ern

The ern package was developed to adapt the EpiEstim package for real world data, including wastewater and clinical data. Specifically the package:

disaggregates clinical reports into a shorter time unit to enable estimation of \(R_t\) using an intrinsic generation interval on a useful timescale;
provides a framework to estimate \(R_t\) from wastewater data, consistent with an estimation based on clinical data;
provides a user-friendly interface geared at public-health practitioners that may have limited proficiency in the R programming language;
uses EpiEstim for efficient and rapid estimation.

This package combines the following methods:

including an additional module for disaggregation of data into shorter time units.

Features
Ability to nowcast/forecast	No
Incorporates delay distributions	Includes incubation period and reporting delay for clinical data
Estimates expected cases	Doing this from wastewater or aggregated clincal case data
Communicates uncertainty	Uncertainty from both EpiEstim approach, as well as assumptions made in estimating incident cases through resampling approach
Validation
Documentation of package methods	Yes
Documentation of package implementation	Yes

There is a vignette and sample code and worked examples in the Plos One publication for this method Champredon et al. (2024).