README.Rmd

---
output: github_document
---

<!-- README.md is generated from README.Rmd. Please edit that file -->

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

# `SEIRcovid19FR`

`SEIRcovid19FR` is an R package for multi-level inference of epidemic dynamics applied to COVID-19 in France.

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## Installation

You can install the development version of SEIRcovid19FR from [GitHub](https://github.com/) with:

``` r
# install.packages("devtools")
devtools::install_github("sistm/SEIRcovid19")
```

## Updating the Hospitalization data for Monolix :

1. download the new SurSaUD file in `data/raw` from [data.gouv](https://www.data.gouv.fr/fr/datasets/r/941ff2b4-ea24-4cdf-b0a7-655f2a332fb2)
2. update the file name and run the commented code in example of `R/sursaud_covid19.R`
3. reload the package
4. run the example script of `R/prepare_data_4monolix.R`

Mélanie Prague, Dan Dutartre & Boris Hejblum