Update README

2 files changed, 111 insertions, 63 deletions

diff --git a/README.Rmd b/README.Rmd
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+++ b/README.Rmd
@@ -13,37 +13,61 @@ 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 [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).
-
-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.
-
-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
-(SI)](https://en.wikipedia.org/wiki/Serial_interval). This table can be
-exported as a .csv file.
-
-In progress…
+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>.
diff --git a/README.md b/README.md
index 5eb0549..f1dd1c8 100644
--- a/README.md
+++ b/README.md
@@ -8,32 +8,56 @@ 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).
-
-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.
-
-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
-(SI)](https://en.wikipedia.org/wiki/Serial_interval). This table can be
-exported as a .csv file.
-
-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>.