Diagnostics for Vaccine Impact Modelling Consortium Burden and
Impact Estimates
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Documentation for package ‘vimcheck’ version 0.0.5
Help Pages
| vimcheck-package | vimcheck: Diagnostics for Vaccine Impact Modelling Consortium Burden and Impact Estimates |
| basic_burden_sanity | Sanity checks on burden estimates |
| burden_outcome_names | Package constants |
| check_demography_alignment | Check incoming burden cohort size against interpolated population |
| colnames_df_missing_cols | Package constants |
| COLNAMES_INTEREST_PRESSURE_TEST | Package constants |
| COLNAMES_KEY_PRESSURE_TEST | Package constants |
| colnames_plot_demog_compare | Package constants |
| COLOUR_VIMC | Package constants |
| compare_natl_subreg | Compare sub-regional and national estimates |
| constants | Package constants |
| DEF_TOUCHSTONE_NEW | Package constants |
| DEF_TOUCHSTONE_OLD | Package constants |
| DEF_TOUCHSTONE_OLD_OLD | Package constants |
| eg_burden_template | Example of VIMC burden template provided to modellers |
| eg_coverage | Example of scenario coverage data |
| eg_fvps | Example of FVP estimate data |
| eg_fvps_2 | A second FVP data example |
| eg_impact | Example of impact data |
| eg_impact_2 | Second example of impact data |
| eg_wpp | Example of UN-WPP time-series data |
| EXCLUDED_DISEASES | Package constants |
| file_dict_colnames | Package constants |
| filter_excluded_diseases_ts | Filter data for touchstones or diseases |
| filter_impact_data | Filter data for touchstones or diseases |
| filter_invalid_trajectories | Filter data for touchstones or diseases |
| filter_recent_ts | Filter data for touchstones or diseases |
| flag_duplicates | Filter data for touchstones or diseases |
| flag_large_diffs | Flag significant changes in impact estimates |
| generate_diffs | Explore significant changes in deaths and DALYs |
| gen_combined_df | Combine and align data from two touchstones |
| gen_national_iqr | Generate IQR for key outcomes |
| IMPACT_OUTCOMES | Package constants |
| MAX_TS_MONTH | Package constants |
| MAX_TS_YEAR | Package constants |
| MIN_TS_MONTH | Package constants |
| MIN_TS_YEAR | Package constants |
| N_TS_MIN_CHARS | Package constants |
| N_TS_YEAR_CHARS | Package constants |
| PINE | Package constants |
| plotting_theme | Plotting theme for vimcheck |
| plot_age_patterns | Plot burden and impact diagnostics |
| plot_burden_diagnostics | Plot burden and impact diagnostics |
| plot_compare_demography | Plot burden and impact diagnostics |
| plot_coverage_fvps | Plot coverage and fully vaccinated persons (FVPs) |
| plot_coverage_set | Plot burden and impact diagnostics |
| plot_cumul | Create impact diagnostics plots |
| plot_diff | Create impact diagnostics plots |
| plot_fvp | Plot burden and impact diagnostics |
| plot_global_burden | Plot burden and impact diagnostics |
| plot_global_burden_decades | Plot burden and impact diagnostics |
| plot_impact | Plot central impact estimates by cohort and year |
| plot_impact_diagnostics | Create impact diagnostics plots |
| plot_modelling_group_variation | Create impact diagnostics plots |
| plot_prep_burden_diagnostics | Prepare data for plotting |
| plot_prep_impact_diagnostics | Prepare impact diagnostics for plotting |
| plot_sig_diff | Create impact diagnostics plots |
| plot_vaccine_gavi | Create impact diagnostics plots |
| prep_plot_age | Prepare data for plotting |
| prep_plot_burden_decades | Prepare data for plotting |
| prep_plot_coverage_set | Prepare data for plotting |
| prep_plot_cumul | Prepare impact diagnostics for plotting |
| prep_plot_demography | Prepare data for plotting |
| prep_plot_fvp | Prepare data for plotting |
| prep_plot_global_burden | Prepare data for plotting |
| prep_plot_mod_grp_varn | Prepare impact diagnostics for plotting |
| prep_plot_vax_gavi | Prepare impact diagnostics for plotting |
| save_outputs | Save pressure-testing diagnostics to local file |
| scenario_data_colnames | Package constants |
| theme_vimc | Plotting theme for vimcheck |
| theme_vimc_noxaxis | Plotting theme for vimcheck |
| validate_complete_incoming_files | Validate files in a burden estimate |
| validate_file_dict_template | Validate file dictionary template |
| validate_template_alignment | Check incoming burden set against template |
| vimcheck | vimcheck: Diagnostics for Vaccine Impact Modelling Consortium Burden and Impact Estimates |
| who_subregions | Data on countries in WHO subregions |