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55 changes: 27 additions & 28 deletions README.md
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@@ -1,49 +1,49 @@

## *vaccineff*: An R package with tools for estimating vaccine effectiveness and vaccine related metrics <img src="man/figures/vaccineff.png" align="right" width="130"/>
## *{{ packagename }}*: An R package with tools for estimating vaccine effectiveness and vaccine related metrics <img src="man/figures/vaccineff.png" align="right" width="130"/>

<!-- badges: start -->

[![License:
MIT](https://img.shields.io/badge/License-MIT-yellow.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)
[![R-CMD-check](https://github.com/%7B%7B%20gh_repo%20%7D%7D/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/%7B%7B%20gh_repo%20%7D%7D/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)
coverage](https://codecov.io/gh/%7B%7B%20gh_repo%20%7D%7D/branch/main/graph/badge.svg)](https://app.codecov.io/gh/%7B%7B%20gh_repo%20%7D%7D?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)
[![CRAN
status](https://www.r-pkg.org/badges/version/vaccineff)](https://CRAN.R-project.org/package=vaccineff)
status](https://www.r-pkg.org/badges/version/%7B%7B%20packagename%20%7D%7D)](https://CRAN.R-project.org/package=%7B%7B%20packagename%20%7D%7D)
[![lifecycle-experimental](https://raw.githubusercontent.com/reconverse/reconverse.github.io/master/images/badge-experimental.svg)](https://www.reconverse.org/lifecycle.html#concept)

<!-- badges: end -->

*vaccineff* is developed at [Pontificia Universidad
*{{ 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/).

*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
([Torvaldsen and McIntyre 2020](#ref-torvaldsen2002)). The current
version of the package provides a set of features for preparing,
*{{ packagename }}* 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 ([Torvaldsen and McIntyre 2002](#ref-torvaldsen2002)). 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](https://github.com/) using the `pak` package.
The current development version of *{{ packagename }}* can be installed
from [GitHub](https://github.com/) using the `pak` package.

``` r
if(!require("pak")) install.packages("pak")
pak::pak("epiverse-trace/vaccineff")
pak::pak("{{ gh_repo }}")
```

## Quick start

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

``` r
# Load example `cohortdata` included in the package
Expand All @@ -65,21 +65,21 @@ head(cohortdata, 5)

## Package vignettes

More details on how to use *vaccineff* can be found in the [online
documentation as package
vignettes](https://epiverse-trace.github.io/vaccineff/), in the article
“Get Started with vaccineff”.
More details on how to use *{{ packagename }}* can be found in the
[online documentation as package
vignettes](https://epiverse-trace.github.io/%7B%7B%20packagename%20%7D%7D/),
in the article “Get Started 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).
[issue](https://github.com/%7B%7B%20gh_repo%20%7D%7D/issues/new/choose).

## Contribute

Contributions to *vaccineff* are welcomed. Please follow the [package
contributing
guide](https://github.com/epiverse-trace/vaccineff/blob/main/.github/CONTRIBUTING.md).
Contributions to *{{ packagename }}* are welcomed. Please follow the
[package contributing
guide](https://github.com/%7B%7B%20gh_repo%20%7D%7D/blob/main/.github/CONTRIBUTING.md).

Contributors to the project include:

Expand All @@ -98,19 +98,18 @@ Abril-Bermúdez](https://github.com/fsabrilb)

## Code of conduct

Please note that the *vaccineff* project is released with a [Contributor
Code of
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

<div id="refs" class="references csl-bib-body hanging-indent"
entry-spacing="0">
<div id="refs" class="references csl-bib-body hanging-indent">

<div id="ref-torvaldsen2002" class="csl-entry">

Torvaldsen, S., and P. B. McIntyre. 2020. “Observational Methods in
Torvaldsen, S., and P. B. McIntyre. 2002. “Observational Methods in
Epidemiologic Assessment of Vaccine Effectiveness.” *Communicable
Diseases Intelligence Quarterly Report* 26 (3).
<https://pubmed.ncbi.nlm.nih.gov/12416713/>.
Expand Down
2 changes: 1 addition & 1 deletion vignettes/references.json
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@@ -1,3 +1,3 @@
[
{"id":"torvaldsen2002","accessed":{"date-parts":[[2024,5,2]]},"author":[{"family":"Torvaldsen","given":"S."},{"family":"McIntyre","given":"P. B."}],"citation-key":"torvaldsen2002","container-title":"Communicable Diseases Intelligence Quarterly Report","issue":"3","issued":{"date-parts":[[2020,8,23]]},"publisher":"Australian Government Department of Health","source":"health.gov.au","title":"Observational methods in epidemiologic assessment of vaccine effectiveness","type":"article-journal","URL":"https://pubmed.ncbi.nlm.nih.gov/12416713/","volume":"26"}
{"id":"torvaldsen2002","accessed":{"date-parts":[[2024,5,2]]},"author":[{"family":"Torvaldsen","given":"S."},{"family":"McIntyre","given":"P. B."}],"citation-key":"torvaldsen2002","container-title":"Communicable Diseases Intelligence Quarterly Report","issue":"3","issued":{"date-parts":[[2002,8,23]]},"publisher":"Australian Government Department of Health","source":"health.gov.au","title":"Observational methods in epidemiologic assessment of vaccine effectiveness","type":"article-journal","URL":"https://pubmed.ncbi.nlm.nih.gov/12416713/","volume":"26"}
]
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