├── .Rbuildignore ├── .covrignore ├── .gitattributes ├── .github ├── .gitignore └── workflows │ ├── R-CMD-check.yaml │ ├── pkgdown.yaml │ ├── render-readme.yaml │ └── test-coverage.yaml ├── .gitignore ├── .travis.yml ├── DESCRIPTION ├── JointAI.Rproj ├── NAMESPACE ├── NEWS.md ├── R ├── JAGSmodel_clm.R ├── JAGSmodel_clmm.R ├── JAGSmodel_glm.R ├── JAGSmodel_glmm.R ├── JAGSmodel_mlogit.R ├── JAGSmodel_mlogitmm.R ├── JAGSmodel_surv.R ├── JointAI.R ├── JointAIObject.R ├── add_samples.R ├── build_model.R ├── convergence_criteria.R ├── datasets.R ├── deprecated.R ├── divide_matrices.R ├── extract_state.R ├── get_MIdat.R ├── get_data_list.R ├── get_model_dimensions.R ├── get_model_info.R ├── get_modeltypes.R ├── get_params.R ├── get_refs.R ├── get_subset.R ├── helpfunctions.R ├── helpfunctions_JAGS.R ├── helpfunctions_JAGSmodel.R ├── helpfunctions_checks.R ├── helpfunctions_divide_matrices.R ├── helpfunctions_formulas.R ├── helpfunctions_formulas_general.R ├── helpfunctions_info_list.R ├── helpfunctions_melt.R ├── helpfunctions_model_imp.R ├── helpfunctions_prediction.R ├── helpfunctions_print-paste.R ├── helpfunctions_ranefs.R ├── helpfunctions_summary.R ├── helpfunctions_survival.R ├── helpfunctions_tests.R ├── helpfunctions_vcov.R ├── list_models.R ├── md_pattern.R ├── methods.R ├── model_imp.R ├── parameters.R ├── plot_imp_distr.R ├── plots.R ├── plots_ppc.R ├── predict.R ├── residuals.R ├── scaling.R ├── simulate_data.R ├── splines.R └── summary.JointAI.R ├── README.Rmd ├── README.md ├── _pkgdown.yml ├── codecov.yml ├── cran-comments.md ├── data ├── NHANES.RData ├── longDF.RData ├── pbc.RData ├── simLong.RData ├── simWide.RData └── wideDF.RData ├── inst ├── CITATION └── WORDLIST ├── man ├── GR_crit.Rd ├── JointAI.Rd ├── JointAIObject.Rd ├── MC_error.Rd ├── NHANES.Rd ├── PBC.Rd ├── Surv.Rd ├── add_linebreaks.Rd ├── add_samples.Rd ├── all_vars.Rd ├── bs.Rd ├── check_classes.Rd ├── check_data.Rd ├── check_duplicate_groupings.Rd ├── check_formula_list.Rd ├── check_full_blockdiag.Rd ├── check_rd_vcov.Rd ├── check_rd_vcov_list.Rd ├── check_unnecessary_grouping_levels.Rd ├── check_vars_in_data.Rd ├── clean_names.Rd ├── clean_survname.Rd ├── combine_formula_lists.Rd ├── combine_formulas.Rd ├── compare_data_structure.Rd ├── convert_variables.Rd ├── default_hyperpars.Rd ├── densplot.Rd ├── difftime_df.Rd ├── drop_levels.Rd ├── duration_obj.Rd ├── expand_rd_vcov_full.Rd ├── extract_fixef_formula.Rd ├── extract_grouping.Rd ├── extract_lhs_string.Rd ├── extract_lhs_varnames.Rd ├── extract_ranef_formula.Rd ├── extract_state.Rd ├── figures │ ├── JointAI_191.png │ ├── JointAI_square.png │ ├── README-unnamed-chunk-3-1.png │ ├── README-unnamed-chunk-4-1.png │ ├── README-unnamed-chunk-5-1.png │ ├── README-unnamed-chunk-6-1.png │ └── logo.png ├── get_MIdat.Rd ├── get_Mlist.Rd ├── get_family.Rd ├── get_groups.Rd ├── get_listelement.Rd ├── get_missinfo.Rd ├── get_modeltype.Rd ├── get_nranef.Rd ├── get_resp_mat.Rd ├── hc_rdslope_info.Rd ├── hc_rdslope_interact.Rd ├── list_models.Rd ├── longDF.Rd ├── md_pattern.Rd ├── model_imp.Rd ├── ns.Rd ├── parameters.Rd ├── paste_coef.Rd ├── paste_data.Rd ├── paste_linpred.Rd ├── paste_scale.Rd ├── paste_scaling.Rd ├── plot.JointAI.Rd ├── plot_all.Rd ├── plot_imp_distr.Rd ├── predDF.Rd ├── predict.JointAI.Rd ├── rd_terms_by_grouping.Rd ├── rd_vcov.Rd ├── reformat_difftime.Rd ├── remove_formula_grouping.Rd ├── remove_grouping.Rd ├── remove_lhs.Rd ├── replace_nan_with_na.Rd ├── residuals.JointAI.Rd ├── set_refcat.Rd ├── sharedParams.Rd ├── simLong.Rd ├── split_formula_list.Rd ├── sum_duration.Rd ├── summary.JointAI.Rd ├── traceplot.Rd ├── two_value_to_factor.Rd └── wideDF.Rd ├── pkgdown ├── extra.css └── favicon │ ├── apple-touch-icon-120x120.png │ ├── apple-touch-icon-152x152.png │ ├── apple-touch-icon-180x180.png │ ├── apple-touch-icon-60x60.png │ ├── apple-touch-icon-76x76.png │ ├── apple-touch-icon.png │ ├── favicon-16x16.png │ ├── favicon-32x32.png │ └── favicon.ico ├── tests ├── testthat.R └── testthat │ ├── _snaps │ ├── clm.md │ ├── clmm.md │ ├── coxph.md │ ├── glm.md │ ├── glmm.md │ ├── mlogit.md │ ├── mlogitmm.md │ ├── printfcts.md │ └── survreg.md │ ├── test-add_samples.R │ ├── test-auxvars.R │ ├── test-clm.R │ ├── test-clmm.R │ ├── test-coxph.R │ ├── test-get_models.R │ ├── test-glm.R │ ├── test-glmm.R │ ├── test-groupings.R │ ├── test-helpfunctions.R │ ├── test-helpfunctions_checks.R │ ├── test-helpfunctions_formulas.R │ ├── test-helpfunctions_formulas_general.R │ ├── test-helpfunctions_melt.R │ ├── test-helpfunctions_ranefs.R │ ├── test-helpfunctions_vcov.R │ ├── test-mlogit.R │ ├── test-mlogitmm.R │ ├── test-modeltypes.R │ ├── test-plots.R │ ├── test-printfcts.R │ ├── test-survival.R │ └── test-survreg.R └── vignettes ├── AfterFitting.Rmd ├── AfterFitting.Rmd.orig ├── MCMCsettings.Rmd ├── MinimalExample.Rmd ├── MinimalExample.Rmd.orig ├── ModelSpecification.Rmd ├── ModelSpecification.Rmd.orig ├── SelectingParameters.Rmd ├── SelectingParameters.Rmd.orig 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