| analyze_x_posterior | Analyze an input density by calculating the mean and... |
| apply_cat_spec | Apply a category specification to an input vector of original... |
| build_cindep_model | Build a multivariate, conditionally independent model using... |
| build_file_path | Build the path to a file in the data directory |
| build_lr_var | Build a left/right variable from the base variable, side... |
| build_univariate_cont_problems | Build a list of univariate continuous problems |
| build_univariate_ord_problems | Build a list of univariate ordinal problems |
| build_var_names | Build a complete vector of variable names for the input data... |
| calc_bin_prob | Calculate bin probabilities for a univariate ordinal dataset |
| calc_ci_ord | Calculate ordinal model confidence intervals |
| calc_cond_gauss_int_inputs | Calculate the inputs to the conditional Gaussian integral |
| calc_conditional_gaussian_integral | Calculate the conditional multivariate Gaussian integral over... |
| calc_joint | Calculate the joint density probability p(x,y|th_x,th_y) |
| calc_kl_div | Calculate the Kullback-Leibler (KL) divergence of a posterior... |
| calc_mean | Calculate the mean response for a yada mean specification |
| calc_mean_univariate_cont | Calculate the mean for a univariate continuous model |
| calc_mean_univariate_ord | Calculate the mean for a univariate ordinal model |
| calc_neg_log_lik_cont | Calculate the negative log-likelihood for a continuous model |
| calc_neg_log_lik_multivariate | Calculate the overall (summed) negative log-likelihood |
| calc_neg_log_lik_ord | Calculate the negative log-likelihood for an ordinal model |
| calc_neg_log_lik_scalar_multivariate | Calculate the negative log-likelihood for a single... |
| calc_neg_log_lik_vect_cont | Calculate the vector of negative log-likelihoods for a... |
| calc_neg_log_lik_vect_multivariate | Use a parallel for loop to calculate the vector of negative... |
| calc_neg_log_lik_vect_multivariate_chunk_inner | The inner function for calculating the negative... |
| calc_neg_log_lik_vect_multivariate_chunk_outer | The outer function for calculating the negative... |
| calc_neg_log_lik_vect_ord | Calculate the vector of negative log-likelihoods for an... |
| calc_noise | Calculate the noise for a yada noise specification |
| calc_noise_univariate_cont | Calculate the noise for a univariate continuous model |
| calc_noise_univariate_ord | Calculate the noise for a univariate ordinal model |
| calc_q | Calculate the likelihood for a univariate ordinal model as a... |
| calc_trapez_weights | Calculate integration weights assuming the midpoint rule |
| calc_weib_mix_density | Caculate the density for a Weibull mixture model |
| calc_weib_mix_density_matrix | Calculate the probability density function (PDF) matrix for a... |
| calc_x_density | Calculate the density for a model th_x, p(x|th_x) |
| calc_x_posterior | Calculate the posterior density of x |
| clear_temp_dir | Clear all the files in the temporary directory |
| comb | Calculate the combinadic |
| crossval_multivariate_models | Calculate multivariate (cindep and cdep)... |
| crossval_univariate_models | Cross-validation of univariate models |
| dual | Calculate the dual |
| elem | Calculate the element |
| elem_to_index | Convert the element (a vector) to the corresponding index (a... |
| extract_univariate_param_vect | Extract the parameter vector for a univariate fit from a... |
| fail_for_beta2 | A helper function to check whether the fits in TH_y fail for... |
| fit_multivariate | Fit a multivariate mixed cumulative probit model. |
| fit_univariate_cont | Fit a univariate continuous model |
| fit_univariate_ord | Fit a univariate ordinal model |
| generate_cv_problems | A wrapper to generate the cross-validation problems |
| generate_mod_spec | Generate mod_spec list for use in yada functions |
| generate_ord_ci | Generate the confidence intervals for a given a... |
| get_approx_x_range_cont | Get the approximate range of x-values given a single, known... |
| get_approx_x_range_ord | Get the approximate range of x-values given a single, known... |
| get_best_univariate_params | Get the parameters of the best cross-validated fits |
| get_J | Get J for a yada model specification |
| get_K | Get K for a yada model specification |
| get_mean_transform_categories | Return the transform categories (see... |
| get_multivariate_transform_categories | Return the categories used by [param_constr2uncontr] and... |
| get_noise_transform_categories | Return the transform categories (see... |
| get_non_singleton_groups | Get the non-singleton groups for the input group vector |
| get_num_folds | A helper function to identify univariate fit in a folder and... |
| get_num_training_problems | A helper function to identify the number of training problems... |
| get_num_var_mean | Get the number of variables for a yada mean specification |
| get_num_var_multivariate | Get the number of parameters for named variables of a... |
| get_num_var_noise | Get the number of variables for a yada noise specification |
| get_num_var_univariate_cont | Get the number of parameters for named variables of a... |
| get_num_var_univariate_ord | Get the number of parameters for named variables of a... |
| get_univariate_cont_transform_categories | Get the tranform categories for a univariate continuous model |
| get_univariate_indices | For a multivariate model, get the indices in the full... |
| get_univariate_ord_transform_categories | Get the tranform categories for a univariate ordinal model |
| get_univariate_variable_cases | A helper function to check the files in data_dir to get the... |
| get_var_index_multivariate | Get the indices in the parameter vector th_y of named... |
| get_var_index_multivariate_fast | Quickly get the indices in the parameter vector th_y of named... |
| get_var_index_multivariate_mapping | A helper function to build the mapping for... |
| get_var_index_univariate_cont | Get the variable indices for a univariate, continuous model... |
| get_var_index_univariate_ord | Get the variable indices for a univariate, ordinal model... |
| get_z_full_fast | Quickly extract the correlation vector, z |
| get_z_length | Get the number of correlation terms for a yada model... |
| hjk_nll_wrapper | A wrapper for calculating the negative log-likehood in... |
| init_univariate_ord | Initialize a univariate ordinal model |
| is_cdep | Is this model conditionally dependent? |
| load_best_univariate_model | Load the best univariate model using saved univariate... |
| load_cp_data | Load cumulative probit data from file |
| load_var_info | Load variable information from file |
| mean_spec_int_to_str | Convert from an integer to string representation of the mean... |
| merge_lr_var | Merge a variable that has distinct left and right... |
| merge_multiple_lr_var | Merge multiple variables that have distinct left and right... |
| noise_spec_int_to_str | Convert from an integer to string representation of the noise... |
| param_constr_to_unconstr | Transform a vector from a constrained to an unconstrained... |
| param_unconstr_to_constr | Transform a vector from an unconstrained to a constrained... |
| parse_cat_spec | Parse a category specification |
| parse_joined_model | Parse a joined model to get the individual mean and noise... |
| parse_NA_values | Parse missing value information from var_info |
| plot_x_posterior | Plot the posterior density using the result of a call to... |
| prep_for_neg_log_lik_multivariate | Prepare for the negative log-likelihood calculations |
| remove_missing_variables | For a single observation, remove missing variables and... |
| renumber_groups | Renumber the groups in the input vector group0 so that the... |
| sample_x_posterior | Sample from the posterior density of x |
| save_problem | Wrapper function to save problem files |
| sim_multivariate | Create simulated observations for a multivarate mixed... |
| sim_univariate_cont | Simulate a univariate ordinal model |
| sim_univariate_ord | Simulate a univariate ordinal model |
| solve_cont_problem | Solve a univariate continuous problem |
| solve_ord_problem | Solve a univariate ordinal problem |
| vis_cont_fit | Visualize a continuous fit |
| vis_ord_fit | Visualize an ordinal fit |
| write_continuous_report | Make an Rmarkdown document in the results folder for a... |
| write_matrix | A helper function to write a matrix to an Rmd file |
| write_ordinal_report | Make an Rmarkdown document in the results folder for an... |
| yada_sample_mcmc | Sample a likelihood function at a given temperature using an... |
| yada_tailored_annealing | Do a tailored optimization using simulated annealing |
