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Coronavirus - Modelling Aspects Only

The home for all non-political Coronavirus (Covid-19) discussions on The Lemon Fool
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This is the home for all non-political Coronavirus (Covid-19) discussions on The Lemon Fool
Lootman
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Re: Coronavirus - Modelling Aspects Only

#346665

Postby Lootman » October 10th, 2020, 9:45 am

servodude wrote:
Lootman wrote:
servodude wrote:Indeed! And it is done so everywhere in the world; irrespective of the absolute weather

Are you saying that there is more flu in Australia in December, January and February, even though that is summer there?

Otherwise I am not sure what point you are making.

Autumn/Winter is flu season all over the world.
The winter is at different times depending on where you are
One place's Winter might be closer to another's Summer.
It's not the absolute weather that causes the flu to spread better in winter: it's what the people do that does

Ah, OK, so in any country it is the colder part of the year when colds and flu are more prevalent? That makes sense.

That said the UK's numbers started going up in August so clearly the virus doesn't really care what month it is nor what the season is.

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Re: Coronavirus - Modelling Aspects Only

#346666

Postby Itsallaguess » October 10th, 2020, 9:45 am

johnhemming wrote:
I don't have figures to compare various regions in France. However, the weather today in Paris is ranging from 11-14 C.

London is 8-13, Birmingham is 8-11. Manchester 10-13.

I would not say with those figures that Paris is substantially warmer than the UK cities.


But then neither is London substantially warmer than Birmingham or Manchester from those figures, and yet you're happy to use relative UK temperatures as part of your weather-based theory...

I'm sorry, but that seems inconsistent John.

Cheers,

Itsallaguess
Last edited by Itsallaguess on October 10th, 2020, 9:46 am, edited 1 time in total.

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Re: Coronavirus - Modelling Aspects Only

#346667

Postby johnhemming » October 10th, 2020, 9:45 am

The paper on humidity is interesting:
Overall, a decrease in relative humidity of 1% was associated with an increase in cases of 7–8%. Overall, we found no relationship with between cases and temperature, rainfall or wind speed. Information generated in this study confirms humidity as a driver of SARS‐CoV‐2 transmission.


Obviously humidity is affected by temperature, but that is not the only factor.

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Re: Coronavirus - Modelling Aspects Only

#346668

Postby Lootman » October 10th, 2020, 9:50 am

johnhemming wrote:The paper on humidity is interesting:
Overall, a decrease in relative humidity of 1% was associated with an increase in cases of 7–8%. Overall, we found no relationship with between cases and temperature, rainfall or wind speed. Information generated in this study confirms humidity as a driver of SARS‐CoV‐2 transmission.

Obviously humidity is affected by temperature, but that is not the only factor.

100 years ago the "cure" for TB was often being told to move to Arizona or New Mexico for its very low humidity.

Is the suggestion now to move somewhere with high humidity like, er, the UK?

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Re: Coronavirus - Modelling Aspects Only

#346670

Postby johnhemming » October 10th, 2020, 9:52 am

Itsallaguess wrote:But then neither is London substantially warmer than Birmingham or Manchester, and yet you're happy to use relative UK temperatures as part of your weather-based theory...

I'm sorry, but that seems inconsistent John.


What I have said is that weather (and it may be primarily the humidity, but we need to see more on that) has an impact on the infectiousness of the disease. There is a variation in England. We will have difficulty having absolute certainty as to why there is a variation. Comparing things to earlier in the year it is clear that the North is doing worse than the South. That could be weather (possibly humidity) and it could be because a higher proportion of people in London and the south were infected earlier in the year. I think the latter is going to be part of the cause. It may also be that humidity is lower in the North, but I don't have any figures to check that.

I don't think that is inconsistent. I do not have figures to enable me to come to any conclusions about France. Getting reliable stats in England is not that easy. I think the hospital figures are probably a bit lumpy because of testing delays.

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Re: Coronavirus - Modelling Aspects Only

#346673

Postby Itsallaguess » October 10th, 2020, 9:58 am

johnhemming wrote:
Itsallaguess wrote:
But then neither is London substantially warmer than Birmingham or Manchester, and yet you're happy to use relative UK temperatures as part of your weather-based theory...

I'm sorry, but that seems inconsistent John.


What I have said is that weather (and it may be primarily the humidity, but we need to see more on that) has an impact on the infectiousness of the disease. There is a variation in England. We will have difficulty having absolute certainty as to why there is a variation. Comparing things to earlier in the year it is clear that the North is doing worse than the South. That could be weather (possibly humidity) and it could be because a higher proportion of people in London and the south were infected earlier in the year. I think the latter is going to be part of the cause. It may also be that humidity is lower in the North, but I don't have any figures to check that.

I don't think that is inconsistent. I do not have figures to enable me to come to any conclusions about France. Getting reliable stats in England is not that easy. I think the hospital figures are probably a bit lumpy because of testing delays.


I think it's inconsistent to want to compare North/South UK temperatures, but then stop that comparison at the English Channel.

I also think it's inconsistent to think that North/South UK humidity might be a potential driver, but again, wish to ignore any resurgence past the White Cliffs of Dover.

A weather-related 'Due-south is better' theory that stops at the channel doesn't, on the face of it, deliver a great deal of confidence..

We probably won't get any further with this particular discussion at this moment in time, other than for me to raise this disparity with you to perhaps consider, and then we shall wait to see how things progress, of course.

Cheers,

Itsallaguess

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Re: Coronavirus - Modelling Aspects Only

#346675

Postby Lootman » October 10th, 2020, 10:06 am

Itsallaguess wrote:neither is London substantially warmer than Birmingham or Manchester

Although there is a (moderate) north/south difference in average temperature, there is also an east/west divide. The east of the UK is typically hotter in summer and colder in winter. So for instance the west coast of Scotland can be milder than Suffolk on a winter's day, but is unlikely to be hotter than Sussex in the summer.

Humidity is generally higher in the west as well.

The town with the mildest winter temperature in Great Britain, when I looked into it, was Teignbridge in Devon, sheltered to the west by Dartmoor and by ocean breezes from the south and east. Locals there claim that they have to regularly mow their lawns in winter. That said the weather there isn't great because nowhere in the UK has great weather.

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Re: Coronavirus - Modelling Aspects Only

#346900

Postby gryffron » October 11th, 2020, 11:49 am

Moderator Message:
Please remember that this thread is ONLY for specific modelling aspects related to CoronaVirus.

I have removed a number of recent posts which were a very general discussion on the influence of the weather. That should be, and has been, discussed on the Snug thread and PD.

If you have SPECIFIC weather data relevant to modelling, please post here. General discussion about thoughts and influences should take place elsewhere.

Thank You.
Gryffron

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Re: Coronavirus - Modelling Aspects Only

#347221

Postby scotia » October 12th, 2020, 10:25 pm

When the current resurgence of the virus infections began, I wondered if a fear factor as daily cases grew would modify persons’ behaviour and hence would affect the exponential rise. So I thought that daily admissions would be the best statistic to model, since they probably more closely match those who are most likely to be concerned.
The differential equation for an exponential rise is dN/dt = Lambda*N where Lambda is a constant, usually described as the Growth Rate. To reduce the Growth Rate with increasing N, I decided to try Lambda = a – b*N. This gives dN/dt = (a-b*N)*N. The derivative goes to zero when N=a/b, hence the value of N will (ultimately) climb asymptotically to that value. Normalising N to 1 at t=0, with time units as days I selected a=0.09, and the 4 displayed (blue) curves, from the top down are for b=0, a/b = 15, a/b = 10 and a/b = 5. Solution was by numerical integration (variable step length RK4).

Image

The (green) plotted points are Daily Admissions statistics for England, modified by creating a moving average over 7 days to reduce statistical noise and eliminate day-of-the-week bias. They are also normalised to 1 at time zero. The final point includes data up to 7/10/20.
I’m afraid there is not much agreement between the data points and any of the curves. Bang goes a simple theory. I suppose there have been a number of local areas put under stricter controls, which may have caused sharper step-downs in the growth rate. But the data for the last 10 points is puzzling – first a significant reduction in growth rate for the first 5, then a significant increase in the final 5. Could this have been caused by the recently reported data loss, and its subsequent re-entry (possibly in the wrong place?). Alternatively, if the data is correct, what is the cause of such a worrying turn-around in the growth of admissions?

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Re: Coronavirus - Modelling Aspects Only

#347229

Postby servodude » October 13th, 2020, 12:48 am

scotia wrote:When the current resurgence of the virus infections began, I wondered if a fear factor as daily cases grew would modify persons’ behaviour and hence would affect the exponential rise. So I thought that daily admissions would be the best statistic to model, since they probably more closely match those who are most likely to be concerned.


Admissions as a data set does have a lot less of the uncertainty that is around other metrics
- cue shouts from the gallery of "But are they admitted with COVID of from COVID!? Huzah!"
- I think you can also use them to propagate backwards (assume a % of cases require admission)

scotia wrote:The (green) plotted points are Daily Admissions statistics for England, modified by creating a moving average over 7 days to reduce statistical noise and eliminate day-of-the-week bias. They are also normalised to 1 at time zero. The final point includes data up to 7/10/20.
I’m afraid there is not much agreement between the data points and any of the curves. Bang goes a simple theory. I suppose there have been a number of local areas put under stricter controls, which may have caused sharper step-downs in the growth rate. But the data for the last 10 points is puzzling – first a significant reduction in growth rate for the first 5, then a significant increase in the final 5. Could this have been caused by the recently reported data loss, and its subsequent re-entry (possibly in the wrong place?). Alternatively, if the data is correct, what is the cause of such a worrying turn-around in the growth of admissions?


AFAIK the data loss was only for "downstream" test and tracing use
- I don't believe it was lost from the accounting and I don't think it involved admissions

I think the "dip and resurgence" in admissions is just a different form of superimposed noise
- if you find the a/b that puts your line down the best fit for these it will look less pronounced

FWIW I just think that this boils down to the "growth rate" varying day to day
- and that the "growth rate" for admissions is proportional to the virus spread and the ability/capacity/readiness of hospitals to admit

It's a huge lumped system and I wouldn't read too much in to it more than it's getting better or worse
- the trick being to identify the amount of data upon which you can base those

-sd

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Re: Coronavirus - Modelling Aspects Only

#347319

Postby scotia » October 13th, 2020, 11:15 am

servodude wrote:[

It's a huge lumped system and I wouldn't read too much in to it more than it's getting better or worse
- the trick being to identify the amount of data upon which you can base those

-sd

Agreed - but it was good fun oiling up my ancient works and getting down to doing a bit of real programming again :)

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Re: Coronavirus - Modelling Aspects Only

#347341

Postby servodude » October 13th, 2020, 12:04 pm

scotia wrote:
servodude wrote:[

It's a huge lumped system and I wouldn't read too much in to it more than it's getting better or worse
- the trick being to identify the amount of data upon which you can base those

-sd

Agreed - but it was good fun oiling up my ancient works and getting down to doing a bit of real programming again :)

Indeed. It's been a while since I saw a Runge Kutta reference on the fool ;)

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Re: Coronavirus - Modelling Aspects Only

#347517

Postby zico » October 13th, 2020, 9:37 pm

For anyone interested, I've managed to discover how the "deaths within 60 days from diagnosis" compares with the headline reported figure of "deaths from 28 days".
On average across England, using the "60 day" definition gives 68% more deaths than the headline figure. This is based on cumulative deaths from week 27 to week 41 (6th October) which is approximately the last 3.5 months (so from end-June).

This is based on the attached file from Public Health England (buried on page 55)

https://assets.publishing.service.gov.u ... _FINAL.pdf

However, to find out the total deaths to date under both definitions, I needed to find an Excel file under the link in the document (

Numbers are as follows :-
45,488 deaths after positive Covid test (no time limit at all - the originally used definition). As was pointed out at the time, this would inevitably lead to progressively greater overcounts because it assumed that once you'd had a positive test, if you died, it was because of Covid.
41,769 deaths within 60 days of positive test OR Covid-19 on death certificate.
37,688 deaths within 28 days of positive test (the currently used definition).

As you may remember, I think the 60 day definition is more representative of the true picture, because the "headline" definition excludes anyone dying more than 28 days after a positive Covid test - even if Covid is mentioned on the death certificate.

Quite a few interesting graphs in the report, including one on Page 15 by ethnicity, showing very large differences of weekly incidence of Covid per 100,000 people.
250 for Pakistani (Asian or Asian British)
220 for "Other" Ethnic groups
150 Indian (Asian or Asian British)
110 Other Asian/ Asian British
100 White
60 Black / African / Caribbean / Black British
55 Mixed / Multiple Ethnic groups

Page 21 shows outbreaks rocketing for educational establishment (obviously co-inciding with schools & universities reopening). This is by far the biggest source of outbreaks.
Page 22 shows that outbreaks associated with food outlets increased sharply around end-August (remember "Eat Out to Help Out" was throughout August) but has declined a little since then (though still higher than pre-August).
Page 22 shows workplace outbreaks increasing sharply a week or two later (probably co-inciding with the government calls for people to go back to their workplaces).

There an interesting (well, interesting to me!) graph on page 54 showing that for the last 3-4 weeks, the "28 day" and "60 day" definitions have been very close. This may be because a lot of "60 day" deaths not recorded were people who'd been affected badly in the first wave and never recovered, dying 2 (or more) months after first testing positive.

A reminder of the definitions (from the report).

The current definitions used for mortality surveillance of COVID-19 in England are:(a)28 day definition: A death in a person with a laboratory-confirmed positive COVID-19 test and died within (equal to or less than) 28 days of the first positive specimen date
(b)60 day definition: A death in a person with a laboratory-confirmed positive COVID-19 test and either: died within 60 days of the first specimen date OR died more than 60 days after the first specimen date only if COVID-19 is mentioned on the death certificate

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Re: Coronavirus - Modelling Aspects Only

#347522

Postby servodude » October 13th, 2020, 10:06 pm

This is the immediately interesting bit for me
zico wrote:died within (equal to or less than) 28 days of the first positive specimen date

- so it doesn't get reset on subsequent tests

The median time on a ventilator should you require one is ~3weeks (varies across the world a bit based on resources and policy)
I find it strange to think that you could wait out that period being kept alive and then not be counted... but there's strange everywhere

-sd

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Re: Coronavirus - Modelling Aspects Only

#347523

Postby zico » October 13th, 2020, 10:10 pm

servodude wrote:This is the immediately interesting bit for me
zico wrote:died within (equal to or less than) 28 days of the first positive specimen date

- so it doesn't get reset on subsequent tests

The median time on a ventilator should you require one is ~3weeks (varies across the world a bit based on resources and policy)
I find it strange to think that you could wait out that period being kept alive and then not be counted... but there's strange everywhere

-sd


In the New York epidemic, I remember the Cuomo saying the longer someone was on a ventilator, the worse their chances of survival.
I agree it's very strange that a death after 29+ days with Covid on the death certificate is NOT counted as a Covid death.

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Re: Coronavirus - Modelling Aspects Only

#347526

Postby zico » October 13th, 2020, 10:15 pm

Although posted by Andy Burnham (Manchester), these statistics are still a good guide to why, after the initial national lockdown, continuing with same rules for everyone wasn't appropriate for all regions of the country.

(All figures are 7 day cases per 100,000 population)

30th April (Past peak)
63.1 Greater Manchester (GM)
30.2 London

10th May ("Stay Alert")
47.8 GM
16.8 London

1st June (Schools Re-open)
28.9 GM
4.6 London

4th July (Pubs Reopen)
13.4 GM
3.2 London

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Re: Coronavirus - Modelling Aspects Only

#347527

Postby servodude » October 13th, 2020, 10:20 pm

zico wrote:
servodude wrote:This is the immediately interesting bit for me
zico wrote:died within (equal to or less than) 28 days of the first positive specimen date

- so it doesn't get reset on subsequent tests

The median time on a ventilator should you require one is ~3weeks (varies across the world a bit based on resources and policy)
I find it strange to think that you could wait out that period being kept alive and then not be counted... but there's strange everywhere

-sd


In the New York epidemic, I remember the Cuomo saying the longer someone was on a ventilator, the worse their chances of survival.
I agree it's very strange that a death after 29+ days with Covid on the death certificate is NOT counted as a Covid death.


Well it's being counted; but as a lesser statistic (perhaps intentionally)
I reckon that there's a date when the patient gets entered in the system for the initial positive result and that's what they're basing this on
- what would be really interesting would be a distribution curve; what does it look like over 2 months
- I'd expect spikes really early for the DNR component and one a lot later at the cessation of ventilation

-sd

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Re: Coronavirus - Modelling Aspects Only

#347545

Postby johnhemming » October 14th, 2020, 6:56 am

zico wrote:Although posted by Andy Burnham (Manchester), these statistics are still a good guide to why, after the initial national lockdown, continuing with same rules for everyone wasn't appropriate for all regions of the country.

...

1st June (Schools Re-open)
28.9 GM
4.6 London


I don't remember the precise details, but I think that a large proportion of the state schools did not reopen before autumn term and schools only actually reopened part way through July. (for two weeks in the case of my Son's school).

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Re: Coronavirus - Modelling Aspects Only

#347582

Postby scotia » October 14th, 2020, 10:11 am

zico wrote:https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/925324/Weekly_Flu_and_COVID-19_report_W41_FINAL.pdf


Many thanks for the link to the 76 page report (I'll put it down on my reading list!)
And thanks for your work in extracting interesting mortality statistics. The part that has always bothered me about the number of Covid-19 certified mortality deaths is the very significant under-reporting of such deaths during the peak month of April - reaching around 30% - as can be seen in the weekly excess deaths statistics:-
https://fingertips.phe.org.uk/static-reports/mortality-surveillance/excess-mortality-in-england-latest.htmlMortality
Was this possibly down to an overstretched NHS, and medical inexperience? Are we now improving the detection rate?

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Re: Coronavirus - Modelling Aspects Only

#347583

Postby scotia » October 14th, 2020, 10:14 am

servodude wrote:Indeed. It's been a while since I saw a Runge Kutta reference on the fool ;)

Surely not - after all this is a science and modelling board! :D


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