EpiFilter

REF	Parag (2021)
Docs
Github	https://github.com/kpzoo/EpiFilter
Last commit	Dec 9, 2023
Installation

Brief description

Copied from the developer site

Maximally informed, mean square error optimised estimates of reproduction numbers (R) over time.

Uses Bayesian recursive filtering and smoothing to maximise the information extracted from the incidence data used. Takes a forward-backward approach and provides estimates that combine advantages of EpiEstim and the Wallinga-Teunis method. Method is exact (and optimal given a grid over R) and deterministic (produces the same answer on the same data).

Methods

This package contains the following methods to solve for \(R(t)\) in time:

• filtering

Assessment

Features
Ability to nowcast/forecast	No
Incorporates delay distributions	No, although some right-censoring is included
Estimates expected cases	No
Communicates uncertainty	Yes
Validation
Documentation of package methods	Yes
Documentation of package implementation	No

Sample code

The primary sample code comes from this R script.

Parag KV. 2021. Improved estimation of time-varying reproduction numbers at low case incidence and between epidemic waves. PLOS Computational Biology 17:e1009347; doi:10.1371/journal.pcbi.1009347.