Package index

Package-level documentation

vimcheck vimcheck-package

vimcheck: Diagnostics for Vaccine Impact Modelling Consortium Burden and Impact Estimates

Burden estimate diagnostics

Check burden estimates

basic_burden_sanity()

Sanity checks on burden estimates

check_demography_alignment()

Check incoming burden cohort size against interpolated population

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

Prepare burden estimates for plotting

prep_plot_demography() prep_plot_age() prep_plot_burden_decades() prep_plot_global_burden() prep_plot_coverage_set() prep_plot_fvp()

Prepare data for plotting

Plot burden estimates

plot_compare_demography() plot_age_patterns() plot_global_burden_decades() plot_global_burden() plot_coverage_set() plot_fvp()

Plot burden and impact diagnostics

Impact estimate diagnostics

Check impact estimates

compare_natl_subreg()

Compare sub-regional and national estimates

filter_recent_ts() filter_excluded_diseases_ts() flag_duplicates() filter_invalid_trajectories()

Filter data for touchstones or diseases

flag_large_diffs()

Flag significant changes in impact estimates

gen_combined_df()

Combine and align data from two touchstones

gen_national_iqr()

Generate IQR for key outcomes

generate_diffs()

Explore significant changes in deaths and DALYs

save_outputs()

Save pressure-testing diagnostics to local file

Prepare impact estimate checks for plotting

prep_plot_mod_grp_varn() prep_plot_vax_gavi() prep_plot_cumul()

Prepare impact diagnostics for plotting

Plot impact estimates

plot_sig_diff() plot_diff() plot_modelling_group_variation() plot_vaccine_gavi() plot_cumul()

Create impact diagnostics plots

Plotting helper functions

theme_vimc() theme_vimc_noxaxis()

Plotting theme for vimcheck

Internal functions

adaptive_round()

Adaptively round numerics

add_campaign_id()

Add campaign id to dataframe

make_novax_scenario()

Make data for a no-vaccination scenario

round_numeric()

Round numeric columns of a data.frame

validate_ts_year()

Check and return touchstone year-month

Package data

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_impact

Example of impact data

eg_wpp

Example of UN-WPP time-series data

who_subregions

Data on countries in WHO subregions

Package constants

file_dict_colnames scenario_data_colnames burden_outcome_names colnames_plot_demog_compare colnames_df_missing_cols COLNAMES_KEY_PRESSURE_TEST COLNAMES_INTEREST_PRESSURE_TEST IMPACT_OUTCOMES EXCLUDED_DISEASES N_TS_MIN_CHARS N_TS_YEAR_CHARS MIN_TS_YEAR MAX_TS_YEAR MIN_TS_MONTH MAX_TS_MONTH DEF_TOUCHSTONE_OLD DEF_TOUCHSTONE_NEW DEF_TOUCHSTONE_OLD_OLD COLOUR_VIMC

Package constants