├── .Rbuildignore ├── DESCRIPTION ├── NAMESPACE ├── NEWS ├── R ├── .DS_Store ├── 00_codeOrganization.R ├── 00_steps_to_implement_distribution.R ├── 00_steps_to_implement_estimator.R ├── 00_steps_to_implement_model.R ├── 01_classes.R ├── 02_algebrahelpers_Solve.R ├── 02_algebrahelpers_blockToeplitz.R ├── 02_algebrahelpers_checkJacobian.R ├── 02_algebrahelpers_expected_latent_residual_covs.R ├── 02_algebrahelpers_expectedmodel.R ├── 02_algebrahelpers_kronecker.R ├── 02_algebrahelpers_lavUtils.R ├── 02_algebrahelpers_matrixexponent.R ├── 02_algebrahelpers_maxcor.R ├── 02_algebrahelpers_modelMatrix.R ├── 02_algebrahelpers_quantiletransform.R ├── 02_algebrahelpers_spectralshift.R ├── 02_algebrahelpers_trysolve.R ├── 02_algebrahelpers_vectorize.R ├── 02_algebrahelpers_vectorizeMatrices.R ├── 02_algebrahelpers_weighted_geomean.R ├── 02_modelformation_PCCPDC.R ├── 03_modelformation_adjust_p_values.R ├── 03_modelformation_defaultoptimizer.R ├── 03_modelformation_factorstart.R ├── 03_modelformation_fixAdj.R ├── 03_modelformation_fixMatrix.R ├── 03_modelformation_fixMu.R ├── 03_modelformation_fixTau.R ├── 03_modelformation_formModelMatrices.R ├── 03_modelformation_generateParameterTable.R ├── 03_modelformation_impliedcovstructures.R ├── 03_modelformation_labtoind.R ├── 03_modelformation_matrixSetup_Isingbeta.R ├── 03_modelformation_matrixSetup_Isingtau.R ├── 03_modelformation_matrixSetup_SD.R ├── 03_modelformation_matrixSetup_beta.R ├── 03_modelformation_matrixSetup_cholesky.R ├── 03_modelformation_matrixSetup_delta.R ├── 03_modelformation_matrixSetup_isingomega.R ├── 03_modelformation_matrixSetup_kappa.R ├── 03_modelformation_matrixSetup_lambda.R ├── 03_modelformation_matrixSetup_mu.R ├── 03_modelformation_matrixSetup_omega.R ├── 03_modelformation_matrixSetup_rho.R ├── 03_modelformation_matrixSetup_sigma.R ├── 03_modelformation_matrixSetup_tau.R ├── 03_modelformation_missingpatterns.R ├── 03_modelformation_missingpatterns_covs.R ├── 03_modelformation_samplestats.R ├── 03_modelformation_samplestats_norawts.R ├── 03_modelformation_samplestats_rawts.R ├── 03_modelformation_sparseordense.R ├── 03_modelformation_startvaluesandbounds.R ├── 03_modelformation_tsData.R ├── 04_generalFit_fitfunction.R ├── 04_generalFit_gradient.R ├── 04_generalFit_logLikelihood.R ├── 04_generalfit_FisherInformation.R ├── 04_generalfit_VCOV.R ├── 04_generalfit_impliedModel.R ├── 04_generalfit_loglikelihood_Ising.R ├── 04_generalfit_loglikelihood_gauss.R ├── 04_generalfit_prepareModel.R ├── 04_modelformation_matrixSetup_flexcov.R ├── 05_MLestimator_expected_hessian_Gauss.R ├── 05_MLestimator_expected_hessian_Ising.R ├── 05_MLestimator_fit_Gauss.R ├── 05_MLestimator_fit_Ising.R ├── 05_MLestimator_fitfunction.R ├── 05_MLestimator_gradient_Gauss.R ├── 05_MLestimator_gradient_Ising.R ├── 06_ULS_expectedHessian.R ├── 06_ULS_fitfunction.R ├── 06_ULS_gradient.R ├── 06_weightsMatrix.R ├── 07_FIMLestimator_expected_hessian_Gauss.R ├── 07_FIMLestimator_fit_Gauss.R ├── 07_FIMLestimator_fitfunction.R ├── 07_FIMLestimator_gradient_Gauss.R ├── 08_outputHelpers_NAtoFALSE.R ├── 08_outputHelpers_NAtoTRUE.R ├── 08_outputHelpers_goodNum.R ├── 08_outputHelpers_logo.R ├── 09_modelmodification_clearpars.R ├── 09_modelmodifivation_emergencystart.R ├── 14_varcov_derivatives.R ├── 14_varcov_implied.R ├── 14_varcov_prepare.R ├── 15_lvm_derivatives.R ├── 15_lvm_identify.R ├── 15_lvm_implied.R ├── 15_lvm_prepare.R ├── 16_var1_derivatives.R ├── 16_var1_implied.R ├── 16_var1_prepare.R ├── 18_dlvm1_derivatives.R ├── 18_dlvm1_identify.R ├── 18_dlvm1_implied.R ├── 18_dlvm1_prepare.R ├── 19_tsdlvm1_derivatives.R ├── 19_tsdlvm1_identify.R ├── 19_tsdlvm1_implied.R ├── 19_tsdlvm1_prepare.R ├── 20_meta_varcov_derivatives.R ├── 20_meta_varcov_implied.R ├── 20_meta_varcov_prepare.R ├── 21_Ising_derivatives.R ├── 21_Ising_helperfunctions.R ├── 21_Ising_identify.R ├── 21_Ising_implied.R ├── 21_Ising_prepare.R ├── 22_ml_lvm_derivatives.R ├── 22_ml_lvm_identify.R ├── 22_ml_lvm_implied.R ├── 22_ml_lvm_prepare.R ├── RcppExports.R ├── a_models_Ising.R ├── a_models_bifactor.R ├── a_models_cholesky.R ├── a_models_corr.R ├── a_models_dlvm1.R ├── a_models_frombootnet.R ├── a_models_ggm.R ├── a_models_gvar.R ├── a_models_joingroups.R ├── a_models_latentgrowth.R ├── a_models_lnm.R ├── a_models_lrnm.R ├── a_models_lvm.R ├── a_models_meta_ggm.R ├── a_models_meta_varcov.R ├── a_models_ml_lnm.R ├── a_models_ml_lrnm.R ├── a_models_ml_lvm.R ├── a_models_ml_rnm.R ├── a_models_ml_tsdlvm1.R ├── a_models_ml_tslvgvar.R ├── a_models_panelgvar.R ├── a_models_precision.R ├── a_models_ri_clpm.R ├── a_models_rnm.R ├── a_models_sem.R ├── a_models_tsdlvm1.R ├── a_models_tslvgvar.R ├── a_models_var1.R ├── a_models_varcov.R ├── b_modelexpansions_addMIs.R ├── b_modelexpansions_addSEs.R ├── b_modelexpansions_addfit.R ├── b_modelexpansions_identify.R ├── b_modelexpansions_updateModel.R ├── c_runmodel.R ├── d_stepup.R ├── e_modelmodifications_fixpar.R ├── e_modelmodifications_fixstart.R ├── e_modelmodifications_freepar.R ├── e_modelmodifications_groupequal.R ├── e_modelmodifications_groupfree.R ├── e_modelmodifications_intersectionmodel.R ├── e_modelmodifications_partialprune.R ├── e_modelmodifications_prune.R ├── e_modelmodifications_ri_clpm_stationarity.R ├── e_modelmodifications_setequal.R ├── e_modelmodifications_transmod.R ├── e_modelmodifications_unionmodel.R ├── f_conveneince_changedata.R ├── f_conveneince_fake_optimr.R ├── f_conveneince_fakeoptimr.R ├── f_conveneince_generate.R ├── f_conveneince_setEstimator.R ├── f_conveneince_setoptimizer.R ├── f_conveneince_setverbose.R ├── f_conveneince_usecpp.R ├── f_convenience_CIplot.R ├── f_convenience_MIs.R ├── f_convenience_aggregate_bootstraps.R ├── f_convenience_bootstrap.R ├── f_convenience_bootstrap_SEs.R ├── f_convenience_bootstrap_warning.R ├── f_convenience_covML.R ├── f_convenience_ergodicity.R ├── f_convenience_factorscores.R ├── f_convenience_fit.R ├── f_convenience_getmatrix.R ├── f_convenience_logbook.R ├── f_convenience_modelCompare.R ├── f_convenience_parameters.R ├── f_convenience_printMethod.R ├── f_convenience_printMethod_bootstrap.R ├── f_convenience_residuals.R ├── f_convenience_simplestructure.R ├── g_simulations_replicator.R └── h_modelsearch.R ├── README_figs ├── README-unnamed-chunk-19-1.png └── README-unnamed-chunk-38-1.png ├── data ├── Jonas.RData └── StarWars.RData ├── logo.png ├── man ├── .DS_Store ├── CIplot.Rd ├── Ising.Rd ├── Jonas.Rd ├── MIs.Rd ├── StarWars.Rd ├── aggregate_bootstraps.Rd ├── algebraMatrices.Rd ├── bifactor.Rd ├── bootstrap.Rd ├── changedata.Rd ├── compare.Rd ├── convenience.Rd ├── covML.Rd ├── diagnostics.Rd ├── dlvm1_family.Rd ├── emergencystart.Rd ├── esa.Rd ├── factorscores.Rd ├── fit.Rd ├── fixpar_freepar.Rd ├── fixstart.Rd ├── generate.Rd ├── getVCOV.Rd ├── getmatrix.Rd ├── groupequal_groupfree.Rd ├── latentgrowth.Rd ├── logbook.Rd ├── lvm_family.Rd ├── meta_varcov.Rd ├── ml_lvm.Rd ├── ml_tsdlvm1.Rd ├── modelsearch.Rd ├── modelupdate.Rd ├── parameters.Rd ├── parequal.Rd ├── partialprune.Rd ├── prune.Rd ├── psychonetrics-class.Rd ├── psychonetrics-package.Rd ├── psychonetrics_bootstrap-class.Rd ├── psychonetrics_log-class.Rd ├── ri_clpm.Rd ├── runmodel.Rd ├── setverbose.Rd ├── simplestructure.Rd ├── stepup.Rd ├── transmod.Rd ├── tsdlvm1_family.Rd ├── unionmodel_intersectionmodel.Rd ├── var1_family.Rd └── varcov_family.Rd ├── readme.md └── src ├── 02_algebragelpers_kronecker.h ├── 02_algebrahelpers_RcppHelpers.cpp ├── 02_algebrahelpers_RcppHelpers.h ├── 02_algebrahelpers_kronecker.cpp ├── 02_algebrahelpers_modelMatrix_cpp.cpp ├── 02_algebrahelpers_modelMatrix_cpp.h ├── 03_modelformation_formModelMatrices_cpp.cpp ├── 03_modelformation_formModelMatrices_cpp.h ├── 03_modelformation_impliedcovstructures.cpp ├── 03_modelformation_impliedcovstructures.h ├── 03_modelinformation_sparseordense_cpp.cpp ├── 03_modelinformation_sparseordense_cpp.h ├── 04_generalFit_FisherInformation_cpp.cpp ├── 04_generalFit_gradient_cpp.cpp ├── 04_generalFit_gradient_cpp.h ├── 04_generalFit_implied_and_prepare.h ├── 04_generalfit_fitfunction_cpp.cpp ├── 04_generalfit_fitfunction_cpp.h ├── 04_generalfit_implied_and_prepare.cpp ├── 04_generalfit_loglik_fimlcpp.cpp ├── 04_generalfit_psychonetrics_BFGS.cpp ├── 05_MLestimator_expected_Hessian_Gauss_cpp.cpp ├── 05_MLestimator_expected_Hessian_Gauss_cpp.h ├── 05_MLestimator_fit_Gauss_cpp.cpp ├── 05_MLestimator_fit_Gauss_cpp.h ├── 05_MLestimator_fit_Ising.cpp ├── 05_MLestimator_fit_Ising.h ├── 05_MLestimator_gradient_Gauss_cpp.cpp ├── 05_MLestimator_gradient_Gauss_cpp.h ├── 05_MLestimator_gradient_Ising_cpp.cpp ├── 05_MLestimator_gradient_Ising_cpp.h ├── 06_DWLS_Wmat.cpp ├── 06_ULS_expectedHessian_cpp.cpp ├── 06_ULS_expectedHessian_cpp.h ├── 06_ULS_fitfunction_cpp.cpp ├── 06_ULS_fitfunction_cpp.h ├── 06_ULS_gradient_cpp.cpp ├── 06_ULS_gradient_cpp.h ├── 06_WLS_Wmat.cpp ├── 07_FIMLestimator_expected_hessian_gauss_cppversion.cpp ├── 07_FIMLestimator_expected_hessian_gauss_cppversion.h ├── 07_FIMLestimator_fitfunction_cppversion.cpp ├── 07_FIMLestimator_fitfunction_cppversion.h ├── 07_FIMLestimator_jacobian_gauss.cpp ├── 07_FIMLestimator_jacobian_gauss.h ├── 10_ordinal_covPrepare.cpp ├── 10_ordinal_cppFuns.cpp ├── 10_ordinal_cppFuns.h ├── 14_varcov_derivatives_cpp.cpp ├── 14_varcov_derivatives_cpp.h ├── 14_varcov_implied_cpp.cpp ├── 14_varcov_implied_cpp.h ├── 14_varcov_prepare_cpp.cpp ├── 14_varcov_prepare_cpp.h ├── 15_lvm_derivatives_cpp.cpp ├── 15_lvm_derivatives_cpp.h ├── 15_lvm_implied_cpp.cpp ├── 15_lvm_implied_cpp.h ├── 15_lvm_prepare_cpp.cpp ├── 15_lvm_prepare_cpp.h ├── 16_var1_derivatives_cpp.cpp ├── 16_var1_derivatives_cpp.h ├── 16_var1_implied_cpp.cpp ├── 16_var1_implied_cpp.h ├── 16_var1_prepare_cpp.cpp ├── 16_var1_prepare_cpp.h ├── 18_dlvm1_derivatives_cpp.cpp ├── 18_dlvm1_derivatives_cpp.h ├── 18_dlvm1_implied_cpp.cpp ├── 18_dlvm1_implied_cpp.h ├── 18_dlvm1_prepare_cpp.cpp ├── 18_dlvm1_prepare_cpp.h ├── 19_tsdlvm1_derivatives.cpp ├── 19_tsdlvm1_derivatives_cpp.h ├── 19_tsdlvm1_implied_cpp.cpp ├── 19_tsdlvm1_implied_cpp.h ├── 19_tsdlvm1_prepare_cpp.cpp ├── 19_tsdlvm1_prepare_cpp.h ├── 20_meta_varcov_derivatives_cpp.cpp ├── 20_meta_varcov_derivatives_cpp.h ├── 20_meta_varcov_implied.cpp ├── 20_meta_varcov_implied_cpp.h ├── 20_meta_varcov_prepare_cpp.cpp ├── 20_meta_varcov_prepare_cpp.h ├── 21_Ising_derivatives.cpp ├── 21_Ising_derivatives_cpp.h ├── 21_Ising_expectedHessian.cpp ├── 21_Ising_helperfunctions.cpp ├── 21_Ising_helperfunctions.h ├── 21_Ising_implied_cpp.cpp ├── 21_Ising_implied_cpp.h ├── 21_Ising_prepare_cpp.cpp ├── 21_Ising_prepare_cpp.h ├── 22_ml_lvm_derivatives.cpp ├── 22_ml_lvm_derivatives_cpp.h ├── 22_ml_lvm_implied_cpp.cpp ├── 22_ml_lvm_implied_cpp.h ├── 22_ml_lvm_prepare_cpp.cpp ├── 22_ml_lvm_prepare_cpp.h ├── Makevars ├── Makevars.win ├── RcppExports.cpp ├── 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