Man pages for JointAI
Joint Analysis and Imputation of Incomplete Data
| add_linebreaks | Add line breaks to a linear predictor string |
| add_samples | Continue sampling from an object of class JointAI |
| all_vars | Extract names of variables from several objects |
| auto_corr | Autocorrelation of MCMC samples |
| bs | B-Spline Basis for Polynomial Splines |
| check_classes | Check classes of all variables used in the model |
| check_data | Run all data related checks |
| check_duplicate_groupings | Check for duplicate grouping levels |
| check_fixed_random | Check whether fixed or formula contains a random effects... |
| check_formula_list | Ensure object is a (list of) formula(s) |
| check_full_blockdiag | Replace a full with a block-diagonal variance covariance... |
| check_groups_vary_within_lvl | Check if a grouping variable varies within another grouping... |
| check_na_groupings | Check for missing values in grouping variables |
| check_rd_vcov | Check / create the random effects variance-covariance matrix... |
| check_rd_vcov_list | First validation for rd_vcov |
| check_redundant_lvls | Check for unnecessary grouping levels |
| check_vars_in_data | Check that all variables in formulas are in the data |
| choose_default_model | Choose default analysis model based on outcome and data level |
| clean_names | Replace ":" with "_" in a string |
| clean_survname | Convert a survival outcome to a model name |
| combine_formula_lists | Combine fixed and random effects formulas |
| combine_formulas | Combine a fixed and random effects formula |
| compare_data_structure | Compare the structure of two data.frames |
| convert_variables | Convert variables |
| cross_corr | Cross-correlation of MCMC samples |
| default_hyperpars | Get the default values for hyper-parameters |
| densplot | Plot the posterior density from object of class JointAI |
| difftime_df | Converts a 'difftime' object to a 'data.frame' |
| drop_levels | Check for empty factor levels |
| duration_obj | Create a duration object |
| expand_rd_vcov_full | Expand rd_vcov using variable names in case "full" is used |
| extract_fixef_formula | Extract fixed effects formula from lme4-type formula |
| extract_grouping | Extract grouping variables from a (list of) formula(s) |
| extract_lhs_string | Extract the left hand side of a formula |
| extract_lhs_varnames | Extract variable names from the left-hand side of a formula |
| extract_ranef_formula | Extract random effects formula from lme4-type formula |
| extract_state | Return the current state of a 'JointAI' model |
| factor_to_integer | Convert a factor to an integer representation |
| get_datlvls | Determine grouping level of data |
| get_family | Identify the family from the covariate model type |
| get_grouping_levels | Get grouping levels |
| get_groups | Get grouping information |
| get_listelement | Get an element of a list, return a default value if it does... |
| get_MIdat | Extract multiple imputed datasets from an object of class... |
| get_missinfo | Obtain a summary of the missing values involved in an object... |
| get_Mlist | Re-create the full 'Mlist' from a "JointAI" object |
| get_modeltype | Identify the general model type from the covariate model type |
| get_nranef | Extract the number of random effects |
| get_resp_mat | Identify the data matrix containing a given response variable |
| GR_crit | Gelman-Rubin criterion for convergence |
| hc_rdslope_info | Get info on main effects in a rd slope structure for a level... |
| hc_rdslope_interact | Get info on the interactions with random slopes for a given... |
| internal_clean_survname | Convert a survival outcome to a model name |
| JointAI | JointAI: Joint Analysis and Imputation of Incomplete Data |
| JointAIObject | Fitted object of class 'JointAI' |
| list_models | List model details |
| longDF | Longitudinal example dataset |
| MC_error | Calculate and plot the Monte Carlo error |
| md_pattern | Missing data pattern |
| merge_call_args | Merge call arguments with default formals |
| model_imp | Joint Analysis and Imputation of incomplete data |
| NHANES | National Health and Nutrition Examination Survey (NHANES)... |
| normalize_formula_args | Normalize formula arguments in arglist |
| ns | Generate a Basis Matrix for Natural Cubic Splines |
| parameters | Parameter names of an JointAI object |
| paste_analysis_type | Paste analysis type with family information |
| paste_coef | Write the coefficient part of a linear predictor |
| paste_data | Write the data element of a linear predictor |
| paste_linpred | Write a linear predictor |
| paste_scale | Create the scaling in a data element of a linear predictor |
| paste_scaling | Wrap a data element of a linear predictor in scaling syntax |
| PBC | PBC data |
| plot_all | Visualize the distribution of all variables in the dataset |
| plot_imp_distr | Plot the distribution of observed and imputed values |
| plot.JointAI | Plot an object object inheriting from class 'JointAI' |
| predDF | Create a new data frame for prediction |
| predict.JointAI | Predict values from an object of class JointAI |
| prep_arglist | Prepare list of arguments for model_imp() |
| rd_terms_by_grouping | Extract terms by grouping variables from a formula |
| rd_vcov | Extract the random effects variance covariance matrix |
| reformat_difftime | Set all elements of a 'difftime' object to the same, largest... |
| remove_formula_grouping | Remove grouping part from (random effects) formula |
| remove_grouping | Remove grouping part from (random effects) formulas |
| remove_lhs | Remove the left hand side of a (list of) formula(s) |
| replace_nan_with_na | Replace NaN values with NA |
| residuals.JointAI | Extract residuals from an object of class JointAI |
| resolve_family_obj | Resolve family object |
| set_refcat | Specify reference categories for all categorical covariates... |
| sharedParams | Parameters used by several functions in JointAI |
| simLong | Simulated Longitudinal Data in Long and Wide Format |
| split_formula_list | Split a list of formulas into fixed and random effects parts. |
| sum_duration | Calculate the sum of the computational duration of a JointAI... |
| summary.JointAI | Summarize the results from an object of class JointAI |
| Surv | Create a Survival Object |
| traceplot | Create traceplots for a MCMC sample |
| two_value_to_factor | Convert two-value vectors to factors |
| varname_to_modelframe | Create data.frame from variable term and data |
| wideDF | Cross-sectional example dataset |
