Describing connectivity of farms in the landscape: How do approximations of contiguity compare?

1. Describing connectivity of farms in the landscape: How do approximations of contiguity compare? Jessica Flood, ThibaudPorphyre, Michael Tildesley and Mark Woolhouse GeoVet 23/08/2013

2. Background • Effective contact for transmission to occur • Requires conducive environment • Foot-and-mouth disease: • Livestock movements • Nose-nose contact • Contaminated fomites (on people, vehicles, blown by wind between pastures) Host Environment Pathogen

3. What is contiguity? • To be contiguous • To be neighbouring in such a way that enables disease transmission • Local spread, excluding movement of livestock between farms • Foot-and-mouth 2001 • Contiguous premises (CPs) pre-emptively culled • ‘On-the-ground’ decision

4. Why does it matter? • Foot-and-mouth 2001 local spread modelled byapproximations • Approximations not previously assessed for accuracy in identifying contiguous premises (CPs) • Stochastic models using these approximations: • Just 12% of model-predicted infected premises (IPs) were truly infected over the course of the 2001 outbreak (Tildesleyet al., 2008) From Keeling et al. (2001)

5. 1. The kernel Decay of risk of transmission with increasing distance from infected premises Relative risk of transmission • Assumes: • That the landscape is homogeneous • Resulting in an isotropic process (i.e. infection transmits equally in all directions from the farm premises) • And that Euclidean distance is appropriate, between point locations of farm premises 6 2 4 Distance (km)

6. 2. Area-weighted Voronoi tessellation Tries to approximate field adjacency • Approximates adjacency of fields using point locations • Assumes no landscape features would act as barriers to prevent transmission

7. Don’t forget landscape features Savillet al. (2006) • Large scale • Kernel based on shortest road distance better at explaining transmission around estuaries Bessellet al. (2008) • Smaller scale (<3km from infected premise) • Rivers & railways protect against transmission

8. So how do approximations compare to this?

9. Defining a gold standard • Field location data (IACS data) • Individual field parcel areas • Farms may have fragmented field clusters • Topographical data (OS MasterMap data) • Rivers • Roads/tracks • Railways • Ditches Gold standard termed as “map-based contiguity”

10. Key questions • How accurate are approximations in identifying map-based CPs? • How many map-based CPs are missed by approximation methods? • How many CPs do approximation methods pick up that are not map-based CPs? • Overall discrimination between map-based CPs/non-CPs • How do different CP definitions change the properties of the transmission network? • Mean degree (number of neighbours) • Density (the proportion of possible connections that actually exist)

11. Methods Two sample areas: • Aberdeenshire (n=107) • Beef/sheep breeding and finishing • Cropping • Ayrshire (n=184) • Dairy units • Densely packed Aberdeenshire Ayrshire

12. Methods • Point locations within areas ~15x15 km • Holdings paired if <7km point distance apart • Each holding pair (<7km point distance) checked by eye to see if contiguous according to gold-standard: • Shared boundary (0m between field edge) • Close boundary (<15m between field edge) • Presence of rivers, roads/tracks, railways, ditches

13. Compared to approximations 1. Point distance-based: <1km, <3km, <5km 2. Shared polygon edge - Area-weighted Voronoi polygon

14. Measuring agreement between the approximation and map-based measures • Sensitivity = TP / (TP + FN) • PPV = TP / (TP + FP) • TSS = (sensitivity + specificity - 1), where Specificity = TN / (FP + TN) TP=true positive, FP=false positive, TN=true negative, FN=false negative

15. Sensitivity: the proportion of map-based CPs correctly identified by approximation method • Low value => small proportion are CPs by approximation method (therefore high proportion of false negatives) The average sensitivity across all map-based definitions is shown

16. PPV: the proportion of approximation method CPs that are map-based CPs • Low value => small proportion are map-based CPs (therefore high proportion of false positives) The average PPV across all map-based definitions is shown

17. TSS: Overall measure of accuracy • How well do the approximation methods discriminate between map-based CPs/non-CPs? Average TSS across all map-based definitions shown

18. Network properties: Mean degree (number of neighbours) Approximations Map-based measures

19. Network properties: Density (proportion of possible connections that exist) Approximations Map-based measures

20. Aberdeenshire Effect of landscape features on network properties: Number of neighbours under different map-based definitions Ayrshire

21. Conclusions: How good are approximations of contiguity? • Approximations perform fairly consistently between locations • But no approximations are fantastic! • <3km point distance performs best out of point distance measures against map-based contiguity • Area-weighted tessellation overall best approximation measure of contiguity compared to map-based contiguity • Landscape not homogeneous – landscape features frequently act to alter contiguity definitions

22. Implications • Some inaccuracy of models may in part be due to not taking into account landscape heterogeneity and farm contiguity • Assuming contiguous mechanisms of spread are important → CPs should be given elevated level of risk → shape of kernel likely to be altered • <1km point distance – about 70% map-based CPs being missed • <5km point distance – still some map-based CPs being identified • Worth taking another look at road distance kernel in conjunction with map-based contiguity • Next step to look at spatial patterns from simulations to see how patterns compare, and if becomes slightly more deterministic

23. Thank you Supervisors: Prof. Mark Woolhouse Dr.ThibaudPorphyre Prof. Steve Albon Collaborators: Dr. Mike Tildesley Prof. Matt Keeling Dr. Paul Bessell

24. Aberdeenshire CPs captured with increasing distance between point locations Ayrshire