---
output: github_document
---

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

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
```

# Rnaught <a href="https://MI2YorkU.github.io/Rnaught"><img src="man/figures/logo.svg" align="right" height="139" alt="Rnaught Logo"></a>

<!-- badges: start -->
[![R-CMD-check](https://github.com/MI2YorkU/Rnaught/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/MI2YorkU/Rnaught/actions/workflows/R-CMD-check.yaml)
<!-- badges: end -->

Rnaught is an R package and web application for estimating the
[basic reproduction number (*R*<sub>0</sub>)](
https://en.wikipedia.org/wiki/Basic_reproduction_number) of infectious diseases.

An instance of the web application is available at
<https://immune.math.yorku.ca/Rnaught>.


## Installation

You can install the development version of Rnaught using the [devtools](
https://devtools.r-lib.org) package. Run the following commands in an R session:

``` r
install.packages("devtools") # If not already installed.
devtools::install_github("MI2YorkU/Rnaught", build_vignettes = TRUE)
```


## Documentation

The package documentation is available online at
<https://MI2YorkU.github.io/Rnaught>.

For a quick introduction, see the [Get started](
https://MI2YorkU.github.io/Rnaught/articles/Rnaught.html) page. This can also be
accessed from an R session with `vignette("Rnaught", package = "Rnaught")`.

To view the documentation locally, run `?Rnaught::<function>`. A list of all
functions is shown in the package index by executing
`help(package = "Rnaught")`.


## Contributing

The source code for this package is available on
[GitHub](https://github.com/MI2YorkU/Rnaught). 

To report a bug, request a new feature, give feedback, or ask questions, open a
new [issue](https://github.com/MI2YorkU/Rnaught/issues).

Submit new estimators, features, bug fixes, or patches by creating a
[pull request](https://github.com/MI2YorkU/Rnaught/pulls).


## License

This program is free software: you can redistribute it and/or modify it under
the terms of the GNU Affero General Public License as published by the Free
Software Foundation, either version 3 of the License, or (at your option) any
later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY
WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.

You should have received a copy of the GNU Affero General Public License along
with this program. If not, see <https://www.gnu.org/licenses>.