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Merge pull request #46 from epiverse-trace/fix-vignettes-urls
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doc: update vignettes urls in the README as well as the installation repository
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zmcucunuba authored Apr 13, 2023
2 parents 585d51b + 1838892 commit a325d08
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16 changes: 8 additions & 8 deletions README.Rmd
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Expand Up @@ -21,16 +21,16 @@ knitr::opts_chunk$set(

[![License:
MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
[![R-CMD-check](https://github.com/TRACE-LAC/serofoi/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/TRACE-LAC/serofoi/actions/workflows/R-CMD-check.yaml)
[![R-CMD-check](https://github.com/epiverse-trace/serofoi/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/epiverse-trace/serofoi/actions/workflows/R-CMD-check.yaml)
[![Codecov test
coverage](https://codecov.io/gh/TRACE-LAC/serofoi/branch/dev/graph/badge.svg)](https://app.codecov.io/gh/TRACE-LAC/serofoi/tree/dev/R?displayType=list)
coverage](https://codecov.io/gh/epiverse-trace/serofoi/branch/dev/graph/badge.svg)](https://app.codecov.io/gh/epiverse-trace/serofoi/tree/dev/R?displayType=list)
[![lifecycle-concept](https://raw.githubusercontent.com/reconverse/reconverse.github.io/master/images/badge-concept.svg)](https://www.reconverse.org/lifecycle.html#concept)

<!-- badges: end -->

***serofoi*** is an R package to estimate the *Force-of-Infection (FoI)* of a given pathogen from age-disaggregated population-based cross-sectional serosurveys, using a Bayesian framework. The package provides a set of features for assessing model fitting, convergence and visualisation.

***serofoi*** relies on the [`rstan`](https://mc-stan.org/users/interfaces/rstan) package, which provides an R interface for the Stan programming language for statistical Bayesian modelling. Particularly, ***serofoi*** relies on the use of a *Hamiltonian Monte Carlo (HCM)* algorithm implemented by *Stan for Markov chain Monte Carlo (MCMC)* sampling. The implemented methods are outlined in [@cucunubá2017] and [@carrera2020] (see [FoI Models](https://trace-lac.github.io/serofoi/articles/foi_models.html) for further details)
***serofoi*** relies on the [`rstan`](https://mc-stan.org/users/interfaces/rstan) package, which provides an R interface for the Stan programming language for statistical Bayesian modelling. Particularly, ***serofoi*** relies on the use of a *Hamiltonian Monte Carlo (HCM)* algorithm implemented by *Stan for Markov chain Monte Carlo (MCMC)* sampling. The implemented methods are outlined in [@cucunubá2017] and [@carrera2020] (see [FoI Models](https://epiverse-trace.github.io/serofoi/articles/foi_models.html) for further details)

***serofoi*** is part of the [Epiverse Initiative](https://data.org/initiatives/epiverse/).

Expand All @@ -40,7 +40,7 @@ You can install the **development version** of ***serofoi*** from [GitHub](https

``` r
if(!require("remotes")) install.packages("remotes")
remotes::install_github("TRACE-LAC/serofoi")
remotes::install_github("epiverse-trace/serofoi")
```

## Quick start
Expand Down Expand Up @@ -90,14 +90,14 @@ Contributors to the project include:

More details on how to use ***serofoi*** can be found in the
[online documentation](https://epiverse-trace.github.io/serofoi/) as package vignettes, under
[**Get Started**](https://trace-lac.github.io/serofoi/articles/serofoi.html),
[**FoI Models**](https://trace-lac.github.io/serofoi/articles/foi_models.html) and
[**Use Cases**](https://trace-lac.github.io/serofoi/articles/use_cases.html)
[**Get Started**](https://epiverse-trace.github.io/serofoi/articles/serofoi.html),
[**FoI Models**](https://epiverse-trace.github.io/serofoi/articles/foi_models.html) and
[**Use Cases**](https://epiverse-trace.github.io/serofoi/articles/use_cases.html)

## Help

To report a bug please open an
[issue](https://github.com/TRACE-LAC/serofoi/issues).
[issue](https://github.com/epiverse-trace/serofoi/issues).

## Contribute

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16 changes: 8 additions & 8 deletions README.md
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Expand Up @@ -5,9 +5,9 @@

[![License:
MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
[![R-CMD-check](https://github.com/TRACE-LAC/serofoi/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/TRACE-LAC/serofoi/actions/workflows/R-CMD-check.yaml)
[![R-CMD-check](https://github.com/epiverse-trace/serofoi/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/epiverse-trace/serofoi/actions/workflows/R-CMD-check.yaml)
[![Codecov test
coverage](https://codecov.io/gh/TRACE-LAC/serofoi/branch/dev/graph/badge.svg)](https://app.codecov.io/gh/TRACE-LAC/serofoi/tree/dev/R?displayType=list)
coverage](https://codecov.io/gh/epiverse-trace/serofoi/branch/dev/graph/badge.svg)](https://app.codecov.io/gh/epiverse-trace/serofoi/tree/dev/R?displayType=list)
[![lifecycle-concept](https://raw.githubusercontent.com/reconverse/reconverse.github.io/master/images/badge-concept.svg)](https://www.reconverse.org/lifecycle.html#concept)

<!-- badges: end -->
Expand All @@ -26,7 +26,7 @@ the use of a *Hamiltonian Monte Carlo (HCM)* algorithm implemented by
*Stan for Markov chain Monte Carlo (MCMC)* sampling. The implemented
methods are outlined in ([Cucunubá et al. 2017](#ref-cucunubá2017)) and
([Carrera et al. 2020](#ref-carrera2020)) (see [FoI
Models](https://trace-lac.github.io/serofoi/articles/foi_models.html)
Models](https://epiverse-trace.github.io/serofoi/articles/foi_models.html)
for further details)

***serofoi*** is part of the [Epiverse
Expand All @@ -39,7 +39,7 @@ You can install the **development version** of ***serofoi*** from

``` r
if(!require("remotes")) install.packages("remotes")
remotes::install_github("TRACE-LAC/serofoi")
remotes::install_github("epiverse-trace/serofoi")
```

## Quick start
Expand Down Expand Up @@ -96,16 +96,16 @@ Contributors to the project include:
More details on how to use ***serofoi*** can be found in the [online
documentation](https://epiverse-trace.github.io/serofoi/) as package
vignettes, under [**Get
Started**](https://trace-lac.github.io/serofoi/articles/serofoi.html),
Started**](https://epiverse-trace.github.io/serofoi/articles/serofoi.html),
[**FoI
Models**](https://trace-lac.github.io/serofoi/articles/foi_models.html)
Models**](https://epiverse-trace.github.io/serofoi/articles/foi_models.html)
and [**Use
Cases**](https://trace-lac.github.io/serofoi/articles/use_cases.html)
Cases**](https://epiverse-trace.github.io/serofoi/articles/use_cases.html)

## Help

To report a bug please open an
[issue](https://github.com/TRACE-LAC/serofoi/issues).
[issue](https://github.com/epiverse-trace/serofoi/issues).

## Contribute

Expand Down
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