diff options
| -rw-r--r-- | README.Rmd | 92 | ||||
| -rw-r--r-- | README.md | 82 |
2 files changed, 111 insertions, 63 deletions
@@ -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>. @@ -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>. |