Calibration and evaluation of individual-based models using Approximate Bayesian Computation

Authored by Richard M Sibly, der Vaart Elske van, Mark A Beaumont, Alice S A Johnston

Date Published: 2015

DOI: 10.1016/j.ecolmodel.2015.05.020

Sponsors: Natural Environmental Resource Council

Platforms: NetLogo

Model Documentation: Other Narrative Flow charts Mathematical description

Model Code URLs: Model code not found

Abstract

This paper investigates the feasibility of using Approximate Bayesian Computation (ABC) to calibrate and evaluate complex individual-based models (IBMs). As ABC evolves, various versions are emerging, but here we only explore the most accessible version, rejection-ABC. Rejection-ABC involves running models a large number of times, with parameters drawn randomly from their prior distributions, and then retaining the simulations closest to the observations. Although well-established in some fields, whether ABC will work with ecological IBMs is still uncertain. Rejection-ABC was applied to an existing 14-parameter earthworm energy budget IBM for which the available data consist of body mass growth and cocoon production in four experiments. ABC was able to narrow the posterior distributions of seven parameters, estimating credible intervals for each. ABC's accepted values produced slightly better fits than literature values do. The accuracy of the analysis was assessed using cross-validation and coverage, currently the best-available tests. Of the seven unnarrowed parameters, ABC revealed that three were correlated with other parameters, while the remaining four were found to be not estimable given the data available. It is often desirable to compare models to see whether all component modules are necessary. Here, we used ABC model selection to compare the full model with a simplified version which removed the earthworm's movement and much of the energy budget. We are able to show that inclusion of the energy budget is necessary for a good fit to the data. We show how our methodology can inform future modelling cycles, and briefly discuss how, more advanced versions of ABC may be applicable to IBMs. We conclude that ABC has the potential to represent uncertainty in model structure, parameters and predictions, and to embed the often complex process of optimising an IBM's structure and parameters within an established statistical framework, thereby making the process more transparent and objective. (C) 2015 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY license

Tags

Agent-based models parameterization systems growth Populations Inference Monte-carlo Ecological models Eisenia-foetida savigny Simulation-models