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Data from: Hidden variable models reveal the effects of infection from changes in host survival


Ferguson, Jake et al. (2023), Data from: Hidden variable models reveal the effects of infection from changes in host survival, Dryad, Dataset,


The impacts of disease on host vital rates can be demonstrated using longitudinal studies, but these studies can be expensive and logistically challenging. We examined the utility of hidden variable models to infer the individual effects of infectious disease from population-level measurements of survival when longitudinal studies are not possible. Our approach seeks to explain temporal deviations in population-level survival after introducing a disease causative agent when disease prevalence cannot be directly measured by coupling survival and epidemiological models. We tested this approach using an experimental host system (Drosophila melanogaster) with multiple distinct pathogens to validate the ability of the hidden variable model to infer per-capita disease rates. We then applied the approach to a disease outbreak in harbor seals (Phoca vituline) that had data on observed strandings but no epidemiological data. We found that our hidden variable modeling approach could successfully detect the per-capita effects of disease from monitored survival rates in both the experimental and wild populations. Our approach may prove useful for detecting epidemics from public health data in regions where standard surveillance techniques are not available and in the study of epidemics in wildlife populations, where longitudinal studies can be especially difficult to implement.


Fly survival data was collected from an experimental design that monitored daily survival in populations of flies that were challenged with the Drosophila C virus (DCV) and Drosophila X virus (DXV).

Seal stranding data was digitized from an existing report by Brasseur, "Stranding and Rehabilitation in Numbers: Population development and stranding data on the Dutch coasts 1990-2016".  Surveys covered the coastline of the Dutch Wadden Sea and nearby areas.

Usage notes

JAGS ( and R ( need to be installed to reproduce these analyses.


National Institute of General Medical Sciences, Award: P20GM104420

National Institute of General Medical Sciences, Award: P30GM103324

National Science Foundation, Award: DBI-0939454

National Science Foundation, Award: DMS-1029485