epinowcast

REF	Lison et al. (2024)
Docs	epinowcast.org/
Github	github.com/epinowcast
Last commit	Sep 30, 2024
Installation	CRAN

Description

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Tools to enable flexible and efficient hierarchical nowcasting of right-truncated epidemiological time-series using a semi-mechanistic Bayesian model with support for a range of reporting and generative processes. Nowcasting, in this context, is gaining situational awareness using currently available observations and the reporting patterns of historical observations. This can be useful when tracking the spread of infectious disease in real-time: without nowcasting, changes in trends can be obfuscated by partial reporting or their detection may be delayed due to the use of simpler methods like truncation. While the package has been designed with epidemiological applications in mind, it could be applied to any set of right-truncated time-series count data.

Methods

This package contains the following methods:

• random walk

Assessment

Features
Ability to nowcast/forecast	Nowcasting
Incorporates delay distributions	Yes
Estimates expected cases	Yes
Communicates uncertainty	Yes
Validation
Documentation of package methods	Yes
Documentation of package implementation	Yes

Sample code

A list of helpful vignettes are given here.

Lison A, Abbott S, Huisman J, Stadler T. 2024. Generative bayesian modeling to nowcast the effective reproduction number from line list data with missing symptom onset dates. PLoS Computational Biology 20: e1012021.