├── .github └── workflows │ └── test-all.yaml ├── .gitignore ├── .travis.yml ├── LICENSE ├── README.md ├── UserManual ├── .DS_Store └── nCompiler_user_manual │ ├── .gitignore │ ├── _book │ ├── argument_passing.html │ ├── controlling_compilation.html │ ├── developer_basic_objects.html │ ├── developer_compilation_stages.html │ ├── developer_cppDefs.html │ ├── developer_cppImpl.html │ ├── developer_exprClass.html │ ├── developer_nCompile.html │ ├── developer_new_opDefs.html │ ├── developer_opDefs.html │ ├── developer_types.html │ ├── index.html │ ├── nCompiler-User-Manual.pdf │ ├── nFunctions.html │ ├── search.json │ ├── site_libs │ │ ├── bootstrap │ │ │ ├── bootstrap-icons.css │ │ │ ├── bootstrap-icons.woff │ │ │ ├── bootstrap.min.css │ │ │ └── bootstrap.min.js │ │ ├── clipboard │ │ │ └── clipboard.min.js │ │ ├── quarto-html │ │ │ ├── anchor.min.js │ │ │ ├── popper.min.js │ │ │ ├── quarto-syntax-highlighting.css │ │ │ ├── quarto.js │ │ │ ├── tippy.css │ │ │ └── tippy.umd.min.js │ │ ├── quarto-nav │ │ │ ├── headroom.min.js │ │ │ └── quarto-nav.js │ │ └── quarto-search │ │ │ ├── autocomplete.umd.js │ │ │ ├── fuse.min.js │ │ │ └── quarto-search.js │ ├── supported_operations.html │ ├── types.html │ └── types_in_function_code.html │ ├── _quarto.yml │ ├── argument_passing.qmd │ ├── controlling_compilation.qmd │ ├── cover.png │ ├── developer_basic_objects.qmd │ ├── developer_compilation_stages.qmd │ ├── developer_cppDefs.qmd │ ├── developer_cppImpl.qmd │ ├── developer_exprClass.qmd │ ├── developer_nCompile.qmd │ ├── developer_new_opDefs.qmd │ ├── developer_opDefs.qmd │ ├── developer_types.qmd │ ├── index.qmd │ ├── nCompiler_user_manual.Rproj │ ├── nFunctions.qmd │ ├── references.bib │ ├── references.qmd │ ├── supported_operations.qmd │ ├── types.qmd │ └── types_in_function_code.qmd ├── archived_tests ├── tests_to_be_fixed │ ├── README.txt │ ├── test-TBB-NOTWORKING.R_noscan │ ├── test-nOptim-NOTWORKING.R_noscan │ └── test-packaging-NOTWORKING.R_noscan └── v1tests │ ├── AD_utils.R_noscan │ ├── README_noscan.txt │ ├── known_failures.R_noscan │ ├── math_utils.R_noscan │ ├── serialization_test_in_new_R_session.R_noscan │ ├── serialization_test_utils │ ├── .gitignore │ ├── README.txt │ ├── testserial_create_Package.R_noscan │ ├── testserial_read_Full.R_noscan │ ├── testserial_read_Generic.R_noscan │ ├── testserial_read_Multiple.R_noscan │ ├── testserial_read_Package.R_noscan │ ├── testserial_save_Full.R_noscan │ ├── testserial_save_Generic.R_noscan │ ├── testserial_save_Multiple.R_noscan │ └── testserial_save_Package.R_noscan │ ├── status.txt │ ├── test-AD.R_noscan │ ├── test-ADfun.R_noscan │ ├── test-NF_CompilerClass.R_noscan │ ├── test-NF_derivs.R_noscan │ ├── test-RcppTypes.R_noscan │ ├── test-Rcpp_nCompilerPacket.R_noscan │ ├── test-StridedTensorMap.R_noscan │ ├── test-TBB.R_noscan │ ├── test-aliasChecks.R_noscan │ ├── test-argumentPassing.R_noscan │ ├── test-as_wrap_Rcpp.R_noscan │ ├── test-callingBetweenNFs.R_noscan │ ├── test-compileErrorTrapping.R_noscan │ ├── test-compilerStage-setToEigen.R_noscan │ ├── test-compilerStages.R_noscan │ ├── test-concatenate.R_noscan │ ├── test-cppLiteral.R_noscan │ ├── test-cppVariables.R_noscan │ ├── test-cpp_nClassClass.R_noscan │ ├── test-cpp_nFunctionClass.R_noscan │ ├── test-eigenShapeFlex.R_noscan │ ├── test-header_mgmt.R_noscan │ ├── test-hellotest.R_noscan │ ├── test-indexing-cpp.R_noscan │ ├── test-indexing.R_noscan │ ├── test-labelAbstractTypes.R_noscan │ ├── test-math.R_noscan │ ├── test-nClass_interface.R_noscan │ ├── test-nClass_uncompiled.R_noscan │ ├── test-nCompile.R_noscan │ ├── test-nCompile_nClass.R_noscan │ ├── test-nCompile_nFunction.R_noscan │ ├── test-nFunction_uncompiled.R_noscan │ ├── test-nOptim.R_noscan │ ├── test-nParse_nDeparse.R_noscan │ ├── test-normalizeCalls.R_noscan │ ├── test-packaging.R_noscan │ ├── test-predefined.R_noscan │ ├── test-recycling_rule.R_noscan │ ├── test-rep.R_noscan │ ├── test-repClass.R_noscan │ ├── test-seq.R_noscan │ ├── test-seqClass.R_noscan │ ├── test-serialization.R_noscan │ ├── test-setInputOutputTypes.R_noscan │ ├── test-setWhich.R_noscan │ ├── test-substituteMangledArgumentNames.R_noscan │ ├── test-tensorCreation.R_noscan │ ├── test-tensorOperations_accessors.R_noscan │ ├── test-tensorOperations_linear_algebra.R_noscan │ ├── test-tensorOperations_reshaping.R_noscan │ ├── test-tensorOperations_sparse.R_noscan │ ├── test-tensorOperations_sparse_multiplication.R_noscan │ ├── test-types-NOTWORKING.R_noscan │ ├── test-which.R_noscan │ ├── testing_operatorLists.R_noscan │ └── testing_utils.R_noscan ├── ci-extra-packages.txt ├── generatePredefinedCpp.R ├── install_requirements.R ├── nCompiler ├── .DS_Store ├── .Rbuildignore ├── DESCRIPTION ├── NAMESPACE ├── R │ ├── NC.R │ ├── NC_Compile.R │ ├── NC_CompilerClass.R │ ├── NC_FullCompiledInterface.R │ ├── NC_InternalsClass.R │ ├── NC_LoadedObjectEnv.R │ ├── NC_Serialize.R │ ├── NC_SimpleInterface.R │ ├── NC_Utils.R │ ├── NF.R │ ├── NF_Compile.R │ ├── NF_CompilerClass.R │ ├── NF_CompilerStages.R │ ├── NF_CompilerUtils.R │ ├── NF_InternalsClass.R │ ├── NF_PassByReference.R │ ├── NF_ProcessCompilerStages.R │ ├── NF_Utils.R │ ├── NF_derivs.R │ ├── RcppExports.R │ ├── Rcpp_check.R │ ├── Rcpp_nCompiler.R │ ├── Rcpp_nCompiler_plugin.R │ ├── Rexecution.R │ ├── Rhooks.R │ ├── all_utils.R │ ├── changeKeywords.R │ ├── compileNimble.R │ ├── compile_aaa_operatorLists.R │ ├── compile_addDebug.R │ ├── compile_eigenization.R │ ├── compile_exprClass.R │ ├── compile_finalTransformations.R │ ├── compile_generateCpp.R │ ├── compile_insertAssertions.R │ ├── compile_labelAbstractTypes.R │ ├── compile_liftMaps.R │ ├── compile_nParse.R │ ├── compile_normalizeCalls.R │ ├── compile_processAD.R │ ├── compile_simpleIntermediates.R │ ├── compile_simpleTransformations.R │ ├── compile_zzz_operatorLists.R │ ├── cppDefs_ADutils.R │ ├── cppDefs_R_interface_calls.R │ ├── cppDefs_TBB.R │ ├── cppDefs_core.R │ ├── cppDefs_nClass.R │ ├── cppDefs_nFunction.R │ ├── cppDefs_serialize.R │ ├── cppDefs_utils.R │ ├── cppDefs_variables.R │ ├── developerTools.R │ ├── distributions_implementations.R │ ├── distributions_inputList.R │ ├── distributions_processInputList.R │ ├── local_DLL.R │ ├── nCompile.R │ ├── nConstructor.R │ ├── nList.R │ ├── nTry.R │ ├── nimbleModels.R │ ├── options.R │ ├── packaging.R │ ├── symbolTable.R │ ├── symbolTableClass.R │ ├── symbolTable_utils.R │ ├── testingTools.R │ ├── typeDeclarations.R │ └── zzz_NC_Predefined.R ├── doc │ └── nExternalCall-with-user-packages.Rmd ├── inst │ ├── include │ │ └── nCompiler │ │ │ ├── .DS_Store │ │ │ ├── AD │ │ │ ├── derivsMgr.h │ │ │ ├── nCompiler_CppAD.h │ │ │ └── nCompiler_CppAD_old.h │ │ │ ├── ET_Rcpp_ext │ │ │ ├── .DS_Store │ │ │ ├── ET_Rcpp_ext_forward_declarations.h │ │ │ ├── ET_Rcpp_ext_post_Rcpp.h │ │ │ ├── ET_Rcpp_ext_pre_Rcpp.h │ │ │ ├── ETaccessor.h │ │ │ └── post_Rcpp │ │ │ │ ├── ET_Rcpp_as_wrap.h │ │ │ │ ├── ET_SEXP_converter.h │ │ │ │ ├── ETaccessor_post_Rcpp.h │ │ │ │ ├── SEXP_2_EigenTensor.h │ │ │ │ └── SEXP_indices_2_IndexArray.h │ │ │ ├── ET_ext │ │ │ ├── ET_ext_post_Rcpp.h │ │ │ ├── ET_ext_pre_Rcpp.h │ │ │ ├── StridedTensorMap.h │ │ │ ├── StridedTensorMapInfo.h │ │ │ ├── index_block.h │ │ │ ├── nCompiler_Eigen_EnableErrors.h_deprecated │ │ │ ├── post_Rcpp │ │ │ │ ├── recyclingRule.h │ │ │ │ ├── setWhich.h │ │ │ │ ├── tensorCreation.h │ │ │ │ ├── tensorFlex.h │ │ │ │ ├── tensorFlex_CppAD.h │ │ │ │ ├── tensorIndexingOps.h │ │ │ │ ├── tensorOperations.h │ │ │ │ ├── tensorUtils.h │ │ │ │ ├── tensor_cat_op.h │ │ │ │ ├── tensor_rep_op.h │ │ │ │ ├── tensor_seq_op.h │ │ │ │ └── typedefs.h │ │ │ ├── repClass.h_deprecated │ │ │ └── seqClass.h_deprecated │ │ │ ├── EigenDecomp_pkg.cpp │ │ │ ├── EigenDecomp_pkg.h │ │ │ ├── INCLUDE_RULES.txt │ │ │ ├── OptimControlList_pkg.cpp │ │ │ ├── OptimControlList_pkg.h │ │ │ ├── OptimResultList_pkg.cpp │ │ │ ├── OptimResultList_pkg.h │ │ │ ├── Rcpp_extensions │ │ │ ├── .DS_Store │ │ │ └── Rcpp_forward_declarations.h │ │ │ ├── SVDDecomp_pkg.cpp │ │ │ ├── SVDDecomp_pkg.h │ │ │ ├── cWiseUnary_external.h │ │ │ ├── derivClass_pkg.cpp │ │ │ ├── derivClass_pkg.h │ │ │ ├── localDLL_dummy.R │ │ │ ├── nC_cereal │ │ │ ├── archives.h │ │ │ ├── nC_cereal_post_Rcpp.h │ │ │ ├── nC_cereal_pre_Rcpp.h │ │ │ └── post_Rcpp │ │ │ │ ├── Rcpp_types_cereal.h │ │ │ │ ├── save_load_Rcpp_types.h │ │ │ │ └── serialization_mgr.h │ │ │ ├── nC_inter │ │ │ ├── .DS_Store │ │ │ ├── expand_call_method.h │ │ │ ├── generic_class_interface.h │ │ │ ├── loadedObjectsHook.h │ │ │ ├── nC_factory.h │ │ │ ├── nC_inter_post_Rcpp.h │ │ │ ├── nC_inter_pre_Rcpp.h │ │ │ ├── nCompiler_class_interface_old.h │ │ │ ├── post_Rcpp │ │ │ │ ├── generic_class_interface_Rcpp_steps.h │ │ │ │ ├── loadedObjectHookC_impl.h │ │ │ │ ├── nCompiler_compileNimble_support.h │ │ │ │ ├── nCompiler_model_base_devel.h │ │ │ │ └── process_call_args.h │ │ │ ├── shared_ptr_as_wrap.h_defunct │ │ │ └── shared_ptr_holder.h_defunct │ │ │ ├── nC_inter_Rcpp_ext │ │ │ ├── nC_inter_Rcpp_ext_post_Rcpp.h │ │ │ ├── nC_inter_Rcpp_ext_pre_Rcpp.h │ │ │ ├── post_Rcpp │ │ │ │ └── shared_ptr_as_wrap.h │ │ │ └── shared_ptr_as_wrap_forward_declarations.h │ │ │ ├── nCompiler_omnibus.h │ │ │ ├── nCompiler_omnibus_pre_Rcpp.h │ │ │ ├── nCompiler_stacktrace.h │ │ │ ├── nList │ │ │ ├── nList_forward_declarations.h │ │ │ ├── nList_post_Rcpp.h │ │ │ ├── nList_pre_Rcpp.h │ │ │ └── post_Rcpp │ │ │ │ └── nList.h │ │ │ ├── nOptim.h │ │ │ ├── omnibus_fxns.h │ │ │ ├── parallel │ │ │ └── nCompiler_TBB.h │ │ │ ├── predef │ │ │ ├── README.txt │ │ │ ├── calcInstrList_nC │ │ │ │ ├── calcInstrList_nC_copyFiles.txt │ │ │ │ ├── calcInstrList_nC_cppContent.cpp │ │ │ │ ├── calcInstrList_nC_filebase.txt │ │ │ │ ├── calcInstrList_nC_hContent.h │ │ │ │ ├── calcInstrList_nC_manifest.txt │ │ │ │ ├── calcInstrList_nC_post_cpp_compiler.txt │ │ │ │ └── calcInstrList_nC_preamble.cpp │ │ │ ├── calcInstr_nClass │ │ │ │ ├── calcInstr_nClass_copyFiles.txt │ │ │ │ ├── calcInstr_nClass_cppContent.cpp │ │ │ │ ├── calcInstr_nClass_filebase.txt │ │ │ │ ├── calcInstr_nClass_hContent.h │ │ │ │ ├── calcInstr_nClass_manifest.txt │ │ │ │ ├── calcInstr_nClass_post_cpp_compiler.txt │ │ │ │ └── calcInstr_nClass_preamble.cpp │ │ │ ├── modelBase_nClass │ │ │ │ ├── modelBase_nClass_copyFiles.txt │ │ │ │ ├── modelBase_nClass_cppContent.cpp │ │ │ │ ├── modelBase_nClass_filebase.txt │ │ │ │ ├── modelBase_nClass_hContent.h │ │ │ │ ├── modelBase_nClass_manifest.txt │ │ │ │ ├── modelBase_nClass_post_cpp_compiler.txt │ │ │ │ └── modelBase_nClass_preamble.cpp │ │ │ ├── nodeFxnBase_nClass │ │ │ │ ├── nodeFxnBase_nClass_copyFiles.txt │ │ │ │ ├── nodeFxnBase_nClass_cppContent.cpp │ │ │ │ ├── nodeFxnBase_nClass_filebase.txt │ │ │ │ ├── nodeFxnBase_nClass_hContent.h │ │ │ │ ├── nodeFxnBase_nClass_manifest.txt │ │ │ │ ├── nodeFxnBase_nClass_post_cpp_compiler.txt │ │ │ │ └── nodeFxnBase_nClass_preamble.cpp │ │ │ └── nodeInstr_nClass │ │ │ │ ├── nodeInstr_nClass_copyFiles.txt │ │ │ │ ├── nodeInstr_nClass_cppContent.cpp │ │ │ │ ├── nodeInstr_nClass_filebase.txt │ │ │ │ ├── nodeInstr_nClass_hContent.h │ │ │ │ ├── nodeInstr_nClass_manifest.txt │ │ │ │ ├── nodeInstr_nClass_post_cpp_compiler.txt │ │ │ │ └── nodeInstr_nClass_preamble.cpp │ │ │ ├── predefined.cpp_defunct │ │ │ ├── predefined.h_defunct │ │ │ ├── test_predefined_pkg.cpp │ │ │ ├── test_predefined_pkg.h │ │ │ └── utils.h │ └── nCompLocal_files │ │ └── loadedObjectEnv.cpp ├── man │ ├── CAR-Normal.Rd │ ├── Categorical.Rd │ ├── Constraint.Rd │ ├── Dirichlet.Rd │ ├── Exponential.Rd │ ├── Interval.Rd │ ├── Inverse-Gamma.Rd │ ├── Inverse-Wishart.Rd │ ├── Multinomial.Rd │ ├── Multivariate-t.Rd │ ├── MultivariateNormal.Rd │ ├── NCinternals-set.Rd │ ├── NCinternals.Rd │ ├── NFinternals.Rd │ ├── Wishart.Rd │ ├── asDense.Rd │ ├── asSparse.Rd │ ├── buildLocalDLLpackage.Rd │ ├── buildPackage.Rd │ ├── cpp_nCompiler.Rd │ ├── createLocalDLLpackage.Rd │ ├── deregisterDistributions.Rd │ ├── distributionInfo.Rd │ ├── documentNClass.Rd │ ├── documentNFunction.Rd │ ├── erasePackage.Rd │ ├── flat.Rd │ ├── get_nOption.Rd │ ├── installLocalDLLpackage.Rd │ ├── isCompiledNCgenerator.Rd │ ├── isNC.Rd │ ├── isNCgenerator.Rd │ ├── isNF.Rd │ ├── nChol.Rd │ ├── nClass.Rd │ ├── nCompile_nClass.Rd │ ├── nCompile_nFunction.Rd │ ├── nDeparse.Rd │ ├── nDerivs.Rd │ ├── nDiag.Rd │ ├── nDim.Rd │ ├── nEigen.Rd │ ├── nFunction.Rd │ ├── nMatrix.Rd │ ├── nMul.Rd │ ├── nNumeric.Rd │ ├── nParse.Rd │ ├── nRep.Rd │ ├── nimEigen.Rd │ ├── nimSvd.Rd │ ├── read_nClass.Rd │ ├── registerDistributions.Rd │ ├── requireLocalDLLpackage.Rd │ ├── save_nClass.Rd │ ├── set_nOption.Rd │ ├── setup_nCompLocal.Rd │ ├── setup_wrt.Rd │ ├── t.Rd │ ├── writeCode.Rd │ └── writePackage.Rd ├── nCompiler.Rproj ├── src │ ├── Makevars │ ├── Makevars.win │ ├── RcppExports.cpp │ ├── nimbleClassInterface.cpp_temp │ ├── predefined.cpp_temp │ ├── predefined.h_temp │ └── rcpp_hw.cpp └── tests │ ├── .DS_Store │ ├── nimble │ ├── test-allocations.R │ ├── test-compileNimbleProxy.R │ ├── test-coreR.R │ └── test-math.R │ └── testthat │ ├── .DS_Store │ ├── README.txt │ ├── cpp │ ├── StridedTensorMap_tests.cpp │ ├── as_wrap_tests.cpp │ ├── general_indexing_examples.cpp │ ├── preamble.h │ ├── repClass_tests.cpp │ ├── seqClass_tests.cpp │ ├── setWhich_tests.cpp │ └── tensorCreation_tests.cpp │ ├── cpp_tests │ ├── test-ETaccess.R │ ├── test-StridedTensorMap.R │ ├── test-as_wrap_Rcpp.R │ ├── test-indexing-cpp.R │ ├── test-repClass-cpp.R │ ├── test-seqClass-cpp.R │ └── test-setWhich-cpp.R │ ├── gold_files │ ├── AD_abs.gold │ ├── AD_cube.gold │ ├── AD_div.gold │ ├── AD_exp.gold │ ├── AD_log.gold │ ├── AD_minus.gold │ ├── AD_mult.gold │ ├── AD_plus.gold │ ├── AD_rsqrt.gold │ ├── AD_sqrt.gold │ ├── AD_square.gold │ ├── AD_squaredNorm.gold │ ├── AD_tanh.gold │ ├── math_abs.gold │ ├── math_acos.gold │ ├── math_acosh.gold │ ├── math_all.gold │ ├── math_and.gold │ ├── math_any.gold │ ├── math_asin.gold │ ├── math_asinh.gold │ ├── math_atan.gold │ ├── math_atanh.gold │ ├── math_ceiling.gold │ ├── math_cloglog.gold │ ├── math_cos.gold │ ├── math_cube.gold │ ├── math_div.gold │ ├── math_eq.gold │ ├── math_exp.gold │ ├── math_expit.gold │ ├── math_floor.gold │ ├── math_ge.gold │ ├── math_gt.gold │ ├── math_icloglog.gold │ ├── math_ilogit.gold │ ├── math_iprobit.gold │ ├── math_le.gold │ ├── math_length.gold │ ├── math_lfactorial.gold │ ├── math_lgamma.gold │ ├── math_log.gold │ ├── math_log1p.gold │ ├── math_logfact.gold │ ├── math_loggam.gold │ ├── math_logit.gold │ ├── math_lt.gold │ ├── math_max.gold │ ├── math_mean.gold │ ├── math_min.gold │ ├── math_minus.gold │ ├── math_mod.gold │ ├── math_mult.gold │ ├── math_neq.gold │ ├── math_or.gold │ ├── math_phi.gold │ ├── math_plus.gold │ ├── math_pmax.gold │ ├── math_pmin.gold │ ├── math_pow.gold │ ├── math_probit.gold │ ├── math_prod.gold │ ├── math_round.gold │ ├── math_rsqrt.gold │ ├── math_sin.gold │ ├── math_sqrt.gold │ ├── math_square.gold │ ├── math_sum.gold │ ├── math_tan.gold │ ├── math_tanh.gold │ └── math_trunc.gold │ ├── math_tests │ ├── test-math.R │ ├── test-recyclingRule.R │ └── test-recycling_rule.R │ ├── math_utils.R │ ├── nClass_tests │ ├── test-nClass_constructor.R │ ├── test-nClass_destructor.R │ ├── test-nClass_inherit.R │ ├── test-nClass_interface.R │ ├── test-nClass_nested.R │ └── test-nClass_uncompiled.R │ ├── nCompile_tests │ ├── test-Rcpp_nCompilerPacket.R │ ├── test-argumentPassing.R │ ├── test-callingBetweenNFs.R │ ├── test-compileErrorTrapping.R │ ├── test-compileNimble.R │ ├── test-cppLiteral.R │ ├── test-eigenShapeFlex.R │ ├── test-indexing.R │ ├── test-nCompile.R │ ├── test-nCompile_C_fun.R │ ├── test-nCompile_deps.R │ ├── test-nList.R │ └── test-userOps.R │ ├── nimble_tests │ ├── test-compileNimble.R │ └── test-nimbleModel.R │ ├── predefined_tests │ └── test-predefined.R │ ├── serialization_test_in_new_R_session.R │ ├── serialization_tests │ └── test-serialization.R │ ├── specificOp_tests │ ├── test-rep.R │ ├── test-seq.R │ └── 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