Small moan about models and parameters in COVID. R - the number of infections each person makes on average is a parameter but it is also something that one can measure. Each infected person has their own "R" - it is a count - and one could in theory measure all these little Rs
This R is both something one can measure and the average R, or the distribution of R is often components of model. It is a "real measurable thing" and it is "part of our COVID models".
You might want to model other things; one is the distribution of how R varies between people/events. A sensible choice is a negative binomial. Often people use k as a parameter (in fact, in other uses, they often use the letter r as a parameter, but this would be confusing!)
k here is not measureable in the same way as R. It doesn't have meaning on an individual level and one can't subdivide k into different groups. You fit k with data. k is part of COVID models, but a modelling choice not a measurable thing at the limit.
Does this matter? Not much I suspect. But ... it's good to keep these things straight.
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Right. Deep Breath. RT-PCR "false positives" and Ct numbers (again). tl;dr it is complex, but the RT-PCR testing systems deployed across the world are sound and the people who run them report positives are positives and little can be improved obviously.
Context: I am a genomics/genetics + computational biology expert. I know a large number of infectious disease testing experts. I have a COI in that I am a long established consultant for a company (ONT) that makes a new test here; this gives me additional insight
There a number of classes of false positives which don't concern the current debate (eg, sample swaps, lab contamination). To repeat an early point all the people I know in this are paranoid about this, test and check in a rather detailed way and these are looooow.
Again, a briefing for journalists, this time on vaccine trials, types of vaccine, efficacy and safety.
(Context: I am a two-steps expert away from vaccine development; I am a one-step away from clinical trials; I am an expert on genetics + computational data science. I am, finally, on one of these clinical trials as a participant)
Standard context: SARS_CoV_2 is an infectious virus that causes a nasty disease, often leading to death, in a subset of humans. It will continue to be a massive issue to manage until we either have good enough vaccines or good enough treatments for the disease.
It's great to see this paper on scaled up Cactus graphs (Progressive Cactus) - on 600 vertebrate genomes - from the great team lead by @BenedictPatennature.com/articles/s4158…
This paper is a very much a methods paper, but I hope Benedict and colleagues will also dive into the data - I don't think we have use the realised ancestor reconstructions (reminds me of the older Enredo days - also with Benedict!). There is a treasure trove in there
Just repeat evolution I think is fascinating here, but also niche-loss pseudogenes for example.
A riff on data, models and intervention in a COVID world.
When you don't have data, you absolutely need models - it helps you understand what could happen, good and bad scenarios and what you need to measure to understand more thing. With no - or little - data, models are king.
When you have data, the role of models change. In fast moving epidemic even working out what is happening *right now* is complex; your data is coming in different streams, it has biases (which change over time), technical issues (also time dependent) >>
There are debates - important debates - to have in these COVID times, but there are some either stupid debates or misguided in my view debates. Here's my list with brief rejoinders.
1. False positives on tests are grossly inflating the number of cases. Straightforwardly they are not; the system understands false positives, goes to a lot of length to prevent them, and, acknowledging that they can never be 0, carefully models them in analysis.
2. "Hard" Stratify and Shield (or segmentation) is a solution. By "Hard" I mean placing all the at risk people in entirely COVID "safe" environments (extremely low risk of infection) and then having the remaining people at low risk live normal lives, and get the infection.
It is somewhat hard to know which strand on England's November lockdown to pick apart - a large number of people in the press (and twitter) are commenting ("hot takes" in the US parlance) - most heat and not so much light.
Yesterday, before the announcement, I tweeted on this here: