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

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.Comment: 21 pages, 11 figures. v2 matches published version: improved presentation (including title, abstract and references), results and conclusions unchange

Using a Socioeconomic Segregation Burn-in Model to Initialise an Agent-Based Model for Infectious Diseases

Socioeconomic status can have an important effect on health. In this paper we: (i) propose using house price data as a publicly available proxy for socioeconomic status to examine neighbourhood socioeconomic status at a more fine grained resolution than is available in Irish Central Statistics Office data; (ii) use a dissimilarity index to demonstrate and measure the existence of socioeconomic clustering at a neighbourhood level; (iii) demonstrate that using a standard ABM initialisation process based on CSO small area data results in ABMs systematically underestimating the socioeconomic clustering in Irish neighbourhoods; (iv) demonstrate that ABM models are better calibrated towards socioeconomic clustering after a segregation models has been run for a burn-in period after initial model setup; and (v) that running a socieconomic segregation model during the initiation of an ABM epidemiology model can have an effect on the outbreak patterns of the model. Our results support the use of segregation models as useful additions to the initiation process of ABM for epidemiology

Understanding the assumptions of an SEIR compartmental model using agentization and a complexity hierarchy

Equation-based and agent-based models are popular methods in understanding disease dynamics. Although there are many types of equation-based models, the most common is the SIR compartmental model that assumes homogeneous mixing and populations. One way to understand the effects of these assumptions is by agentization. Equation-based models can be agentized by creating a simple agent-based model that replicates the results of the equationbased model, then by adding complexity to these agentized models it is possible to break the assumptions of homogeneous mixing and populations and test how breaking these assumptions results in different outputs. We report a set of experiments comparing the outputs of an SEIR model and a set of agent-based models of varying levels of complexity, using as a case study a measles outbreak in a town in Ireland. We define and use a six level complexity hierarchy for agent-based models to create a set of progressively more complex variants of an agentized SEIR model for the spread of infectious disease. We then compare the results of the agentbased model at each level of complexity with results of the SEIR model to determine when the agentization breaks. Our analysis shows this occurs on the fourth step of complexity, when scheduled movements are added into the model. When agents networks and behaviours are complex the peak of the outbreak is shifted to the right and is lower than in the SEIR model suggesting that heterogeneous populations and mixing patterns lead to slower outbreaks compared homogeneous populations and mixing patterns

Simulating the Cost of Cooperation: A Recipe for Collaborative Problem-Solving

Collective problem-solving and decision-making, along with other forms of collaboration online, are central phenomena within ICT. There had been several attempts to create a system able to go beyond the passive accumulation of data. However, those systems often neglect important variables such as group size, the difficulty of the tasks, the tendency to cooperate, and the presence of selfish individuals (free riders). Given the complex relations among those variables, numerical simulations could be the ideal tool to explore such relationships. We take into account the cost of cooperation in collaborative problem solving by employing several simulated scenarios. The role of two parameters was explored: the capacity, the group’s capability to solve increasingly challenging tasks coupled with the collective knowledge of a group, and the payoff, an individual’s own benefit in terms of new knowledge acquired. The final cooperation rate is only affected by the cost of cooperation in the case of simple tasks and small communities. In contrast, the fitness of the community, the difficulty of the task, and the groups sizes interact in a non-trivial way, hence shedding some light on how to improve crowdsourcing when the cost of cooperation is high

Validating and Testing an Agent-Based Model for the Spread of COVID-19 in Ireland

Agent-based models can be used to better understand the impacts of lifting restrictions or implementing interventions during a pandemic. However, agent-based models are computationally expensive, and running a model of a large population can result in a simulation taking too long to run for the model to be a useful analysis tool during a public health crisis. To reduce computing time and power while running a detailed agent-based model for the spread of COVID-19 in the Republic of Ireland, we introduce a scaling factor that equates 1 agent to 100 people in the population. We present the results from model validation and show that the scaling factor increases the variability in the model output, but the average model results are similar in scaled and un-scaled models of the same population, and the scaled model is able to accurately simulate the number of cases per day in Ireland during the autumn of 2020. We then test the usability of the model by using the model to explore the likely impacts of increasing community mixing when schools reopen after summer holidays