BlueSkiesResearch.org.uk: Model calibration, nowcasting, and operational prediction of the COVID-19 pandemic

New manuscript! Now up on github too.

Title as post. Yes, this is us dipping our toes into epidemiology. Turns out that calibrating a simple model with observational data is much the same whether it’s paleoclimate or epidemics. The maths and the methods are much the same. In fact this one is a particularly easy one as the model is embarrassingly linear (once you take the logarithm of the time series). I’ve been posting my analyses on Twitter and the other blog, but since this is a real paper with words and figures and references and stuff, it can go here too (plus, I can upload a pdf here unlike blogspot).

We have been doing a very straightforward MCMC calibration of a simple SEIR model (equivalent of energy balance box model in climate science, pretty much). The basic concept is to use the model to invert the time series of reported deaths back through the time series of underlying infections in order to discover the model parameters such as the famous reproductive rate R. It’s actually rather simple and I am still bemused by the fact that none of the experts (in the UK at least) are doing this. I mean what on earth are mathematical epidemiologists actually for, if not this sort of thing? They should have been all over this like a rash. The exponential trend in the data is a key diagnostic of the epidemic and the experts didn’t even bother with the most elementary calibration of this in their predictions that our entire policy is based on. It’s absolutely nuts. It’s as if someone ran a simulation with a climate model and presented the prediction without any basic check on whether it reproduced the recent warming. You’d get laughed out of the room if you tried that at any conference I was attending. By me if no-one else (no, really, I wouldn’t be the only one).

Anyway, the basic result is that the method works like a charm and we can reliably deduce the changes in R due to imposed controls, and it looks increasing clear that it’s been less than 1 in the UK for several weeks now, while the experts are still talking about the peak being a couple of weeks away. The whole experience is just…so strange.

Anyway, I did try talking politely to some of the experts but just got brushed off which may partly explain the tone in the manuscript. Or maybe that’s just me

The paper has been submitted to medrxiv but who knows what they will make of it. My experiences when I have poked my nose into other peoples’ fields has not usually be a very encouraging one so I’m half expecting them to reject it anyway. So be it.

Here is today’s forecast to encourage you to read the paper.