Big picture | Function organisation | Package data | Package dependencies | Data frames and tibbles | Testing
Package: vimcheck 0.0.4
Pratik Gupte
vimcheck: Diagnostics for Vaccine Impact Modelling Consortium Burden and Impact Estimates
Run diagnostics on burden estimates submitted by modellers in the Vaccine Impact Modelling Consortium (VIMC) and impact estimates calculated by the VIMC Science & Policy team.
Authors:
vimcheck_0.0.4.tar.gz
vimcheck_0.0.4.zip(r-4.7)vimcheck_0.0.4.zip(r-4.6)vimcheck_0.0.4.zip(r-4.5)
vimcheck_0.0.4.tgz(r-4.6-any)vimcheck_0.0.4.tgz(r-4.5-any)
vimcheck_0.0.4.tar.gz(r-4.7-any)vimcheck_0.0.4.tar.gz(r-4.6-any)
vimcheck_0.0.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
vimcheck/json (API)
| # Install 'vimcheck' in R: |
| install.packages('vimcheck', repos = c('https://vimc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/vimc/vimcheck/issues
Pkgdown/docs site:https://vimc.github.io
Datasets:
- 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
Last updated from:df208a4ba8 (on main). Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 176 | ||
| source / vignettes | OK | 190 | ||
| linux-release-x86_64 | OK | 177 | ||
| macos-release-arm64 | OK | 95 | ||
| macos-oldrel-arm64 | OK | 105 | ||
| windows-devel | OK | 121 | ||
| windows-release | OK | 124 | ||
| windows-oldrel | OK | 104 | ||
| wasm-release | OK | 132 |
Exports:basic_burden_sanityburden_outcome_namescheck_demography_alignmentcolnames_df_missing_colsCOLNAMES_INTEREST_PRESSURE_TESTCOLNAMES_KEY_PRESSURE_TESTcolnames_plot_demog_compareCOLOUR_VIMCcompare_natl_subregDEF_TOUCHSTONE_NEWDEF_TOUCHSTONE_OLDDEF_TOUCHSTONE_OLD_OLDEXCLUDED_DISEASESfile_dict_colnamesfilter_excluded_diseases_tsfilter_invalid_trajectoriesfilter_recent_tsflag_duplicatesflag_large_diffsgen_combined_dfgen_national_iqrgenerate_diffsIMPACT_OUTCOMESMAX_TS_MONTHMAX_TS_YEARMIN_TS_MONTHMIN_TS_YEARN_TS_MIN_CHARSN_TS_YEAR_CHARSplot_age_patternsplot_compare_demographyplot_coverage_setplot_cumulplot_diffplot_fvpplot_global_burdenplot_global_burden_decadesplot_modelling_group_variationplot_sig_diffplot_vaccine_gaviprep_plot_ageprep_plot_burden_decadesprep_plot_coverage_setprep_plot_cumulprep_plot_demographyprep_plot_fvpprep_plot_global_burdenprep_plot_mod_grp_varnprep_plot_vax_gavisave_outputsscenario_data_colnamestheme_vimctheme_vimc_noxaxisvalidate_complete_incoming_filesvalidate_file_dict_templatevalidate_template_alignment
Dependencies:assertthatbackportsbitbit64checkmateclicliprcpp11crayondiffdfdplyrfarverforcatsgenericsggplot2ggridgesgluegtableherehmsisobandlabelinglifecyclemagrittrpillarpkgconfigprettyunitsprogresspurrrR6RColorBrewerreadrrlangrprojrootS7scalesstringistringrtibbletidyrtidyselecttzdbutf8vctrsviridisLitevroomwithr
Package design decisions
Last update: 2026-06-19
Started: 2026-06-19
Pressure testing functions
Example data | Filtering impact data | Filtering on touchstone | Filtering on diseases | Flagging duplicates | Filtering invalid trajectories | Identifying differences between datasets | Generating differences | Generate national IQRs | Flag large differences | Generate a combined dataset | Comparing national values to regional values | Plotting functions | Plotting significant differences | Plotting modelling group variation | Plotting GAVI vaccination | Plot cumulative values
Last update: 2026-06-19
Started: 2026-06-19
Using plotting and preparation functions
Compare demography | Examine age patterns | Global burden by decade | Global burden timeseries | Coverage sets | Fully-vaccinated persons
Last update: 2026-02-03
Started: 2026-02-03
vimcheck
References
Last update: 2026-02-03
Started: 2025-12-11
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| vimcheck: Diagnostics for Vaccine Impact Modelling Consortium Burden and Impact Estimates | vimcheck-package vimcheck |
| Sanity checks on burden estimates | basic_burden_sanity |
| Check incoming burden cohort size against interpolated population | check_demography_alignment |
| Compare sub-regional and national estimates | compare_natl_subreg |
| Package constants | burden_outcome_names colnames_df_missing_cols COLNAMES_INTEREST_PRESSURE_TEST COLNAMES_KEY_PRESSURE_TEST colnames_plot_demog_compare COLOUR_VIMC constants DEF_TOUCHSTONE_NEW DEF_TOUCHSTONE_OLD DEF_TOUCHSTONE_OLD_OLD EXCLUDED_DISEASES file_dict_colnames IMPACT_OUTCOMES MAX_TS_MONTH MAX_TS_YEAR MIN_TS_MONTH MIN_TS_YEAR N_TS_MIN_CHARS N_TS_YEAR_CHARS scenario_data_colnames |
| Example of VIMC burden template provided to modellers | eg_burden_template |
| Example of scenario coverage data | eg_coverage |
| Example of FVP estimate data | eg_fvps |
| Example of impact data | eg_impact |
| Example of UN-WPP time-series data | eg_wpp |
| Filter data for touchstones or diseases | filter_excluded_diseases_ts filter_impact_data filter_invalid_trajectories filter_recent_ts flag_duplicates |
| Flag significant changes in impact estimates | flag_large_diffs |
| Combine and align data from two touchstones | gen_combined_df |
| Generate IQR for key outcomes | gen_national_iqr |
| Explore significant changes in deaths and DALYs | generate_diffs |
| Plot burden and impact diagnostics | plot_age_patterns plot_burden_diagnostics plot_compare_demography plot_coverage_set plot_fvp plot_global_burden plot_global_burden_decades |
| Create impact diagnostics plots | plot_cumul plot_diff plot_impact_diagnostics plot_modelling_group_variation plot_sig_diff plot_vaccine_gavi |
| Prepare data for plotting | plot_prep_burden_diagnostics prep_plot_age prep_plot_burden_decades prep_plot_coverage_set prep_plot_demography prep_plot_fvp prep_plot_global_burden |
| Prepare impact diagnostics for plotting | plot_prep_impact_diagnostics prep_plot_cumul prep_plot_mod_grp_varn prep_plot_vax_gavi |
| Plotting theme for vimcheck | plotting_theme theme_vimc theme_vimc_noxaxis |
| Save pressure-testing diagnostics to local file | save_outputs |
| Validate files in a burden estimate | validate_complete_incoming_files |
| Validate file dictionary template | validate_file_dict_template |
| Check incoming burden set against template | validate_template_alignment |
| Data on countries in WHO subregions | who_subregions |
