E&W: scientific benchmark list

List

Here is a list of potential benchmarks based off of scientific literature focused on the England & Wales dataset. They are in rough order of preferred implementation and include both spatial and non-spatial phenomena.

• Reproducing critical community size for measles (and expected behavior w/r/t birth rate, RI, R0; cf. Kurt's GR)
• Biennial outbreak periodicity
• Lagged/travelling waves in infections from hub to satellites
• Synchrony between hubs

Notes

• Reproducing critical community size for measles (and expected behavior w/r/t birth rate, RI, R0)
• "Second-order" pieces of CCS in a network - frequency of "0-measles-weeks", outbreaks, and importations that don't take off; period between outbreaks, all vs. population size
• Spatiotemporal phenomena - phase coherence, source-sink dynamics, etc. Note that there isn't like a canonical, accepted way to calibrate models to these phenomena.
• Biennial (2-year) periodicity for outbreaks pre-vaccine, especially in large (>CCS) population centers like London.
• They also find travelling waves from large population centers (like London) to outlying areas. With a wave speed of ~5km/week. This wave is well-defined up to 30km. But both distance from London and population size (or maybe density) contribute to lag/phase.
• The traveling wave from London is clearer than the wave from that from the northwest industrial centers of Manchester/Liverpool/Leeds, in the same way that the ripple from a single large rock in a pond is less complex than the superimposed ripples from chucking 4 large-ish rocks together into the same area of a pond.
• There's a very interesting phenomenon of Cambridge being in sync with London while Norwich (and East Anglia) is 180 degrees out of phase, even though they are relatively near each other. I'd be impressed if we could reduce that to its mathematical essence and reproduce it. They note that while most locations lag London, there are a few locations in the industrial northwest which lead it. That's potentially a result of greater fertility. Again, there's potentially something there worth making sure we can capture.

Tools

• .ipynb notebook demonstrating local wavelet power spectrum

References

• Grenfell et al. (2001); classic travelling waves in E&W dataset
• Kurt Frey's CCS GR presentation
• Finkenstadt & Grenfell (2000); periodicity in E&W dataset
• Ferrari et al. (2008); birth rate vs. seasonal forcing
• Marguta et Parisi (2015); impact of mobility
• Marguta et Parisi (2016); synchrony and periodicity in E&W