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

Elske van der Vaart*, Mark A. Beaumont, Alice S A Johnston, Richard M. Sibly

*Corresponding author for this work

Research output: Contribution to journalArticle (Academic Journal)peer-review

57 Citations (Scopus)
292 Downloads (Pure)

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.

Original languageEnglish
Pages (from-to)182-190
Number of pages9
JournalEcological Modelling
Volume312
Early online date11 Jun 2015
DOIs
Publication statusPublished - 24 Sep 2015

Keywords

  • Approximate Bayesian Computation
  • Individual-based models
  • Model selection
  • Parameter estimation
  • Population dynamics

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