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.

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")

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>

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

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

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

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.