README.Rmd

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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 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…