nmode's Git Repositories - Rnaught/blob - README.Rmd

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   2 output: github_document
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   5 <!-- README.md is generated from README.Rmd. Please edit that file. -->
   6
   7 ```{r, include = FALSE}
   8 knitr::opts_chunk$set(
   9   collapse = TRUE,
  10   comment = "#>"
  11 )
  12 ```
  13
  14 # Rnaught <a href="https://MI2YorkU.github.io/Rnaught"><img src="man/figures/logo.svg" align="right" height="139" alt="Rnaught Logo"></a>
  15
  16 Rnaught is an R package and web application for estimating the [basic
  17 reproduction number
  18 (*R*<sub>0</sub>)](https://en.wikipedia.org/wiki/Basic_reproduction_number)
  19 of infectious diseases.
  20
  21 Currently, this estimation can be done in the web application via four
  22 different methods: White and Panago (WP), sequential Bayes (seqB),
  23 incidence decay (ID), and incidence decay and exponential adjustment
  24 (IDEA).
  25
  26 Datasets can be uploaded as a .csv file, or can be entered manually into
  27 the application. The data is visualized in the application through plots
  28 that show the case counts (either weekly or daily). If multiple datasets
  29 are uploaded/manually entered, the trends corresponding to these
  30 datasets are populated in the same plot and can be compared. This plot
  31 can be exported as a .png file. Further, the dataset entered can be
  32 exported into a .csv file. Two sample datasets are included: weekly
  33 Canadian COVID-19 case count data from March 3rd, 2020 to March 31st,
  34 2020, and weekly Ontario COVID-19 case count data from March 3rd, 2020
  35 to March 31st, 2020.
  36
  37 To estimate the basic reproductive number, the user can choose their
  38 preferred estimator, and if applicable, must enter the known serial
  39 interval prior to estimation. If multiple estimates of the basic
  40 reproductive number are calculated, they are all included in a table
  41 where each row represents an estimate. If multiple datasets are being
  42 considered, the basic reproductive number is estimated for all datasets
  43 and the columns of the table correspond to the different datasets
  44 uploaded into the application. The table also consists of a column
  45 corresponding to the value of the [serial interval
  46 (SI)](https://en.wikipedia.org/wiki/Serial_interval). This table can be
  47 exported as a .csv file.
  48
  49 In progress…