Table 1.

Five categories of motivations for modelling, illustrative prompt questions, and focus during model construction.

	Motivations for modelling	Illustrative prompt questions or statements and references	Focus during model construction
Mapping and formalising theory—providing conceptual frameworks	Modelling helps provide a conceptual framework (for self or others)	What are the key entities and processes required to model bTB and how might we formulate them in the most conceptually useful way?	Conceptual clarity of key entities and processes and formalisation of these
	Begin with informal understanding or verbal theory; obtain a precise formal representation of the theory (a full model) or of concepts and subcomponents of it	Are there similar concepts in associated areas that could apply (e.g., how does reproductive potential relate to R0)? (9)
Exploring theory—exploring possibilities	A model formalising theory is used to constrain relationships between entities so that system behaviours can be explored	Is infection invasion success dependent on spatial clustering? (10)	Accurate representation of relevant aspects of the theory in the model
	Begin with a model that formalises theory; obtain a set of possible behaviours given those processes	What is the probability of bTB persisting in cattle herds of different sizes? (11)	No explicit use of data is required
Building theory—generating hypotheses and explanations	The structure of the formalised model focuses our attention on particular processes and parameters, changes to which constitute testable hypotheses	Following the 10-year randomised badger culling trial, bTB incidence in cattle decreased in the badger culling area, but increased in adjoining areas (12)	Observing the way structures and parameters suggest model reformulations
	Begin with an observation or data; obtain precise hypotheses. NB: theory building often conducted iteratively with theory testing (below)	The 1967–1968 UK foot-and-mouth disease (FMD) epidemic was characterised by rapid early spread followed by slower later spread (13)
Testing theory—identifying mechanisms	To generate empirically relevant and measurable predictions, for the purpose of falsification	Does the incorporation of transmission heterogeneity allow us to better explain the data? (14)	Incorporation of mechanisms into a model in ways that allow us to establish whether observed phenomena can be reproduced; structural equivalence between data and model outputs
	Begin with a model that encapsulates a theory; obtain predictions that can be compared with data to help pinpoint incorrect mechanisms
Applying theory—generating accurate predictions	To make forecasts, predict responses under intervention, and examine counterfactual scenarios	How might FMD epidemiological dynamics have differed under alternative culling scenarios during the 2001 FMD outbreak? (15)	Ensuring key mechanisms are replicated as closely as required to accurately reproduce real-world phenomena and data
	Begin with a model that is assumed to be true; obtain hindcasts/forecasts, and predictions relating to counterfactuals and other systems	What difference might incursion location and speed of deployment make to the effectiveness of FMD reactive ring vaccination? (16)