Update README

[Rnaught] / README.Rmd

diff --git a/README.Rmd b/README.Rmd
index f56e18c508bd592c1100bdd0074c176a11d0fd44..b9b38043d5940290825f04a095ca893bceb2379b 100644 (file)
--- a/README.Rmd
+++ b/README.Rmd
@@ -14,7 +14,60 @@ knitr::opts_chunk$set(
 # Rnaught <a href="https://MI2YorkU.github.io/Rnaught"><img src="man/figures/logo.svg" align="right" height="139" alt="Rnaught Logo"></a>
 
 Rnaught is an R package and web application for estimating the
 # Rnaught <a href="https://MI2YorkU.github.io/Rnaught"><img src="man/figures/logo.svg" align="right" height="139" alt="Rnaught Logo"></a>
 
 Rnaught is an R package and web application for estimating the

-[basic reproduction number (_R_~0~)](
+[basic reproduction number (*R*<sub>0</sub>)](

 https://en.wikipedia.org/wiki/Basic_reproduction_number) of infectious diseases.
 
 https://en.wikipedia.org/wiki/Basic_reproduction_number) of infectious diseases.
 

-In progress...
+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>.