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("reconverse/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.