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Mainly for internal use.", "topics": [ "get_art_metadata" ] }, { "page": "get_five_year_age_groups", "title": "Get 5 year age groups", "topics": [ "get_five_year_age_groups" ] }, { "page": "get_meta_indicator", "title": "Get indicator metadata", "topics": [ "get_meta_indicator" ] }, { "page": "get_metadata", "title": "Get indicator metadata as a data frame", "topics": [ "get_metadata" ] }, { "page": "get_plot_type_column_metadata", "title": "Return the translated label & description for a set of plot types", "topics": [ "get_plot_type_column_metadata" ] }, { "page": "get_plotting_metadata", "title": "Get plotting metadata for a particular country", "topics": [ "get_plotting_metadata" ] }, { "page": "get_spec_aggr_interpolation", "title": "Interpolate Spectrum to quarter_id", "topics": [ "get_spec_aggr_interpolation" ] }, { "page": "hintr_calibrate", "title": "Calibrate hintr_output", "topics": [ "hintr_calibrate" ] }, { "page": "hintr_calibrate_plot", "title": "Get data for hintr calibrate plot", "topics": [ "hintr_calibrate_plot" ] }, { "page": "hintr_comparison_plot", "title": "Get data for hintr comparison plot", "topics": [ "hintr_comparison_plot" ] }, { "page": "hintr_prepare_agyw_download", "title": "Prepare AGYW tool download", "topics": [ "hintr_prepare_agyw_download" ] }, { "page": "hintr_prepare_coarse_age_group_download", "title": "Prepare coarse age group download", "topics": [ "hintr_prepare_coarse_age_group_download" ] }, { "page": "hintr_prepare_comparison_report_download", "title": "Prepare comparison report download", "topics": [ "hintr_prepare_comparison_report_download" ] }, { "page": "hintr_prepare_datapack_download", "title": "Prepare Datapack download", "topics": [ "hintr_prepare_datapack_download" ] }, { "page": "hintr_prepare_spectrum_download", "title": "Prepare spectrum download", "topics": [ "hintr_prepare_spectrum_download" ] }, { "page": "hintr_prepare_summary_report_download", "title": "Prepare summary report download", "topics": [ "hintr_prepare_summary_report_download" ] }, { "page": "hintr_run_model", "title": "Run the model and save output", "topics": [ "hintr_run_model" ] }, { "page": "hintr_validate_anc_programme_data", "title": "Run validation for subnational programme data input", "topics": [ "hintr_validate_anc_programme_data" ] }, { "page": "hintr_validate_art_programme_data", "title": "Run validation for subnational programme data input", "topics": [ "hintr_validate_art_programme_data" ] }, { "page": "Imports", "title": "We need to import these as they are used by dependencies (first90) unalified and need to be available in the package environment for the tests to be able to run in a background progress (i.e. when running in parllel)", "topics": [ "Imports" ] }, { "page": "interpolate_population_agesex", "title": "Log-linear interpolation of age/sex stratified population", "topics": [ "interpolate_population_agesex" ] }, { "page": "log_linear_interp", "title": "Log-linear interpolation of NA values", "topics": [ "log_linear_interp" ] }, { "page": "map_outputs", "title": "Create output map plot", "topics": [ "map_outputs" ] }, { "page": "naomi_model_frame", "title": "Construct Model Frames and Adjacency Structures", "topics": [ "naomi_model_frame" ] }, { "page": "naomi_objective_function_r", "title": "R implementation of Naomi model", "topics": [ "naomi_objective_function_r" ] }, { "page": "naomi_output_frame", "title": "Model Frame and Linear Transform for Aggregated Model Outputs", "topics": [ "naomi_output_frame" ] }, { "page": "output_naomi_warning", "title": "Generate naomi warning for specific strata of simulated outputs", "topics": [ "output_naomi_warning" ] }, { "page": "output_package", "title": "Build output package from fit", "topics": [ "output_package" ] }, { "page": "pop_pyramid_outputs", "title": "Create population pyramid plot", "topics": [ "pop_pyramid_outputs" ] }, { "page": "prepare_input_time_series_anc", "title": "Prepare data for ANC input time series plots", "topics": [ "prepare_input_time_series_anc" ] }, { "page": "prepare_input_time_series_art", "title": "Prepare data for ART input time series plots", "topics": [ "prepare_input_time_series_art" ] }, { "page": "prepare_spectrum_naomi_comparison", "title": "Compare aggregated subnational Naomi + spectrum totals for comparison table", "topics": [ "prepare_spectrum_naomi_comparison" ] }, { "page": "prepare_tmb_inputs", "title": "Prepare inputs for TMB model.", "topics": [ "prepare_tmb_inputs" ] }, { "page": "quarter_year_labels", "title": "Time period indexing", "topics": [ "calendar_quarter_labels", "calendar_quarter_labels_short", "calendar_quarter_to_quarter", "calendar_quarter_to_quarter_id", "calendar_quarter_to_year", "convert_calendar_quarter", "convert_quarter_id", "quarter_id_to_calendar_quarter", "quarter_labels", "quarter_number", "quarter_year_labels", "year_labels" ] }, { "page": "read_hintr_output", "title": "Read hintr output", "topics": [ "read_hintr_output" ] }, { "page": "read_population", "title": "Read Naomi structured input files", "topics": [ "read_anc_testing", "read_area_merged", "read_art_number", "read_population", "read_survey_indicators" ] }, { "page": "read_spectrum_projection_name", "title": "Read Spectrum Projection Name from Spectrum PJNZ", "topics": [ "read_spectrum_projection_name" ] }, { "page": "read_spectrum_region_code", "title": "Read Subnational Region Code from Spectrum PJNZ", "topics": [ "read_spectrum_region_code" ] }, { "page": "read_spectrum_region_name", "title": "Read Subnational Region Name from Spectrum PJNZ", "topics": [ "read_spectrum_region_name" ] }, { "page": "report_tmb", "title": "Calculate Posterior Mean and Uncertainty Via TMB 'sdreport()'", "topics": [ "report_tmb" ] }, { "page": "sample_tmb", "title": "Sample TMB fit", "topics": [ "sample_tmb" ] }, { "page": "save_output", "title": "Save outputs to zip file", "topics": [ "save_output" ] }, { "page": "save_output_package", "title": "Save outputs to zip file", "topics": [ "read_output_package", "save_output_package" ] }, { "page": "scale_gmrf_precision", "title": "Scale of GMRF precision matrix", "topics": [ "scale_gmrf_precision" ] }, { "page": "scatter_plotly", "title": "Plotly scatterplot data inputs and naomi outputs", "topics": [ "scatter_plotly" ] }, { "page": "select_naomi_data", "title": "Select data for model fitting", "topics": [ "select_naomi_data" ] }, { "page": "spread_areas", "title": "Spread area hierarchy to wide format", "topics": [ "spread_areas" ] }, { "page": "subset_naomi_output", "title": "Subset the results returned in Naomi output package", "topics": [ "subset_naomi_output" ] }, { "page": "subset_output_package", "title": "Resave a subsetted Naomi output package", "topics": [ "subset_output_package" ] }, { "page": "survey_mf", "title": "Prepare model frames for survey datasets", "topics": [ "survey_mf" ] }, { "page": "th_map", "title": "'ggplot2' theme for plotting maps", "topics": [ "th_map" ] }, { "page": "validate_model_options", "title": "Validate a set of model options", "topics": [ "validate_model_options" ] }, { "page": "write_datapack_csv", "title": "Export naomi outputs to PEPFAR Data Pack format", "topics": [ "write_datapack_csv" ] }, { "page": "write_navigator_checklist", "title": "Write UNAIDS Estimates Navigator checklist CSV", "topics": [ "write_navigator_checklist" ] } ], "_readme": "https://github.com/mrc-ide/naomi/raw/master/README.md", "_rundeps": [ "abind", "anclik", "askpass", "assertthat", "base64enc", "BH", "bigD", "binom", "bit", "bit64", "bitops", "boot", "brio", "bslib", "cachem", "cellranger", "class", "classInt", "cli", "clipr", "commonmark", "cpp11", "crayon", "crosstalk", "curl", "data.table", "data.tree", "DBI", "deldir", "digest", "dplyr", "e1071", "epp", "eppasm", "evaluate", "farver", "fastmap", "fastmatch", "first90", "fontawesome", "forcats", "fs", "generics", "ggplot2", "glue", "gt", "gtable", "highr", "hms", "htmltools", "htmlwidgets", "httr", 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