Man pages for mrc-ide/naomi
Naomi Model for Subnational HIV Estimates
| add_output_labels | Add labels to output indicators |
| age_bar_plotly | Plotly barplot comparing age distribution of survey inputs... |
| aggregate_anc | Aggregate ANC data according to area hierarchy |
| aggregate_art | Aggregate ART data according to area hierarchy |
| align_inputs_outputs | Align model data inputs and model estimates |
| anc_programme_data_warning | Warning for aggregated subnational data input snot equal to... |
| anc_testing_prev_mf | Prepare Model Frames for Programme Datasets |
| artnum_mf | Build artnum model frame |
| art_programme_data_warning | Warning for aggregated subnational data input snot equal to... |
| assert_pjnz_shiny90 | Check whether PJNZ contains .shiny90 file |
| bar_plotly | Plotly barplot comparing geographical distribution of data... |
| build_hierarchy_label | Return the translated label & description for a set of plot... |
| cache_invariant | Make a function cache invariant |
| calculate_prevalence_art_coverage | Calculate prevalence and ART coverage from ANC input data |
| calibrate_outputs | Calibrate naomi model outputs |
| cmc_date | Convert Date to Century Month Code (CMC) |
| create_adj_matrix | Create adjacency matrix from spatial polygons |
| create_area_aggregation | Long data frame mapping area hierarchy areas to model level... |
| create_areas | Create an Areas Object |
| create_edge_list | Create edgelist from adjacency matrix |
| cut_naomi_age_group | Cut Five Year Age Groups |
| data_type_labels | Get id to label mapping for calibration plot data type |
| demo_anc_testing | Programme data: Malawi routine HIV service delivery data |
| demo_area_boundaries | Malawi area boundaries. |
| demo_area_hierarchy | Malawi area hierarchy |
| demo_area_levels | Malawi area levels. |
| demo_population_agesex | Malawi age-sex stratified population data |
| demo_survey_biomarker | Malawi survye biomarkers |
| demo_survey_clusters | Malawi survey clusters |
| demo_survey_hiv_indicators | Malawi HIV indicators |
| demo_survey_individuals | Malawi survey individuals |
| demo_survey_meta | Malawi survey metadata |
| demo_survey_regions | Malawi survey regions |
| disaggregate_0to4_outputs | Disaggregate age 0-4 outputs to <1 / 1-4 |
| district_barplot | Create district bar plot |
| dropdown_buttons | Automatically make drop drop buttons for plotly filter |
| extract_pjnz_naomi | Extract Model Inputs from Spectrum PJNZ |
| extract_pjnz_program_data | Extract ART and ANC testing program data inputs from Spectrum... |
| extract_shiny90_age_sex | Export proportion aware by five year age group from Shiny90 |
| fit_tmb | Fit TMB model |
| generate_comparison_report | Generate and save comparison report at specified path |
| generate_output_summary_report | Generate and save summary report at specified path |
| get_age_group_out | Get age group ids for output |
| get_age_groups | Data frame of age groups |
| get_anc_metadata | Metadata for ANC plot types used in the input time series... |
| get_area_collection | Get a collection of areas |
| get_art_metadata | Metadata for ART plot types used in the input time series... |
| get_colour_scale | Get colour scale and ranges for a particular country |
| get_five_year_age_groups | Get 5 year age groups |
| get_metadata | Get indicator metadata as a data frame |
| get_meta_indicator | Get indicator metadata |
| get_plotting_metadata | Get plotting metadata for a particular country |
| get_plot_type_column_metadata | Return the translated label & description for a set of plot... |
| get_spec_aggr_interpolation | Interpolate Spectrum to quarter_id |
| hintr_calibrate | Calibrate hintr_output |
| hintr_calibrate_plot | Get data for hintr calibrate plot |
| hintr_comparison_plot | Get data for hintr comparison plot |
| hintr_prepare_agyw_download | Prepare AGYW tool download |
| hintr_prepare_coarse_age_group_download | Prepare coarse age group download |
| hintr_prepare_comparison_report_download | Prepare comparison report download |
| hintr_prepare_datapack_download | Prepare Datapack download |
| hintr_prepare_spectrum_download | Prepare spectrum download |
| hintr_prepare_summary_report_download | Prepare summary report download |
| hintr_run_model | Run the model and save output |
| hintr_validate_anc_programme_data | Run validation for subnational programme data input |
| hintr_validate_art_programme_data | Run validation for subnational programme data input |
| Imports | We need to import these as they are used by dependencies... |
| interpolate_population_agesex | Log-linear interpolation of age/sex stratified population |
| log_linear_interp | Log-linear interpolation of NA values |
| map_outputs | Create output map plot |
| naomi_model_frame | Construct Model Frames and Adjacency Structures |
| naomi_objective_function_r | R implementation of Naomi model |
| naomi_output_frame | Model Frame and Linear Transform for Aggregated Model Outputs |
| output_naomi_warning | Generate naomi warning for specific strata of simulated... |
| output_package | Build output package from fit |
| pipe | Pipe operator |
| pop_pyramid_outputs | Create population pyramid plot |
| prepare_anc_spectrum_comparison | Compare aggregated subnational ART inputs + spectrum totals... |
| prepare_art_spectrum_comparison | Compare aggregated district ART inputs + spectrum totals... |
| prepare_input_time_series_anc | Prepare data for ANC input time series plots |
| prepare_input_time_series_art | Prepare data for ART input time series plots |
| prepare_spectrum_naomi_comparison | Compare aggregated subnational Naomi + spectrum totals for... |
| prepare_tmb_inputs | Prepare inputs for TMB model. |
| quarter_year_labels | Time period indexing |
| read_csv_partial_cols | Read CSV with missing columns |
| read_hintr_output | Read hintr output |
| read_metadata | Get indicator metadata as a data frame |
| read_population | Read Naomi structured input files |
| read_spectrum_projection_name | Read Spectrum Projection Name from Spectrum PJNZ |
| read_spectrum_region_code | Read Subnational Region Code from Spectrum PJNZ |
| read_spectrum_region_name | Read Subnational Region Name from Spectrum PJNZ |
| report_tmb | Calculate Posterior Mean and Uncertainty Via TMB 'sdreport()' |
| sample_tmb | Sample TMB fit |
| save_output | Save outputs to zip file |
| save_output_package | Save outputs to zip file |
| scale_gmrf_precision | Scale of GMRF precision matrix |
| scatter_plotly | Plotly scatterplot data inputs and naomi outputs |
| sdreport_joint_precision | Get Joint Precision of TMB Fixed and Random |
| select_naomi_data | Select data for model fitting |
| spread_areas | Spread area hierarchy to wide format |
| subset_naomi_output | Subset the results returned in Naomi output package |
| subset_output_package | Resave a subsetted Naomi output package |
| survey_mf | Prepare model frames for survey datasets |
| tag_data_inputs | Tag data inputs |
| th_map | 'ggplot2' theme for plotting maps |
| validate_model_options | Validate a set of model options |
| write_datapack_csv | Export naomi outputs to PEPFAR Data Pack format |
| write_navigator_checklist | Write UNAIDS Estimates Navigator checklist CSV |
