Disclaimer

This package is a work in progress. Please reach out to the authors before using.

Scope

i2extras adds additional functionality to the incidence2 package.

What does it do?

The main features of the package include:

• fit_curve() and growth_rate(): fit a trend (poisson / negative binomial) to an incidence2 object and calculate the associated growth rate.

• add_rolling_average(): add a rolling average to an incidence2 object.

• bootstrap(): generates a bootstrapped incidence2 object by re-sampling, with replacement, the original dates of events.

• find_peak(): locates the peak time of the epicurve.

• estimate_peak(): uses bootstrap to estimate the peak time (and related confidence interval) of a partially observed outbreak.

Installing the package

Once it is released on CRAN, you will be able to install the stable version of the package with:

install.packages("i2extras")

The development version can be installed from GitHub with:

if (!require(remotes)) {
  install.packages("remotes")
}
remotes::install_github("reconhub/i2extras", build_vignettes = TRUE)

Resources

Vignettes

An overview of i2extras is provided in the included vignettes:

• vignette("peak_estimation", package = "i2extras")

• vignette("fitting_epicurves", package = "i2extras")

Getting help online

Bug reports and feature requests should be posted on github using the issue system. All other questions should be posted on the RECON slack channel see https://www.repidemicsconsortium.org/forum/ for details on how to join.