cos_op.hpp │ │ │ │ │ │ ├── cosh_op.hpp │ │ │ │ │ │ ├── cskip_op.hpp │ │ │ │ │ │ ├── csum_op.hpp │ │ │ │ │ │ ├── discrete_op.hpp │ │ │ │ │ │ ├── div_op.hpp │ │ │ │ │ │ ├── erf_op.hpp │ │ │ │ │ │ ├── exp_op.hpp │ │ │ │ │ │ ├── expm1_op.hpp │ │ │ │ │ │ ├── load_op.hpp │ │ │ │ │ │ ├── log1p_op.hpp │ │ │ │ │ │ ├── log_op.hpp │ │ │ │ │ │ ├── mul_op.hpp │ │ │ │ │ │ ├── neg_op.hpp │ │ │ │ │ │ ├── parameter_op.hpp │ │ │ │ │ │ ├── pow_op.hpp │ │ │ │ │ │ ├── print_op.hpp │ │ │ │ │ │ ├── prototype_op.hpp │ │ │ │ │ │ ├── sign_op.hpp │ │ │ │ │ │ ├── sin_op.hpp │ │ │ │ │ │ ├── sinh_op.hpp │ │ │ │ │ │ ├── sqrt_op.hpp │ │ │ │ │ │ ├── store_op.hpp │ │ │ │ │ │ ├── sub_op.hpp │ │ │ │ │ │ ├── tan_op.hpp │ │ │ │ │ │ ├── tanh_op.hpp │ │ │ │ │ │ ├── unary_op.omh │ │ │ │ │ │ └── zmul_op.hpp │ │ │ │ │ ├── op_code_dyn.hpp │ │ │ │ │ ├── op_code_var.hpp │ │ │ │ │ ├── optimize │ │ │ │ │ │ ├── cexp_info.hpp │ │ │ │ │ │ ├── csum_op_info.hpp │ │ │ │ │ │ ├── csum_stacks.hpp │ │ │ │ │ │ ├── get_cexp_info.hpp │ │ │ │ │ │ ├── get_dyn_previous.hpp │ │ │ │ │ │ ├── get_op_previous.hpp │ │ │ │ │ │ ├── get_op_usage.hpp │ │ │ │ │ │ ├── get_par_usage.hpp │ │ │ │ │ │ ├── hash_code.hpp │ │ │ │ │ │ ├── match_op.hpp │ │ │ │ │ │ ├── optimize_run.hpp │ │ │ │ │ │ ├── record_csum.hpp │ │ │ │ │ │ ├── record_pv.hpp │ │ │ │ │ │ ├── record_vp.hpp │ │ │ │ │ │ ├── record_vv.hpp │ │ │ │ │ │ ├── size_pair.hpp │ │ │ │ │ │ └── usage.hpp │ │ │ │ │ ├── play │ │ │ │ │ │ ├── addr_enum.hpp │ │ │ │ │ │ ├── atom_op_info.hpp │ │ │ │ │ │ ├── player.hpp │ │ │ │ │ │ ├── random_iterator.hpp │ │ │ │ │ │ ├── random_setup.hpp │ │ │ │ │ │ ├── sequential_iterator.hpp │ │ │ │ │ │ └── subgraph_iterator.hpp │ │ │ │ │ ├── pod_vector.hpp │ │ │ │ │ ├── record │ │ │ │ │ │ ├── comp_op.hpp │ │ │ │ │ │ ├── cond_exp.hpp │ │ │ │ │ │ ├── put_dyn_atomic.hpp │ │ │ │ │ │ ├── put_var_atomic.hpp │ │ │ │ │ │ ├── put_var_vecad.hpp │ │ │ │ │ │ ├── recorder.hpp │ │ │ │ │ │ └── recorder.omh │ │ │ │ │ ├── set_get_in_parallel.hpp │ │ │ │ │ ├── sparse │ │ │ │ │ │ ├── binary_op.hpp │ │ │ │ │ │ ├── dev_sparse.omh │ │ │ │ │ │ ├── internal.hpp │ │ │ │ │ │ ├── list_setvec.hpp │ │ │ │ │ │ ├── list_setvec.omh │ │ │ │ │ │ ├── pack_setvec.hpp │ │ │ │ │ │ ├── pack_setvec.omh │ │ │ │ │ │ ├── setvector.omh │ │ │ │ │ │ ├── svec_setvec.hpp │ │ │ │ │ │ └── unary_op.hpp │ │ │ │ │ ├── std_set.hpp │ │ │ │ │ ├── subgraph │ │ │ │ │ │ ├── arg_variable.hpp │ │ │ │ │ │ ├── entire_call.hpp │ │ │ │ │ │ ├── get_rev.hpp │ │ │ │ │ │ ├── info.hpp │ │ │ │ │ │ ├── init_rev.hpp │ │ │ │ │ │ └── sparsity.hpp │ │ │ │ │ ├── sweep │ │ │ │ │ │ ├── call_atomic.hpp │ │ │ │ │ │ ├── dev_sweep.omh │ │ │ │ │ │ ├── dynamic.hpp │ │ │ │ │ │ ├── for_hes.hpp │ │ │ │ │ │ ├── for_jac.hpp │ │ │ │ │ │ ├── forward0.hpp │ │ │ │ │ │ ├── forward1.hpp │ │ │ │ │ │ ├── forward2.hpp │ │ │ │ │ │ ├── rev_hes.hpp │ │ │ │ │ │ ├── rev_jac.hpp │ │ │ │ │ │ └── reverse.hpp │ │ │ │ │ └── utility │ │ │ │ │ │ ├── cppad_vector_itr.hpp │ │ │ │ │ │ └── vector_bool.hpp │ │ │ │ ├── speed │ │ │ │ │ ├── det_33.hpp │ │ │ │ │ ├── det_by_lu.hpp │ │ │ │ │ ├── det_by_minor.hpp │ │ │ │ │ ├── det_grad_33.hpp │ │ │ │ │ ├── det_of_minor.hpp │ │ │ │ │ ├── mat_sum_sq.hpp │ │ │ │ │ ├── ode_evaluate.hpp │ │ │ │ │ ├── sparse_hes_fun.hpp │ │ │ │ │ ├── sparse_jac_fun.hpp │ │ │ │ │ └── uniform_01.hpp │ │ │ │ ├── utility.hpp │ │ │ │ ├── utility │ │ │ │ │ ├── check_numeric_type.hpp │ │ │ │ │ ├── check_simple_vector.hpp │ │ │ │ │ ├── elapsed_seconds.hpp │ │ │ │ │ ├── error_handler.hpp │ │ │ │ │ ├── index_sort.hpp │ │ │ │ │ ├── lu_factor.hpp │ │ │ │ │ ├── lu_invert.hpp │ │ │ │ │ ├── lu_solve.hpp │ │ │ │ │ ├── memory_leak.hpp │ │ │ │ │ ├── nan.hpp │ │ │ │ │ ├── near_equal.hpp │ │ │ │ │ ├── ode_err_control.hpp │ │ │ │ │ ├── ode_gear.hpp │ │ │ │ │ ├── ode_gear_control.hpp │ │ │ │ │ ├── omh │ │ │ │ │ │ ├── cppad_vector.omh │ │ │ │ │ │ ├── dev_cppad_vector.omh │ │ │ │ │ │ ├── dev_utility.omh │ │ │ │ │ │ ├── dev_vector_bool.omh │ │ │ │ │ │ └── utility.omh │ │ │ │ │ ├── omp_alloc.hpp │ │ │ │ │ ├── poly.hpp │ │ │ │ │ ├── pow_int.hpp │ │ │ │ │ ├── romberg_mul.hpp │ │ │ │ │ ├── romberg_one.hpp │ │ │ │ │ ├── rosen_34.hpp │ │ │ │ │ ├── runge_45.hpp │ │ │ │ │ ├── set_union.hpp │ │ │ │ │ ├── sparse2eigen.hpp │ │ │ │ │ ├── sparse_rc.hpp │ │ │ │ │ ├── sparse_rcv.hpp │ │ │ │ │ ├── speed_test.hpp │ │ │ │ │ ├── test_boolofvoid.hpp │ │ │ │ │ ├── thread_alloc.hpp │ │ │ │ │ ├── time_test.hpp │ │ │ │ │ ├── to_string.hpp │ │ │ │ │ ├── track_new_del.hpp │ │ │ │ │ ├── vector.hpp │ │ │ │ │ └── vector_bool.hpp │ │ │ │ └── wno_conversion.hpp │ │ │ ├── cppad_notes_for_nimble.txt │ │ │ ├── nimble │ │ │ │ ├── EigenTypedefs.h │ │ │ │ ├── Model.h │ │ │ │ ├── ModelClassUtils.h │ │ │ │ ├── NamedObjects.h │ │ │ │ ├── NimArr.h │ │ │ │ ├── NimArrBase.h │ │ │ │ ├── RcppNimbleUtils.h │ │ │ │ ├── RcppUtils.h │ │ │ │ ├── Utils.h │ │ │ │ ├── Values.h │ │ │ │ ├── accessorClasses.h │ │ │ │ ├── dists.h │ │ │ │ ├── dllFinalizer.h │ │ │ │ ├── dynamicRegistrations.h │ │ │ │ ├── eigenUsingClasses.h │ │ │ │ ├── nimDerivs_atomic_PDinverse_logdet.h │ │ │ │ ├── nimDerivs_atomic_backsolve.h │ │ │ │ ├── nimDerivs_atomic_cache.h │ │ │ │ ├── nimDerivs_atomic_cholesky.h │ │ │ │ ├── nimDerivs_atomic_classes.h │ │ │ │ ├── nimDerivs_atomic_discrete.h │ │ │ │ ├── nimDerivs_atomic_dyn_ind.h │ │ │ │ ├── nimDerivs_atomic_forwardsolve.h │ │ │ │ ├── nimDerivs_atomic_log_pow_int.h │ │ │ │ ├── nimDerivs_atomic_matinverse.h │ │ │ │ ├── nimDerivs_atomic_matmult.h │ │ │ │ ├── nimDerivs_atomic_pow_int.h │ │ │ │ ├── nimDerivs_atomic_probit.h │ │ │ │ ├── nimDerivs_atomic_solve_base.h │ │ │ │ ├── nimDerivs_atomic_zround.h │ │ │ │ ├── nimDerivs_dists.h │ │ │ │ ├── nimDerivs_vecmat_utils.h │ │ │ │ ├── nimDists.h │ │ │ │ ├── nimIntegrate.h │ │ │ │ ├── nimOptim.h │ │ │ │ ├── nimbleCppAD.h │ │ │ │ ├── nimbleCppADbaseClass.cpp │ │ │ │ ├── nimbleCppADbaseClass.h │ │ │ │ ├── nimbleEigen.h │ │ │ │ ├── nimbleEigenNimArr.h │ │ │ │ ├── nimbleGraph.h │ │ │ │ ├── nodeFun.h │ │ │ │ ├── predefinedNimbleLists.h │ │ │ │ └── smartPtrs.h │ │ │ ├── nimble_ADbase_extensions.hpp │ │ │ ├── nimble_ADbase_tape_link_extensions.hpp │ │ │ ├── nimble_atomic_index.hpp │ │ │ └── tape_link.hpp │ │ └── make │ │ │ ├── .gitignore │ │ │ ├── Makevars.in │ │ │ ├── Makevars.win.in │ │ │ └── Makevars_lib.in │ ├── man │ │ ├── ADNimbleList.Rd │ │ ├── ADbreak.Rd │ │ ├── ADproxyModelClass-class.Rd │ │ ├── BUGSdeclClass-class.Rd │ │ ├── CAR-Normal.Rd │ │ ├── CAR-Proper.Rd │ │ ├── CAR_calcNumIslands.Rd │ │ ├── Categorical.Rd │ │ ├── ChineseRestaurantProcess.Rd │ │ ├── CmodelBaseClass-class.Rd │ │ ├── CnimbleFunctionBase-class.Rd │ │ ├── Constraint.Rd │ │ ├── Dirichlet.Rd │ │ ├── Double-Exponential.Rd │ │ ├── Exponential.Rd │ │ ├── Interval.Rd │ │ ├── Inverse-Gamma.Rd │ │ ├── Inverse-Wishart.Rd │ │ ├── LKJ.Rd │ │ ├── MCMCconf-class.Rd │ │ ├── Multinomial.Rd │ │ ├── Multivariate-t.Rd │ │ ├── MultivariateNormal.Rd │ │ ├── Rmatrix2mvOneVar.Rd │ │ ├── RmodelBaseClass-class.Rd │ │ ├── StickBreakingFunction.Rd │ │ ├── Wishart.Rd │ │ ├── any_na.Rd │ │ ├── as.carAdjacency.Rd │ │ ├── as.carCM.Rd │ │ ├── asRow.Rd │ │ ├── autoBlock.Rd │ │ ├── buildAuxiliaryFilter.Rd │ │ ├── buildBootstrapFilter.Rd │ │ ├── buildEnsembleKF.Rd │ │ ├── buildIteratedFilter2.Rd │ │ ├── buildLiuWestFilter.Rd │ │ ├── buildMCEM.Rd │ │ ├── buildMCMC.Rd │ │ ├── buildMacro.Rd │ │ ├── calculateWAIC.Rd │ │ ├── carBounds.Rd │ │ ├── carMaxBound.Rd │ │ ├── carMinBound.Rd │ │ ├── checkInterrupt.Rd │ │ ├── clearCompiled.Rd │ │ ├── codeBlockClass-class.Rd │ │ ├── compileNimble.Rd │ │ ├── configureMCMC.Rd │ │ ├── configureRJ.Rd │ │ ├── decide.Rd │ │ ├── decideAndJump.Rd │ │ ├── declare.Rd │ │ ├── deregisterDistributions.Rd │ │ ├── derived.Rd │ │ ├── distributionInfo.Rd │ │ ├── eigenNimbleList.Rd │ │ ├── expAv.Rd │ │ ├── expm.Rd │ │ ├── extractControlElement.Rd │ │ ├── flat.Rd │ │ ├── getBUGSexampleDir.Rd │ │ ├── getBound.Rd │ │ ├── getConditionallyIndependentSets.Rd │ │ ├── getDefinition.Rd │ │ ├── getMacroParameters.Rd │ │ ├── getNimbleOption.Rd │ │ ├── getParam.Rd │ │ ├── getSamplesDPmeasure.Rd │ │ ├── getsize.Rd │ │ ├── identityMatrix.Rd │ │ ├── initializeModel.Rd │ │ ├── is.nf.Rd │ │ ├── is.nl.Rd │ │ ├── makeBoundInfo.Rd │ │ ├── makeModelDerivsInfo.Rd │ │ ├── makeParamInfo.Rd │ │ ├── modelBaseClass-class.Rd │ │ ├── modelDefClass-class.Rd │ │ ├── modelInitialization.Rd │ │ ├── modelValues.Rd │ │ ├── modelValuesBaseClass-class.Rd │ │ ├── modelValuesConf.Rd │ │ ├── nfMethod.Rd │ │ ├── nfVar.Rd │ │ ├── nimCat.Rd │ │ ├── nimCopy.Rd │ │ ├── nimDerivs.Rd │ │ ├── nimDim.Rd │ │ ├── nimEigen.Rd │ │ ├── nimIntegrate.Rd │ │ ├── nimMatrix.Rd │ │ ├── nimNumeric.Rd │ │ ├── nimOptim.Rd │ │ ├── nimOptimDefaultControl.Rd │ │ ├── nimOptimMethod.Rd │ │ ├── nimPrint.Rd │ │ ├── nimStop.Rd │ │ ├── nimSvd.Rd │ │ ├── nimble-R-functions.Rd │ │ ├── nimble-internal.Rd │ │ ├── nimble-math.Rd │ │ ├── nimble-package.Rd │ │ ├── nimbleCode.Rd │ │ ├── nimbleExternalCall.Rd │ │ ├── nimbleFunction.Rd │ │ ├── nimbleFunctionBase-class.Rd │ │ ├── nimbleFunctionList-class.Rd │ │ ├── nimbleFunctionVirtual.Rd │ │ ├── nimbleList.Rd │ │ ├── nimbleMCMC.Rd │ │ ├── nimbleModel.Rd │ │ ├── nimbleOptions.Rd │ │ ├── nimbleRcall.Rd │ │ ├── nimbleType-class.Rd │ │ ├── nodeFunctions.Rd │ │ ├── optimControlNimbleList.Rd │ │ ├── optimDefaultControl.Rd │ │ ├── optimResultNimbleList.Rd │ │ ├── parameterTransform.Rd │ │ ├── pow_int.Rd │ │ ├── printErrors.Rd │ │ ├── rankSample.Rd │ │ ├── readBUGSmodel.Rd │ │ ├── registerDistributions.Rd │ │ ├── resize.Rd │ │ ├── run.time.Rd │ │ ├── runCrossValidate.Rd │ │ ├── runLaplace.Rd │ │ ├── runMCMC.Rd │ │ ├── samplers.Rd │ │ ├── setAndCalculate.Rd │ │ ├── setAndCalculateOne.Rd │ │ ├── setSize.Rd │ │ ├── setupMargNodes.Rd │ │ ├── setupOutputs.Rd │ │ ├── simNodes.Rd │ │ ├── simNodesMV.Rd │ │ ├── singleVarAccessClass-class.Rd │ │ ├── summaryLaplace.Rd │ │ ├── svdNimbleList.Rd │ │ ├── t.Rd │ │ ├── testBUGSmodel.Rd │ │ ├── valueInCompiledNimbleFunction.Rd │ │ ├── values.Rd │ │ ├── waic.Rd │ │ ├── waicDetailsNimbleList.Rd │ │ ├── waicNimbleList.Rd │ │ └── withNimbleOptions.Rd │ ├── src │ │ ├── .gitignore │ │ ├── DO_NOT_PUT_CODE_HERE_DO_IN_INST_CPPCODE │ │ ├── Makevars.in │ │ ├── Makevars.win │ │ └── nimble.cpp │ └── tests │ │ └── testthat │ │ ├── AD_distribution_test_lists.R │ │ ├── AD_knownFailures.R │ │ ├── AD_math_test_lists.R │ │ ├── AD_test_utils.R │ │ ├── barkerTestLog_Correct.Rout │ │ ├── bnp_monteCarloTest.Rmd │ │ ├── distributionsTestLog_Correct.Rout │ │ ├── dynamicIndexingTestLists.R │ │ ├── dynamicIndexingTestLog_Correct.Rout │ │ ├── graphStructureTestLog_Correct.Rout │ │ ├── mathTestLists.R │ │ ├── mcemTestLog_Correct.Rout │ │ ├── mcmcTestLog_Correct.Rout │ │ ├── sizeTestLog_Correct.Rout │ │ ├── test-ADbackSolve.R │ │ ├── test-ADbasics.R │ │ ├── test-ADchol.R │ │ ├── test-ADdirsAndInds.R │ │ ├── test-ADdists.R │ │ ├── test-ADdmnorm.R │ │ ├── test-ADdsl.R │ │ ├── test-ADerrorTrapping.R │ │ ├── test-ADforwardSolve.R │ │ ├── test-ADfunctions.R │ │ ├── test-ADmatInverse.R │ │ ├── test-ADmatMult.R │ │ ├── test-ADmatMult_model.R │ │ ├── test-ADmodels-bigmv.R │ │ ├── test-ADmodels.R │ │ ├── test-ADoptim.R │ │ ├── test-allocation.R │ │ ├── test-benchmark-building-steps.R │ │ ├── test-benchmarks.R │ │ ├── test-bnp.R │ │ ├── test-car.R │ │ ├── test-checkDSL.R │ │ ├── test-copy.R │ │ ├── test-coreR.R │ │ ├── test-crossVal.R │ │ ├── test-declare.R │ │ ├── test-derived-quantities.R │ │ ├── test-distributions.R │ │ ├── test-dsl_dists.R │ │ ├── test-dynamicIndexing.R │ │ ├── test-errors.R │ │ ├── test-expandNodeNames.R │ │ ├── test-externalCalls.R │ │ ├── test-getBound.R │ │ ├── test-getDependencies.R │ │ ├── test-getDistributionInfo.R │ │ ├── test-getParam.R │ │ ├── test-graphStructure.R │ │ ├── test-initializeModel.R │ │ ├── test-integrate.R │ │ ├── test-macros.R │ │ ├── test-math.R │ │ ├── test-mcem.R │ │ ├── test-mcmc.R │ │ ├── test-mcmcrj.R │ │ ├── test-misc.R │ │ ├── test-miscAlgorithms.R │ │ ├── test-modelValuesInterface.R │ │ ├── test-models.R │ │ ├── test-nimbleFunctionInterfaces.R │ │ ├── test-nimbleFunctionModelAccess.R │ │ ├── test-nimbleList.R │ │ ├── test-nimbleList_RCfun.R │ │ ├── test-noSMC.R │ │ ├── test-noncenteredSampler.R │ │ ├── test-numericTypes.R │ │ ├── test-optim.R │ │ ├── test-options.R │ │ ├── test-parameterTransform.R │ │ ├── test-polyagamma.R │ │ ├── test-returnTypeErrorTrapping.R │ │ ├── test-setData.R │ │ ├── test-setupMargNodes.R │ │ ├── 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