The basic-reproduction number of infectious diseases in spatially structured host populations

The spatial structure of a host population has a profound effect on the dynamics of infectious diseases. The basic reproduction number, a central quantity in the study of epidemic dynamics, is affected by host clustering as well as host density. Several authors have developed methods to quantify the basic reproduction number in a spatially structured host population. The methods used and the expressions derived are however difficult to apply to real life spatial host structures. In this paper we introduce an explicit expression for the basic reproduction number using the O-ring statistic, developed in spatial statistics, that quantifies the host density as a function of the distance from a randomly selected host individual. The O-ring statistic is frequently used in the study of the ecology of spatially structured plant populations, being a convenient summary of the properties of a landscape by way of a single function. The connection we develop between spatial statistics and epidemic d..., The dataset is computer code supporting the article \"The basic-reproduction number of infectious diseases in spatially structured host populations\" in Oikos by van den Bosch, Helps & Cunniffe., , # Data from: The basic-reproduction number of infectious diseases in spatially structured host populations

[https://doi.org/10.5061/dryad.kh18932fw](https://doi.org/10.5061/dryad.kh18932fw)

Computer code to support the above-named article.

## Description of the data and file structure

Files provided include two .c files and one .h file which can be compiled to create an executable to simulate epidemics using a stochastic individual based model. The .cfg file (as well as command line flags) can be altered to affect the parameterisation of this simulation. There are also three .R files; running one creates a host landscape for the epidemic simulation; the other two can be used to calculate R0 using the methods set out in our paper, and to calculate the same quantity numerically by fitting a (multi-species) branching process model (i.e., a way of checking that the analytic method gives reliable results).

## Sharing/Access information

The code is also available at 

* [https://githu...