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[Rnaught] / README.md

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

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+[![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)
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+

 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.
 
 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.
 

-Currently, this estimation can be done in the web application via four different methods: 
-White and Panago (WP), sequential Bayes (seqB), incidence decay (ID), and incidence decay and exponential adjustment (IDEA).
+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

 
 

-Datasets can be uploaded as a .csv file, or can be entered manually into the application.
-The data is visualized in the application through plots that show the case counts (either weekly or daily).
-If multiple datasets are uploaded/manually entered, the trends corresponding to these datasets are populated in the same plot and can be compared.
-This plot can be exported as a .png file.
-Further, the dataset entered can be exported into a .csv file.
-Two sample datasets are included: weekly Canadian COVID-19 case count data from March 3rd, 2020 to March 31st, 2020, and weekly Ontario COVID-19 case count data from March 3rd, 2020 to March 31st, 2020.
+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.

 
 

-To estimate the basic reproductive number, the user can choose their preferred estimator, and if applicable, must enter the known serial interval prior to estimation.
-If multiple estimates of the basic reproductive number are calculated, they are all included in a table where each row represents an estimate.
-If multiple datasets are being considered, the basic reproductive number is estimated for all datasets and the columns of the table correspond to the different datasets uploaded into the application.
-The table also consists of a column corresponding to the value of the serial interval. 
-This table can be exported as a .csv file. 
+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.

 
 

-In progress...
+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>.