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R package with tools for estimating vaccine effectiveness and vaccine related metrics

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epiverse-trace/vaccineff

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vaccineff: An R package with tools for estimating vaccine effectiveness and vaccine related metrics

License: MIT R-CMD-check Codecov test coverage Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public. CRAN status lifecycle-experimental

vaccineff is developed at Pontificia Universidad Javeriana as part of the Epiverse-TRACE initiative.

vaccineff is an R package that offers tools for estimating vaccine effectiveness, using a series of epidemiological designs including cohort studies, test-negative case-control, and screening methods (Halloran, Longini, and Struchiner 2010). The current version of the package provides a set of features for preparing, visualizing, and managing cohort data, estimating vaccine effectiveness, and assessing the performance of the models. Test-negative design and screening method will be included in future versions.

Installation

The current development version of vaccineff can be installed from GitHub using the pak package.

if(!require("pak")) install.packages("pak")
pak::pak("epiverse-trace/vaccineff")

Quick start

vaccineff provides a minimal cohort dataset that can be used to test out the models.

# Load example `cohortdata` included in the package
data("cohortdata")
head(cohortdata, 5)
#>         id sex age death_date death_other_causes vaccine_date_1 vaccine_date_2
#> 1 afade1b2   F  37       <NA>               <NA>           <NA>           <NA>
#> 2 556c8c76   M  19       <NA>               <NA>           <NA>           <NA>
#> 3 04edf85a   M  50       <NA>               <NA>           <NA>           <NA>
#> 4 7e51a18e   F   8       <NA>               <NA>           <NA>           <NA>
#> 5 c5a83f56   M  66       <NA>               <NA>           <NA>           <NA>
#>   vaccine_1 vaccine_2
#> 1      <NA>      <NA>
#> 2      <NA>      <NA>
#> 3      <NA>      <NA>
#> 4      <NA>      <NA>
#> 5      <NA>      <NA>

Package vignettes

More details on how to use vaccineff can be found in the online documentation as package vignettes, in the article “Get Started with vaccineff”.

Help

To report a bug or to request a new feature please open an issue.

Contribute

Contributions to vaccineff are welcomed. Please follow the package contributing guide.

Contributors to the project include:

Authors: David Santiago Quevedo and Zulma M. Cucunubá (maintainer)

Contributors: Geraldine Gómez, Pratik Gupte, Érika J. Cantor, Santiago Loaiza, Jaime A. Pavlich-Mariscal, Hugo Gruson, Chris Hartgerink, Felipe Segundo Abril-Bermúdez

Code of conduct

Please note that the vaccineff project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

References

Halloran, Elizabeth, Ira Longini, and Claudio Struchiner. 2010. Design and Analysis of Vaccine Studies. Springer.