Automatic readme update

README.md

@@ -1,33 +1,32 @@
 
-## *{{ packagename }}*: Tools for estimating vaccine effectiveness and vaccine related metrics <img src="man/figures/logo.png" align="right" width="130"/>
+## *vaccineff*: Tools for estimating vaccine effectiveness and vaccine related metrics <img src="man/figures/logo.png" align="right" width="130"/>
 
 <!-- badges: start -->
 
 [![License:
 MIT](https://img.shields.io/badge/License-MIT-blue.svg)](https://opensource.org/license/mit)
-[![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)
+[![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)
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+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
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 public.](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip)
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-*{{ packagename }}* is developed at [Pontificia Universidad
+*vaccineff* 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 ([Halloran, Longini, and Struchiner 2010](#ref-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.
+*vaccineff* 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
+([Halloran, Longini, and Struchiner 2010](#ref-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
 
@@ -37,25 +36,25 @@ Our stable versions are released on CRAN, and can be installed using:
 install.packages("vaccineff", build_vignettes = TRUE)
 ```
 
-The current development version of *{{ packagename }}* can be installed
-from [GitHub](https://github.com/) using the `pak` package.
+The current development version of *vaccineff* can be installed from
+[GitHub](https://github.com/) using the `pak` package.
 
 ``` r
 if(!require("pak")) install.packages("pak")
-pak::pak("{{ gh_repo }}")
+pak::pak("epiverse-trace/vaccineff")
 ```
 
 Or using the `remotes` package
 
 ``` r
 if(!require("remotes")) install.packages("remotes")
-remotes::install_github("{{ gh_repo }}")
+remotes::install_github("epiverse-trace/vaccineff")
 ```
 
 ## Quick start
 
-*{{ packagename }}* provides a minimal cohort dataset that can be used
-to test out the models.
+*vaccineff* provides a minimal cohort dataset that can be used to test
+out the models.
 
 ``` r
 # Load example `cohortdata` included in the package
@@ -109,10 +108,10 @@ ve <- estimate_vaccineff(vaccineff_data, at = 180)
 summary(ve)
 #> Vaccine Effectiveness at 180 days computed as VE = 1 - HR:
 #>      VE lower.95 upper.95
-#>  0.6991   0.4975   0.8199
+#>  0.7254   0.5437   0.8347
 #> 
 #> Schoenfeld test for Proportional Hazards assumption:
-#> p-value = 0.1273
+#> p-value = 0.1507
 
 # Generate loglog plot to check proportional hazards
 plot(ve, type = "loglog")
@@ -122,22 +121,21 @@ 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/%7B%7B%20packagename%20%7D%7D/),
-and in the articles “Get Started with vaccineff” and “Introduction to
-cohort design with vaccineff”.
+More details on how to use *vaccineff* 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/%7B%7B%20gh_repo%20%7D%7D/issues/new/choose).
+[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/%7B%7B%20gh_repo%20%7D%7D/pulls).
+Contributions to *vaccineff* are welcomed. Contributions are welcome via
+[pull requests](https://github.com/epiverse-trace/vaccineff/pulls).
 
 Contributors to the project include:
 
@@ -158,14 +156,15 @@ Otero](https://github.com/jd-otero)
 
 ## Code of conduct
 
-Please note that the *{{ packagename }}* project is released with a
-[Contributor Code of
+Please note that the *vaccineff* 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">
+<div id="refs" class="references csl-bib-body hanging-indent"
+entry-spacing="0">
 
 <div id="ref-bookvaccine" class="csl-entry">