Scrutable

shpalman wrote: Wed Mar 04, 2020 12:06 pm The biggest issue is that the model is the wrong one, since it's based on active infections spreading the virus but if someone with symptoms results positive to the test (less than 10% of those considered worth testing) then they are either told to self-isolate or put in hospital (about 50-50) so that's the point at which they stop spreading it. The assumption is also made that asymptomatic carriers don't spread it, which just feels like a bit of an excuse to not test everybody (which is of course unfeasible anyway). The model doesn't even feature an incubation period.

The number of active infections spreading the virus is therefore completely unknown, as is the number of people who quietly got better from a mild infection of it. To fit the data even a little bit I need a very long recovery time which means R0 is far too large. This might just be because recoveries aren't declared until doctors are extremely sure.

Coronavirus Live Updates: Fatality Rate of Covid-19 Is Higher Than the Flu
The World Health Organization announced on Tuesday that the global death rate of the disease caused by the new coronavirus was 3.4 percent.

RIGHT NOW Deaths outside China exceeded those inside the country for the first time since the start of the outbreak.

Bird on a Fire wrote: Wed Mar 04, 2020 12:26 pm

shpalman wrote: Wed Mar 04, 2020 12:06 pm The biggest issue is that the model is the wrong one, since it's based on active infections spreading the virus but if someone with symptoms results positive to the test (less than 10% of those considered worth testing) then they are either told to self-isolate or put in hospital (about 50-50) so that's the point at which they stop spreading it. The assumption is also made that asymptomatic carriers don't spread it, which just feels like a bit of an excuse to not test everybody (which is of course unfeasible anyway). The model doesn't even feature an incubation period.

The number of active infections spreading the virus is therefore completely unknown, as is the number of people who quietly got better from a mild infection of it. To fit the data even a little bit I need a very long recovery time which means R0 is far too large. This might just be because recoveries aren't declared until doctors are extremely sure.

Sounds like this would benefit from a hidden Markov model, which would separate your observation process from the "state process" of interest, i.e. number of cases.

The number of infections today is dependent on the number of infections yesterday, with some multiplying process. But we don't know any of the numbers involved. What we have instead are imperfect observations, which we know a bit about (e.g. number of people tested, sensitivity of the test) which would inform Bayesian priors and you can then use maximum likelihood to find the parameter estimates for the underlying disease process that would most likely generate that sequence of observations, along with associated measures of confidence.

Given the amount of stochasticity involved I'd be surprised if you need a particularly mechanistic model to get something adequately predictive.

jimbob wrote: Wed Mar 04, 2020 4:58 pm An Iranian colleague's wife is still in touch with other medics who stayed in Iran after qualifying as doctors. A
They told her that there were many odd pneumonia cases in Qom in November.

Boustrophedon wrote: Wed Mar 04, 2020 5:16 pm So the government are only going to release infection figures once a week and redacted of geographical information.

https://twitter.com/DHSCgovuk/status/12 ... 4407802880

So there's 6 days for those in the know (IE ministers.) to do a nice little bit of insider trading on companies likely to be affected.

Boustrophedon wrote: Wed Mar 04, 2020 5:16 pm So the government are only going to release infection figures once a week and redacted of geographical information.

https://twitter.com/DHSCgovuk/status/12 ... 4407802880

So there's 6 days for those in the know (IE ministers.) to do a nice little bit of insider trading on companies likely to be affected.

bmforre wrote: Wed Mar 04, 2020 1:27 pm NYTimes right now:

Coronavirus Live Updates: Fatality Rate of Covid-19 Is Higher Than the Flu
The World Health Organization announced on Tuesday that the global death rate of the disease caused by the new coronavirus was 3.4 percent.

RIGHT NOW Deaths outside China exceeded those inside the country for the first time since the start of the outbreak.

shpalman wrote: Wed Mar 04, 2020 11:09 am If I want to model this slowdown I could reduce the susceptible population to some number which isn't several orders of magnitude greater than the number of cases, i.e. 6000 instead of 60 million. But to get the same exponential increase in the first week or so I need to increase the contact parameter so R_0 is now 11.3.

Reducing the susceptible population fudges the idea of quarantine and travel restrictions, so that the virus can't actually reach the entire population of Italy.

It predicts that we'll have 2625 active infections by the end of today.

lpm wrote: Wed Mar 04, 2020 5:13 pm

jimbob wrote: Wed Mar 04, 2020 4:58 pm An Iranian colleague's wife is still in touch with other medics who stayed in Iran after qualifying as doctors. A
They told her that there were many odd pneumonia cases in Qom in November.

None of these "ancient Covid" claims make sense.

It's easy to backtrack to 1st Dec 2019 and a handful of cases. By 31 Dec there would have been in the region of 500 cases in Wuhan, including about 50 in the hospitals - and it was only at the end of Dec that any doctor noticed the anomoly, with that whistle-blower doctor. Of those 50, two-thirds were directly linked to the Wuhan market. It's simply impossible for that profile to fit in with any other origin.

tenchboy wrote: Wed Mar 04, 2020 5:06 pm Fire Flood Pestilence Famine Two Popes and now og hod just pass me the revolver and a glass of port I'll meet you on the other side.
Turn it on turn it on again...

sTeamTraen wrote: Thu Mar 05, 2020 12:45 am

tenchboy wrote: Wed Mar 04, 2020 5:06 pm Fire Flood Pestilence Famine Two Popes and now og hod just pass me the revolver and a glass of port I'll meet you on the other side.
Turn it on turn it on again...

As David Baddiel tweeted, this might not be a great time for three 70-year-olds to spend time with massive crowds of people.

tenchboy wrote: Wed Mar 04, 2020 5:06 pm Fire Flood Pestilence Famine Two Popes and now og hod just pass me the revolver and a glass of port I'll meet you on the other side.
Turn it on turn it on again...

bob sterman wrote: Wed Mar 04, 2020 7:35 pm

Boustrophedon wrote: Wed Mar 04, 2020 5:16 pm So the government are only going to release infection figures once a week and redacted of geographical information.

https://twitter.com/DHSCgovuk/status/12 ... 4407802880

So there's 6 days for those in the know (IE ministers.) to do a nice little bit of insider trading on companies likely to be affected.

The tweet says...

"As of today, due to the number of new cases, we will no longer be tweeting information on the location of each new case. Instead, this information will be released centrally in a consolidated format online, once a week. We are working on this now and plan to share on Friday."

Doesn't this mean they will still tweet the numbers (perhaps each day) but just not tweet the locations.

lpm wrote: Wed Mar 04, 2020 11:43 pm Those guys from that link are pretty dismissive of this latest "new 2nd strain has emerged" theory.

bob sterman wrote: Wed Mar 04, 2020 7:35 pm

Boustrophedon wrote: Wed Mar 04, 2020 5:16 pm So the government are only going to release infection figures once a week and redacted of geographical information.

https://twitter.com/DHSCgovuk/status/12 ... 4407802880

So there's 6 days for those in the know (IE ministers.) to do a nice little bit of insider trading on companies likely to be affected.

The tweet says...

"As of today, due to the number of new cases, we will no longer be tweeting information on the location of each new case. Instead, this information will be released centrally in a consolidated format online, once a week. We are working on this now and plan to share on Friday."

Doesn't this mean they will still tweet the numbers (perhaps each day) but just not tweet the locations.

bob sterman wrote: Thu Mar 05, 2020 10:01 am

lpm wrote: Wed Mar 04, 2020 11:43 pm Those guys from that link are pretty dismissive of this latest "new 2nd strain has emerged" theory.

I had a quick look at the paper - the part where they present an argument about selection pressures leading to a change in the prevalence of different strains is not very clearly written. So it's hard to follow their line of reasoning.

Although the L type (∼70%) is more prevalent than the S type (∼30%), the S type was found to be the ancestral version. Whereas the L type was more prevalent in the early stages of the outbreak in Wuhan, the frequency of the L type decreased after early January 2020. Human intervention may have placed more severe selective pressure on the L type, which might be more aggressive and spread more quickly. On the other hand, the S type, which is evolutionarily older and less aggressive, might have increased in relative frequency due to relatively weaker selective pressure.

Boustrophedon wrote: Thu Mar 05, 2020 10:34 am

bob sterman wrote: Wed Mar 04, 2020 7:35 pm

Boustrophedon wrote: Wed Mar 04, 2020 5:16 pm So the government are only going to release infection figures once a week and redacted of geographical information.

https://twitter.com/DHSCgovuk/status/12 ... 4407802880

So there's 6 days for those in the know (IE ministers.) to do a nice little bit of insider trading on companies likely to be affected.

The tweet says...

"As of today, due to the number of new cases, we will no longer be tweeting information on the location of each new case. Instead, this information will be released centrally in a consolidated format online, once a week. We are working on this now and plan to share on Friday."

Doesn't this mean they will still tweet the numbers (perhaps each day) but just not tweet the locations.

Anyway they have done a U-turn and decided to carry on as before.

lpm wrote: Thu Mar 05, 2020 10:41 am

bob sterman wrote: Thu Mar 05, 2020 10:01 am

lpm wrote: Wed Mar 04, 2020 11:43 pm Those guys from that link are pretty dismissive of this latest "new 2nd strain has emerged" theory.

I had a quick look at the paper - the part where they present an argument about selection pressures leading to a change in the prevalence of different strains is not very clearly written. So it's hard to follow their line of reasoning.

Paper here. S and L types.
https://academic.oup.com/nsr/advance-ar ... 36/5775463

Although the L type (∼70%) is more prevalent than the S type (∼30%), the S type was found to be the ancestral version. Whereas the L type was more prevalent in the early stages of the outbreak in Wuhan, the frequency of the L type decreased after early January 2020. Human intervention may have placed more severe selective pressure on the L type, which might be more aggressive and spread more quickly. On the other hand, the S type, which is evolutionarily older and less aggressive, might have increased in relative frequency due to relatively weaker selective pressure.

bob sterman wrote: Thu Mar 05, 2020 10:48 am

lpm wrote: Thu Mar 05, 2020 10:41 am

bob sterman wrote: Thu Mar 05, 2020 10:01 am

I had a quick look at the paper - the part where they present an argument about selection pressures leading to a change in the prevalence of different strains is not very clearly written. So it's hard to follow their line of reasoning.

Paper here. S and L types.
https://academic.oup.com/nsr/advance-ar ... 36/5775463

Although the L type (∼70%) is more prevalent than the S type (∼30%), the S type was found to be the ancestral version. Whereas the L type was more prevalent in the early stages of the outbreak in Wuhan, the frequency of the L type decreased after early January 2020. Human intervention may have placed more severe selective pressure on the L type, which might be more aggressive and spread more quickly. On the other hand, the S type, which is evolutionarily older and less aggressive, might have increased in relative frequency due to relatively weaker selective pressure.

Yes - that's the bit that I don't think is very clear. E.g. using the term "aggressive" rather than clarifying whether they are referring to harm to the patient or transmissability.