Man pages for mrc-ide/threemc
(Matt's) Multi-Level Model of Male Circumcision in Sub-Saharan Africa
| add_area_id | Change 'area_id' from one hierarchy level to another |
| aggregate_sample | Produce Population Weighted Aggregated Samples |
| aggregate_sample_age_group | Produce Population Weighted Aggregations for Age Groups |
| append_mc_name | Append "mc" to Appropriate Column names |
| brackify | Convert vector to string |
| change_agegroup_convention | Change age group convention to match aggregation results |
| circ_sample_tmb | Sample TMB fit for Circumcision Model |
| combine_areas | Collect results for lower area hierarchies |
| compute_quantiles | Calculate Quantiles for Rates and Cumulative Hazard |
| create_aggregate_structure | Create a List containing the Hierarchy of levels |
| create_design_matrices | Create Design Matrices |
| create_dirs_r | Recursively Create Missing Directories |
| create_hazard_matrix_agetime | Create Matrix Selecting Instantaneous Hazard Rate |
| create_icar_prec_matrix | Create Precision Matrix for ICAR Process |
| create_integration_matrices | Create Integration Matrices for Selecting Instantaneous... |
| create_integration_matrix_agetime | Create Matrix to Estimate Cumulative Hazard Rate |
| create_integration_matrix_agetime_lag | Create Matrix to Estimate Lagged Cumulative Hazard Rate |
| create_rw_prec_matrix | Create Precision Matrix for RWp Process |
| create_shell_dataset | Create Shell Dataset for Estimating Empirical Circumcision... |
| create_survival_matrices | Create Survival Matrices for Selecting Instantaneous Hazard |
| datapack_psnu_area_level | PSNU Area Levels for SSA |
| demo_areas | Malawi shapefiles |
| demo_populations | Malawi populations |
| demo_survey_circumcision | Malawi surveys |
| esa_wca_regions | WCA - ESA key for Sub-Saharan African countries |
| fill_downup_populations | Assume constant historical and future populations |
| match_age_group_to_ages | Create data frame of all ages within provided age group. |
| merge_area_info | Merge Regional Information On Dataset |
| minimise_fit_obj | Minimise Fit Object Size |
| n_circumcised | Calculate Number of People Circumcised |
| normalise_weights_kish | Normalise Survey Weights and apply Kish Coefficients |
| patterns | Pattern matching for 'data.table' |
| posterior_summary_fun | Calculate Summary Statistics From Samples |
| prepare_sample_data | Pull N Circumcision Samples From TMB Fit |
| prepare_survey_data | Prepare Survey Data |
| prevalence_change | Calculate Change in Prevalence/Coverage From a Given Year |
| read_circ_data | Function to read in Circumcision Data |
| reassign_surey_level | Define circumcision type |
| rmvnorm_sparseprec | Take multivariate normal sample from sparse precision matrix |
| sample_tmb | Sample from TMB fit |
| scale_gmrf_precision | Scale of GMRF precision matrix |
| sdreport_joint_precision | Get Joint Precision of TMB Fixed and Random |
| shell_data_spec_area | Subset and Prepare Shell Dataset to Only One Admin Boundary |
| split_mmc_design_matrices_paed | Split MMC Design Matrices between adult and paediatric... |
| spread_areas | Spread area hierarchy to wide format |
| survey_points_dmppt2_convert_convention | Create data frame of all ages within provided age group.... |
| threemc_aggregate | Produce Population Weighted Aggregated Samples for All Area... |
| threemc_empirical_rates | Use model shell dataset to estimate empirical circumcision... |
| threemc_fit_model | Produce TMB model fit with sample, or re-sample from existing... |
| threemc_initial_pars | Initialise 'thremec' (hyper)parameters. |
| threemc_ppc | Posterior Predictive Distribution and checks on OOS survey |
| threemc_ppc2 | Posterior Predictive Distribution and checks on OOS survey |
| threemc_prepare_model_data | Produce Data Matrices for Modelling |
