Explaining transmission rate variations and forecasting epidemic spread in multiple regions with a semiparametric mixed effects SIR model

David A. Buch, James E. Johndrow and David B. Dunson

Biometrics, 2023, vol. 79, issue 4, 2987-2997

Abstract: The transmission rate is a central parameter in mathematical models of infectious disease. Its pivotal role in outbreak dynamics makes estimating the current transmission rate and uncovering its dependence on relevant covariates a core challenge in epidemiological research as well as public health policy evaluation. Here, we develop a method for flexibly inferring a time‐varying transmission rate parameter, modeled as a function of covariates and a smooth Gaussian process (GP). The transmission rate model is further embedded in a hierarchy to allow information borrowing across parallel streams of regional incidence data. Crucially, the method makes use of optional vaccination data as a first step toward modeling of endemic infectious diseases. Computational techniques borrowed from the Bayesian spatial analysis literature enable fast and reliable posterior computation. Simulation studies reveal that the method recovers true covariate effects at nominal coverage levels. We analyze data from the COVID‐19 pandemic and validate forecast intervals on held‐out data. User‐friendly software is provided to enable practitioners to easily deploy the method in public health research.

Date: 2023
References: View references in EconPapers View complete reference list from CitEc
Citations:

Downloads: (external link)
https://doi.org/10.1111/biom.13901

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:bla:biomet:v:79:y:2023:i:4:p:2987-2997

Ordering information: This journal article can be ordered from
http://www.blackwell ... bs.asp?ref=0006-341X

Access Statistics for this article

More articles in Biometrics from The International Biometric Society
Bibliographic data for series maintained by Wiley Content Delivery ().