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@@ -13,8 +13,37 @@ 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_~0~)]( -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. -In progress... +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… |