index.Rmd

---
title: "Nowcaster"
output: github_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
library(badger)
```


<a href='https://github.com/covid19br/nowcaster'><img src='man/figures/nowcaster.png' align="right" width="140" /></a> <a href='https://github.com/covid19br/nowcaster'><img src='man/figures/nowcaster_rev.png' align="right" width="140" /></a>

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`r badger::badge_devel(pkg = "nowcaster", color = "blue")`
`r badger::badge_license(url = "https://github.com/covid19br/nowcaster/blob/main/LICENSE.md")`
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`nowcaster` is an R package for “nowcasting” epidemiological time-series on individual level data.

Every single system of notification has an intrinsic delay between the `date of onset` of the event and the `date of report`. 
`nowcaster` can estimate how many counts of any epidemiological data of interest
(*i.e.*, daily cases and deaths counts) by fitting a negative binomial
model to the time steps of delay between onset date of the event,
(*i.e.*, date of first symptoms for cases or date of occurrence of
death) and the date of report (*i.e.*, date of notification of the case
or death).

## Installing

After have a proper `INLA` installation to install `nowcaster` package simply run the code below in R:

``` r
devtools::install_github("https://github.com/covid19br/nowcaster")
```
If you have any problem installing, please refer to next section on the dependencies of the package.

## Dependencies

`nowcaster` is based on the
[`R-INLA`](https://www.r-inla.org/download-install)
and
[`INLA`](https://inla.r-inla-download.org/r-inla.org/doc/inla-manual/inla-manual.pdf)
packages for “**I**ntegrated **N**ested **L**aplace **A**pproximation”
algorithm to Bayesian inference. `INLA` is a fast alternative to others
methods for Bayesian inference like **MCMC**. An introduction to `INLA`
can be found
[here](https://becarioprecario.bitbucket.io/inla-gitbook/index.html).

`nowcaster` it was built for epidemiological emergency use, it was
constructed for the Brazilian Severe Acute Respiratory Illness (SARI)
surveillance system (SIVEP-Gripe), at the time of Covid-19 pandemic.

Before installing the package certify you have an active installation of `INLA`, 
to do so you can run the following code:

``` r 
install.packages("INLA",
                 repos=c(getOption("repos"),
                         INLA="https://inla.r-inla-download.org/R/stable"), 
                 dep=TRUE)
```

If you want more detail on other possible installations of `INLA`, please refer to the official [page](https://www.r-inla.org/download-install) of the package.

## Similar Initiatives

There are other alternative packages, that can produce nowcasting estimation, here it is some options:

* [Epinow2](https://epiforecasts.io/EpiNow/)
* [Surveillance](https://surveillance.r-forge.r-project.org/pkgdown/index.html)