Package: vimpact 0.1.3

Rich FitzJohn

vimpact: Vaccine Impact Calculation

VIMC IMPACT CALCULATION PACKAGE. This package is mainly for the VIMC Science Team to investigate vaccination impact.

Authors:Rich FitzJohn [aut, cre], Imperial College of Science, Technology and Medicine [cph]

vimpact_0.1.3.tar.gz
vimpact_0.1.3.zip(r-4.5)vimpact_0.1.3.zip(r-4.4)vimpact_0.1.3.zip(r-4.3)
vimpact_0.1.3.tgz(r-4.4-any)vimpact_0.1.3.tgz(r-4.3-any)
vimpact_0.1.3.tar.gz(r-4.5-noble)vimpact_0.1.3.tar.gz(r-4.4-noble)
vimpact_0.1.3.tgz(r-4.4-emscripten)vimpact_0.1.3.tgz(r-4.3-emscripten)
vimpact.pdf |vimpact.html✨
vimpact/json (API)
NEWS

# Install 'vimpact' in R:
install.packages('vimpact', repos = c('https://mrc-ide.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/vimc/vimpact/issues

On CRAN:

4.80 score 2 stars 3 scripts 15 exports 41 dependencies

Last updated 7 months agofrom:7e44aba659 (on master). Checks:OK: 1 NOTE: 6. Indexed: no.

TargetResultDate
Doc / VignettesOKSep 25 2024
R-4.5-winNOTESep 25 2024
R-4.5-linuxNOTESep 25 2024
R-4.4-winNOTESep 25 2024
R-4.4-macNOTESep 25 2024
R-4.3-winNOTESep 25 2024
R-4.3-macNOTESep 25 2024

Exports:calculate_impactcalculate_impact_from_recipecohort_deaths_all_causeextract_vaccination_historyfetch_stochastic_datafetch_stochastic_data_year_groupsget_populationget_touchstoneimpact_by_birth_yearimpact_by_calendar_yearimpact_by_year_of_vaccination_activity_typeimpact_by_year_of_vaccination_birth_cohortimpact_by_year_of_vaccination_cohort_perspectiveimpact_by_year_of_vaccination_country_perspectiverecipe_template

Dependencies:askpassbitbit64blobclicpp11curlDBIdbplyrdplyrfansigenericsgetPassgluehmshttrjsonlitelifecyclelubridatemagrittrmimeopensslpillarpkgconfigplogrpurrrR6rlangRPostgresrstudioapistringistringrsystibbletidyrtidyselecttimechangeutf8vaultrvctrswithr

Using vimpact for estimating vaccine impact

Rob Ashton, Xiang Li, Katy Gaythorpe

Rendered fromusing-vimpact.Rmdusingknitr::rmarkdownon Sep 25 2024.

Last update: 2021-08-19
Started: 2021-08-19

Using vimpact for estimating vaccine impact - internal

Rob Ashton

Rendered frominternal-impact.Rmdusingknitr::rmarkdownon Sep 25 2024.

Last update: 2022-04-07
Started: 2021-11-11

Using vimpact for estimating vaccine impact - VIMC members

Xiang Li

Rendered fromvignette.Rmdusingknitr::rmarkdownon Sep 25 2024.

Last update: 2021-11-11
Started: 2021-08-19

Readme and manuals

Help Manual

Help pageTopics
Calculate impact - requires a DB connection to montagu.calculate_impact
Calculate impact from a recipe - requires a DB connection to montagu.calculate_impact_from_recipe
Extract demographic data - all couse mortality, live birth and under5 mortality ratecohort_deaths_all_cause
Generate target, fvps, coverage for a touchstone This function pulls vaccination and population data from Montagu database, and transform them into target, coverage and fvps. There are two modes of pulling population data: 1.) through touchstone_pop parameter 2.) through demographic_source parameter touchstone_pop is one of touchstone_demographic_dataset.touchstone; this parameter is null-able, when it is null, touchstone_cov is used demographic_source is one of demographic_source.code; by default it is null, when it is not null, it rulls out touchstone_pop parameterextract_vaccination_history
Get data from stochastic tables with specified grouping and filtersfetch_stochastic_data
Get data from stochastic tables with specified grouping and filtersfetch_stochastic_data_year_groups
Extract demographic dataget_population
Determine touchstoneget_touchstone
Determine touchstone idget_touchstone_id
Calculate impact by birth year (lifetime impact)impact_by_birth_year
Calculate impact by calendar yearimpact_by_calendar_year
Calculate impact by year of vaccination: activity typeimpact_by_year_of_vaccination_activity_type
Calculate impact by year of vaccination: birth cohortimpact_by_year_of_vaccination_birth_cohort
Calculate impact by year of vaccination cohort perspectiveimpact_by_year_of_vaccination_cohort_perspective
Calculate impact by year of vaccination country perspectiveimpact_by_year_of_vaccination_country_perspective
Impact recipe templaterecipe_template