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A new formulation of compartmental epidemic modelling for arbitrary distributions of incubation and removal times.

ABSTRACT: The paradigm for compartment models in epidemiology assumes exponentially distributed incubation and removal times, which is not realistic in actual populations. Commonly used variations with multiple exponentially distributed variables are more flexible, yet do not allow for arbitrary distributions. We present a new formulation, focussing on the SEIR concept that allows to include general distributions of incubation and removal times. We compare the solution to two types of agent-based model simulations, a spatially homogeneous one where infection occurs by proximity, and a model on a scale-free network with varying clustering properties, where the infection between any two agents occurs via their link if it exists. We find good agreement in both cases. Furthermore a family of asymptotic solutions of the equations is found in terms of a logistic curve, which after a non-universal time shift, fits extremely well all the microdynamical simulations. The formulation allows for a simple numerical approach; software in Julia and Python is provided.

SUBMITTER: Hernandez P

PROVIDER: S-EPMC7857597 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature

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A new formulation of compartmental epidemic modelling for arbitrary distributions of incubation and removal times.

Hernández Pilar P Pena Carlos C Ramos Alberto A Gómez-Cadenas Juan José JJ

PloS one 20210203 2

The paradigm for compartment models in epidemiology assumes exponentially distributed incubation and removal times, which is not realistic in actual populations. Commonly used variations with multiple exponentially distributed variables are more flexible, yet do not allow for arbitrary distributions. We present a new formulation, focussing on the SEIR concept that allows to include general distributions of incubation and removal times. We compare the solution to two types of agent-based model si ...[more]

PMID: 33534810

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Project description:Controlling for imperfect detection is important for developing species distribution models (SDMs). Occupancy-detection models based on the time needed to detect a species can be used to address this problem, but this is hindered when times to detection are not known precisely. Here, we extend the time-to-detection model to deal with detections recorded in time intervals and illustrate the method using a case study on stream fish distribution modeling. We collected electrofishing samples of six fish species across a Mediterranean watershed in Northeast Portugal. Based on a Bayesian hierarchical framework, we modeled the probability of water presence in stream channels, and the probability of species occupancy conditional on water presence, in relation to environmental and spatial variables. We also modeled time-to-first detection conditional on occupancy in relation to local factors, using modified interval-censored exponential survival models. Posterior distributions of occupancy probabilities derived from the models were used to produce species distribution maps. Simulations indicated that the modified time-to-detection model provided unbiased parameter estimates despite interval-censoring. There was a tendency for spatial variation in detection rates to be primarily influenced by depth and, to a lesser extent, stream width. Species occupancies were consistently affected by stream order, elevation, and annual precipitation. Bayesian P-values and AUCs indicated that all models had adequate fit and high discrimination ability, respectively. Mapping of predicted occupancy probabilities showed widespread distribution by most species, but uncertainty was generally higher in tributaries and upper reaches. The interval-censored time-to-detection model provides a practical solution to model occupancy-detection when detections are recorded in time intervals. This modeling framework is useful for developing SDMs while controlling for variation in detection rates, as it uses simple data that can be readily collected by field ecologists.

Dataset Information

A new formulation of compartmental epidemic modelling for arbitrary distributions of incubation and removal times.

Publications

A new formulation of compartmental epidemic modelling for arbitrary distributions of incubation and removal times.

Similar Datasets

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