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

vaccineff is an R package that offers tools for estimating the vaccine effectiveness, using a series of epidemiological designs including cohort studies, test-negative case-control, and screening methods (Torvaldsen and McIntyre 2020). The package provides a set of features for preparing the data, to analyze different study designs and for assessing the performance of the models.

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

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 minimal datasets that can be used to test out each design (cohortdata, testnegdata, screeningdata)

# Load example `cohortdata` included in the package
data("cohortdata")
head(cohortdata, 5)
#>   sex age subsidy death_date vaccine_date_1 vaccine_date_2 vaccine_1 vaccine_2
#> 1   F   6       0       <NA>           <NA>           <NA>      <NA>      <NA>
#> 2   M  79       0       <NA>     2044-03-31     2044-05-07    BRAND2    BRAND2
#> 3   F  34       0       <NA>     2044-07-26     2044-09-03    BRAND2    BRAND2
#> 4   M  26       0       <NA>           <NA>           <NA>      <NA>      <NA>
#> 5   F  66       0       <NA>     2044-05-20     2044-06-17    BRAND2    BRAND2

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.

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.

Contributions

Contributors to the project include:

• David Santiago Quevedo (author)

• Zulma M. Cucunubá (author)

• Santiago Loaiza (author)

• Geraldine Gómez (contributor)

• Jaime A. Pavlich-Mariscal (contributor)

• Pratik Gupte (contributor)

References

Torvaldsen, S., and P. B. McIntyre. 2020. “Observational Methods in Epidemiologic Assessment of Vaccine Effectiveness.” Communicable Diseases Intelligence Quarterly Report 26 (3). https://doi.org/10.3316/informit.511798489353134.