vaccineff

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

https://github.com/epiverse-trace/vaccineff

Science Score: 67.0%

This score indicates how likely this project is to be science-related based on various indicators:

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CITATION.cff file
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Found codemeta.json file
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Found 3 DOI reference(s) in README
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Links to: zenodo.org
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Keywords

epidemiology epiverse r r-package vaccine-effectiveness

Last synced: 10 months ago · JSON representation ·

Repository

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

Basic Info

Host: GitHub
Owner: epiverse-trace
License: other
Language: R
Default Branch: main
Homepage: https://epiverse-trace.github.io/vaccineff/
Size: 20.5 MB

Statistics

Stars: 16
Watchers: 3
Forks: 4
Open Issues: 3
Releases: 5

Topics

epidemiology epiverse r r-package vaccine-effectiveness

Created almost 4 years ago · Last pushed 12 months ago

Metadata Files

Readme Changelog License Citation

README.Rmd

---
output: github_document
bibliography: vignettes/references.bib
link-citations: true
editor_options: 
  markdown: 
    wrap: 72
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

## *{{ packagename }}*: Tools for estimating vaccine effectiveness and vaccine related metrics 



[![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg)](https://opensource.org/license/mit)
[![R-CMD-check](https://github.com/epiverse-trace/vaccineff/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/epiverse-trace/vaccineff/actions/workflows/R-CMD-check.yaml)
[![Codecov test coverage](https://codecov.io/gh/epiverse-trace/vaccineff/branch/main/graph/badge.svg)](https://app.codecov.io/gh/epiverse-trace/vaccineff?branch=main)
[![Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip)
[![lifecycle-maturing](https://raw.githubusercontent.com/reconverse/reconverse.github.io/master/images/badge-maturing.svg)](https://www.reconverse.org/lifecycle.html#concept)
[![CRAN status](https://www.r-pkg.org/badges/version/vaccineff)](https://CRAN.R-project.org/package=vaccineff)
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.14258965.svg)](https://doi.org/10.5281/zenodo.14258965)



*{{ packagename }}* is developed at [Pontificia Universidad Javeriana](https://www.javeriana.edu.co/inicio) as part of the
[Epiverse-TRACE initiative](https://data.org/initiatives/epiverse/).

*{{ packagename }}* is an R package that offers tools for estimating vaccine effectiveness (VE), using a series of epidemiological designs including cohort studies, test-negative case-control, and screening methods [@bookvaccine]. 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

Our stable versions are released on CRAN, and can be installed using:

```r
install.packages("vaccineff", build_vignettes = TRUE)
```

The current development version of _{{ packagename }}_ can be installed from [GitHub](https://github.com/) using the `pak` package.

```{r, eval = FALSE}
if(!require("pak")) install.packages("pak")
pak::pak("{{ gh_repo }}")
```

Or using the `remotes` package
```{r, eval = FALSE }
if(!require("remotes")) install.packages("remotes")
remotes::install_github("{{ gh_repo }}")
```

## Quick start

```{r cleaning, include = FALSE, echo = TRUE}
library(vaccineff)
```


*{{ packagename }}* provides a minimal cohort dataset that can be used to test out the models.

```{r example, include = TRUE, echo = TRUE}
# Load example `cohortdata` included in the package
data("cohortdata")
head(cohortdata, 5)
```
The function `make_vaccineff_data` allows defining different aspects of the study design—such as vaccination dates, immunization delays, and potential confounding factors—and creates an object of class `vaccineff_data`. Its output is used to estimate VE using a Cox model regression invoked by the function `estimate_vaccineff`, which returns the object `vaccineff`.

The proportional hazard assumption can be tested both through the Schoenfeld test and visually using the `plot` method by setting `type = "loglog"`.

```{r}
# Create `vaccineff_data`
vaccineff_data <- make_vaccineff_data(
  data_set = cohortdata,
  outcome_date_col = "death_date",
  censoring_date_col = "death_other_causes",
  vacc_date_col = "vaccine_date_2",
  vaccinated_status = "v",
  unvaccinated_status = "u",
  immunization_delay = 15,
  end_cohort = as.Date("2021-12-31"),
  match = TRUE,
  exact = "sex",
  nearest = c(age = 1)
)

# Estimate VE
ve <- estimate_vaccineff(vaccineff_data, at = 180)

# Print summary of VE
summary(ve)

# Generate loglog plot to check proportional hazards
plot(ve, type = "loglog")
```

## Package vignettes

More details on how to use _{{ packagename }}_ can be found in the [online documentation as package vignettes](https://epiverse-trace.github.io/vaccineff/), and in the articles "Get Started with vaccineff" and "Introduction to cohort design with vaccineff".

## Help

To report a bug or to request a new feature please open an [issue](https://github.com/epiverse-trace/vaccineff/issues/new/choose).

## Contribute 

Contributions to _{{ packagename }}_ are welcomed. Contributions are welcome via [pull
requests](https://github.com/epiverse-trace/vaccineff/pulls).

Contributors to the project include:

**Authors**: [David Santiago Quevedo](https://github.com/davidsantiagoquevedo) and [Zulma M. Cucunubá](https://github.com/zmcucunuba) (maintainer)

**Contributors**:
[Geraldine Gómez](https://github.com/GeraldineGomez), [Pratik Gupte](https://github.com/pratikunterwegs), [Érika J. Cantor](https://github.com/ErikaCantor), [Santiago Loaiza](https://github.com/santilo9513), [Jaime A. Pavlich-Mariscal](https://github.com/jpavlich), [Hugo Gruson](https://github.com/Bisaloo), [Chris Hartgerink](https://github.com/chartgerink), [Felipe Segundo Abril-Bermúdez](https://github.com/fsabrilb), [Joshua W. Lambert](https://github.com/joshwlambert), [Julian Otero](https://github.com/jd-otero)


## Code of conduct

Please note that the _{{ packagename }}_ project is released with a [Contributor Code of Conduct](https://github.com/epiverse-trace/.github/blob/main/CODE_OF_CONDUCT.md). By contributing to this project, you agree to abide by its terms.

## References

Owner

Name: Epiverse-TRACE
Login: epiverse-trace
Kind: organization

Website: https://epiverse.org
Repositories: 17
Profile: https://github.com/epiverse-trace

Citation (CITATION.cff)

# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "vaccineff" in publications use:'
type: software
license: MIT
title: 'vaccineff: Estimate Vaccine Effectiveness Based on Different Study Designs'
version: 1.0.0.9000
doi: 10.32614/CRAN.package.vaccineff
abstract: Provides tools for estimating vaccine effectiveness and related metrics.
  The 'vaccineff_data' class manages key features for preparing, visualizing, and
  organizing cohort data, as well as estimating vaccine effectiveness. The results
  and model performance are assessed using the 'vaccineff' class.
authors:
- family-names: Quevedo
  given-names: David Santiago
  email: ex-dsquevedo@javeriana.edu.co
  orcid: https://orcid.org/0000-0003-1583-4262
- family-names: Cucunubá
  given-names: Zulma M.
  email: tracelacdev@gmail.com
  orcid: https://orcid.org/0000-0002-8165-3198
repository: https://CRAN.R-project.org/package=vaccineff
repository-code: https://github.com/epiverse-trace/vaccineff
url: https://epiverse-trace.github.io/vaccineff/
contact:
- family-names: Cucunubá
  given-names: Zulma M.
  email: tracelacdev@gmail.com
  orcid: https://orcid.org/0000-0002-8165-3198
keywords:
- epidemiology
- epiverse
- r
- r-package
- vaccine-effectiveness
references:
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    given-names: Michel
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  abstract: 'ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics'
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  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
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  - family-names: Chang
    given-names: Winston
    orcid: https://orcid.org/0000-0002-1576-2126
  - family-names: Henry
    given-names: Lionel
  - family-names: Pedersen
    given-names: Thomas Lin
    email: thomas.pedersen@posit.co
    orcid: https://orcid.org/0000-0002-5147-4711
  - family-names: Takahashi
    given-names: Kohske
  - family-names: Wilke
    given-names: Claus
    orcid: https://orcid.org/0000-0002-7470-9261
  - family-names: Woo
    given-names: Kara
    orcid: https://orcid.org/0000-0002-5125-4188
  - family-names: Yutani
    given-names: Hiroaki
    orcid: https://orcid.org/0000-0002-3385-7233
  - family-names: Dunnington
    given-names: Dewey
    orcid: https://orcid.org/0000-0002-9415-4582
  - family-names: Brand
    given-names: Teun
    name-particle: van den
    orcid: https://orcid.org/0000-0002-9335-7468
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  abstract: 'linelist: Tagging and Validating Epidemiological Data'
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  repository: https://CRAN.R-project.org/package=MatchIt
  authors:
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    orcid: https://orcid.org/0000-0002-2195-5469
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    given-names: Kosuke
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    orcid: https://orcid.org/0000-0002-2748-1022
  - family-names: King
    given-names: Gary
    email: king@harvard.edu
    orcid: https://orcid.org/0000-0002-5327-7631
  - family-names: Stuart
    given-names: Elizabeth
    email: estuart@jhu.edu
    orcid: https://orcid.org/0000-0002-9042-8611
  - family-names: Greifer
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    email: noah.greifer@gmail.com
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  notes: Imports
  url: https://rlang.r-lib.org
  repository: https://CRAN.R-project.org/package=rlang
  authors:
  - family-names: Henry
    given-names: Lionel
    email: lionel@posit.co
  - family-names: Wickham
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    email: hadley@posit.co
  year: '2025'
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  repository: https://CRAN.R-project.org/package=scales
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  - family-names: Pedersen
    given-names: Thomas Lin
    email: thomas.pedersen@posit.co
    orcid: https://orcid.org/0000-0002-5147-4711
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    address: Vienna, Austria
  year: '2025'
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  repository: https://CRAN.R-project.org/package=survival
  authors:
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  doi: 10.32614/CRAN.package.rmarkdown
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  notes: Suggests
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  repository: https://CRAN.R-project.org/package=spelling
  authors:
  - family-names: Ooms
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    email: hadley@posit.co
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GitHub Events

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Create event: 34
Release event: 1
Issues event: 17
Watch event: 4
Delete event: 34
Issue comment event: 21
Push event: 173
Pull request review comment event: 23
Pull request review event: 49
Pull request event: 70
Fork event: 2

Last Year

Create event: 34
Release event: 1
Issues event: 17
Watch event: 4
Delete event: 34
Issue comment event: 21
Push event: 173
Pull request review comment event: 23
Pull request review event: 49
Pull request event: 70
Fork event: 2

Issues and Pull Requests

Last synced: 10 months ago

All Time

Total issues: 23
Total pull requests: 83
Average time to close issues: about 1 month
Average time to close pull requests: 8 days
Total issue authors: 7
Total pull request authors: 10
Average comments per issue: 1.13
Average comments per pull request: 0.25
Merged pull requests: 77
Bot issues: 0
Bot pull requests: 12

Past Year

Issues: 12
Pull requests: 32
Average time to close issues: about 1 month
Average time to close pull requests: 16 days
Issue authors: 3
Pull request authors: 6
Average comments per issue: 0.67
Average comments per pull request: 0.13
Merged pull requests: 28
Bot issues: 0
Bot pull requests: 10

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GeraldineGomez (2)
fsabrilb (2)
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Bisaloo (1)
pratikunterwegs (1)
zmcucunuba (1)
ManuelVelarde2212 (1)

Pull Request Authors

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github-actions[bot] (23)
Bisaloo (15)
GeraldineGomez (10)
chartgerink (8)
ErikaCantor (4)
jpavlich (2)
teunbrand (2)
pratikunterwegs (1)
zmcucunuba (1)

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Packages

Total packages: 1
Total downloads:
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Total dependent packages: 0
Total dependent repositories: 0
Total versions: 1
Total maintainers: 1

cran.r-project.org: vaccineff

Estimate Vaccine Effectiveness Based on Different Study Designs

Homepage: https://github.com/epiverse-trace/vaccineff
Documentation: http://cran.r-project.org/web/packages/vaccineff/vaccineff.pdf
License: MIT + file LICENSE
Latest release: 1.0.0
published over 1 year ago

Versions: 1
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 155 Last month

Rankings

Dependent packages count: 27.6%

Dependent repos count: 34.0%

Average: 49.5%

Downloads: 86.8%

Maintainers (1)

tracelacdev@gmail.com

Last synced: 10 months ago

Dependencies

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DESCRIPTION cran

R >= 3.5.0 depends
checkmate * imports
stats * imports
survival * imports
knitr * suggests
qtl * suggests
rmarkdown * suggests
spelling * suggests
testthat >= 3.0.0 suggests

ecosyste.ms

Data

Tools

Indexes

Applications

Experiments

Open Source Science