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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
9873210
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Re: Coronavirus - Modelling Aspects Only

#315297

Postby 9873210 » June 4th, 2020, 7:23 pm

zico wrote:I've done some more longer-term modelling for a couple of scenarios (graphs below) using as a starting point the government estimate of
1. If a vaccine isn't available until end-2021, herd immunity is unavoidable. Also applies if a vaccine can never be found.

China. Either they are not only lying through their teeth but surgically implanting additional teeth so that they can lie through those, or there is a way to limit the pandemic without a vaccine. I'd bet the latter, but we shall see. There are practical limits on how long anyone could sustain such a monstrous lie.

We still know far too little about the virus. But nothing we know says that a strategy of total lockdown to drive cases down to the single digits followed by contact tracing, testing and quarantining like a mad man to keep cases in the single digits can not work. Unfortunately IMHO we have already squandered the best chance to do that with mono-buttocked lockdowns.

We still know far too little about the virus. We need to learn how the virus spreads to take effective steps to control it and stop wasting effort on ineffective steps that do not control it. It's pretty certain that much of what we are doing is useless or even counter productive, but we don't know which restrictions should be dropped and what steps should be kept and enhanced.

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Re: Coronavirus - Modelling Aspects Only

#315396

Postby servodude » June 5th, 2020, 2:49 am

dspp wrote:
johnhemming wrote:What we know is that the peak rate of hospital deaths in England was on 8th April. We know that lockdown came in on 23rd March. The basic question is one as to whether or not there was enough time between lockdown and the peak rate of hospital deaths for one to have caused the other.

On the information I have there isn't. On the information I have it appears that the peak rate of infection was prior to lockdown.


Official gov lockdown was 23 March. Citizen led lockdown started earlier. So not a classic step function, more of a fast ramp.

Agree with everything else.

regards, dspp


True - agree with you both here
- well I'd probably throw in a "piece-wise linear" because that's how I think of most things having being raise on paper bode plots

I see it as braking a motor
- there was a bit of a press prior to lock down
- then the pressure was really slammed on

The first bit certainly should have made a difference to the ultimate stopping distance
- but its the second that brings you to a standstill

should you not have hit the brakes because your acceleration might have topped out and you would have fun out of fuel eventually?

- sd

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Re: Coronavirus - Modelling Aspects Only

#315397

Postby servodude » June 5th, 2020, 2:53 am

9873210 wrote:But nothing we know says that a strategy of total lockdown to drive cases down to the single digits followed by contact tracing, testing and quarantining like a mad man to keep cases in the single digits can not work.


It has certainly proven to be an effective strategy for New Zealand & Taiwan to pick two off the top of my head
- sd

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Re: Coronavirus - Modelling Aspects Only

#315550

Postby zico » June 5th, 2020, 1:53 pm

Image

Following comments copied from Twitter written by ONS Statistican - Nick Stripe

THREAD – “Non-COVID” excess deaths
Between 7 Mar & 1 May there were 130k deaths registered across E&W. This was 46.4k deaths above 5-yr averages
According to death certs 12.9k (28%) of this “excess” did not mention COVID. 98% are now fully coded enabling detailed analysis

Possible explanations include:

1. COVID was present but undiagnosed, particularly in the presence of other co-morbidities and the absence of a positive test
2. Reluctance to seek care or a delay in receiving care for people with serious health conditions
3. Reduced hospital capacity affecting ongoing care for people with underlying conditions
4. An increase in stress related causes due to lockdown
5. An increase in death registration efficiency introducing a process effect

Our analysis shows:
- Many deaths where COVID was not mentioned were displaced from hospitals to care homes and private homes
- Age-standardised mortality rates (ASMRs) for “non-COVID” deaths were generally higher in regions with higher COVID ASMRs
- Excess deaths where COVID was not mentioned were predominantly in the very eldest
- Men accounted for more at first but from mid-April this switched to women
- Analysis by leading underlying causes of death shows all leading causes above or at their 5-yr averages
- Most notably, they show v significant increases in deaths due to Dementia & Alzheimer Disease and for deaths due to old age & frailty (“signs, symptoms and ill-defined conditions”)

Deaths with these causes account for two thirds of all “non-COVID” excess deaths. Dementia increases are so sharp it’s implausible that they are unrelated to COVID. They generally affect the very old, they would tend to impact women to a greater extent than men simply due to pop structure. Especially once care home epidemics took hold with ltd testing
People with dementia are more likely to have communication problems describing symptoms
Some evidence has been observed for atypical hypoxia in frail COVID patients – well preserved lungs but severely compromised pulmonary gas exchange without signs of respiratory distress

No reason to believe that COVID-19 has been knowingly omitted from death certs. Symptoms may not be apparent.
But we cannot discount the impact of changes to normal routines for vulnerable care home residents following lockdown. These could have had adverse consequences too

The balance of evidence so far points to undiagnosed COVID in the elderly being the most likely explanation for a majority of excess deaths that did not mention CV on certs. This fits: demography, locations, esp where testing was sparse, causes of death & timings of peaks


Some potential evidence for a delay in receiving care. Normal care pathways have been disrupted and we can see increases in deaths due to diabetes, sepsis and asthma outside hospital settings
But some of these are risk factors for CV so could also support under diagnosis
There is some evidence for deaths involving, for example, cancers and renal failure being displaced from hospitals
Little evidence yet of signif increases in overall deaths due to reduced capacity. But these may increase over time as impacts of treatment delays emerge
For stress-related causes there is some evidence of increases due to e.g. hypertension. But due to the need for coroners’ inquests for deaths caused by drugs, violence or suicide, any increases for these will not yet have been registered. Need longer to observe any changes

Some evidence of increased efficiency due to registration process changes. The % of deaths registered by coroners has reduced, but within the context of many more deaths in total. Any effect is likely to be marginal and again this may change as more inquests conclude.

Note- excess deaths during May are so far all accounted for by COVID being mentioned on death certificates.
This may reflect improving knowledge of its complex effects, increased testing, and the fact that some earlier deaths will have been brought forward by COVID

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Re: Coronavirus - Modelling Aspects Only

#315562

Postby zico » June 5th, 2020, 2:50 pm

Lots of bad news in this latest Cambridge modelling group report which feeds into government Covid-19 SAGE, and was produced on 5th June.
(Although things may not be so bad, because this model estimates 16,700 daily infections, but I saw on TV today an estimate for 40,000 weekly infections, which translates to 5,700 daily infections.

https://www.mrc-bsu.cam.ac.uk/now-casting/

I've quoted the findings from the report, then added my own thoughts below that.

Findings

We estimate that across England there are 17,000 (11,000–25,000, 95% credible interval) new infections arising each day
We estimate that the number of deaths each day is likely to fall to between 100–250 by mid-June
We believe it is probable that Rt is below 1 in all regions of England with the exception of the North West and the South West
In the South West, although Rt is around 1, the numbers of new infections occurring in the region on a daily basis is relatively low
There is some evidence that Rt has risen in all regions and we believe that this is probably due to increasing mobility and mixing between households and in public and workplace settings
An increase in Rt will lead to a slowdown in the decrease in new infections and deaths
There is evidence, from the forecast of deaths for the whole of England, that the increases in the regional reproductive numbers may result in the decline in the national death rate being arrested by mid-June



IFR was 0.63% but has now been updated to 0.88% (even worse the confidence interval is 0.77-1.00% so is definitely well above 0.63%)

R-Values VERY close to 1.

East_of_England 0.94
2 London 0.95
3 Midlands 0.90
4 North_East_and_Yorkshire 0.89
5 North_West 1.01
6 South_East 0.97
7 South_West 1.00

Estimate is that 10% of England's population have been infected (that's 6.7 million people).

Below is their latest daily infections estimate

1 England 16,700
2 East_of_England 1,660
3 London 1,310
4 Midlands 2,460
5 North_East_and_Yorkshire 2,450
6 North_West 4,170
7 South_East 2,420
8 South_West 778

This was what they estimated last month - it's very different from what they are now estimating, and looks very strange, because if the R-values have been below 1, how could the estimate of infections have gone up????

Cambridge's estimated new infections by region for May 21st :-
London - 3 (Yes, three!)
East - 524
Midlands 641
North-East & Yorks 2,560 (a whopping 42% of all new infections in England)
North-West 1,180
South-East 594
South-West 399
England 5,960 (this total doesn't quite match the total of the regions because they're based on modelling).
(Cambridge estimate for England new infections on May 28th = 3,960 which would be a 33% reduction).

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Re: Coronavirus - Modelling Aspects Only

#315569

Postby zico » June 5th, 2020, 3:07 pm

ONS report today estimates 53,000 people infected in England and Wales between 17th May-30th May.

These are the figures from all the ONS reports, so a clear downward trend in %of the population infected between the two dates (e.g. 26Apr-2May)
% testing positive for COVID-19
26 April to 2 May 0.44
3 May to 9 May 0.31
10 May to 16 May 0.22
17 May to 23 May 0.16
24 May to 30 May 0.11


There were an estimated 39,000 new COVID-19 infections per week in England (95% confidence interval: 26,000 to 55,000) between 26 April and 30 May 2020


While those who have symptoms are more likely to test positive than those without symptoms, out of those within our study who have ever tested positive for COVID-19, 29% reported any evidence of symptoms at the time of the visit or at either the preceding or following visit.


https://www.ons.gov.uk/peoplepopulation ... /5june2020

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Re: Coronavirus - Modelling Aspects Only

#315608

Postby jfgw » June 5th, 2020, 4:51 pm

zico wrote:ONS report today estimates 53,000 people infected in England and Wales between 17th May-30th May.

These are the figures from all the ONS reports, so a clear downward trend in %of the population infected between the two dates (e.g. 26Apr-2May)
% testing positive for COVID-19
26 April to 2 May 0.44
3 May to 9 May 0.31
10 May to 16 May 0.22
17 May to 23 May 0.16
24 May to 30 May 0.11

...

https://www.ons.gov.uk/peoplepopulation ... /5june2020


That is very close to exponential (think f-stops). The number infected halves about every two weeks.


Julian F. G. W.

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Re: Coronavirus - Modelling Aspects Only

#315616

Postby vrdiver » June 5th, 2020, 5:08 pm

jfgw wrote:
zico wrote:ONS report today estimates 53,000 people infected in England and Wales between 17th May-30th May.

These are the figures from all the ONS reports, so a clear downward trend in %of the population infected between the two dates (e.g. 26Apr-2May)
% testing positive for COVID-19
26 April to 2 May 0.44
3 May to 9 May 0.31
10 May to 16 May 0.22
17 May to 23 May 0.16
24 May to 30 May 0.11

...

https://www.ons.gov.uk/peoplepopulation ... /5june2020


That is very close to exponential (think f-stops). The number infected halves about every two weeks.

(My bold)
If everything else was static, I'd accept that, but I don't think the conditions for test selection have remained constant over the period presented, so I'm not sure you can extrapolate with any confidence. If I remember correctly, there were reports in April of NHS workers with symptoms but unable to get tests? My assumption is that tests were being given at that point in time as confirmation, rather than determination, whereas now it's possible to book a test by answering a few questions, which might skew the statistics towards more negative results being included. That's before we discuss the efficacy of self-administered testing...

I'd suggest it will only be when we have a proper, large scale, randomised testing regime, that such a claim could be substantiated.

VRD

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Re: Coronavirus - Modelling Aspects Only

#315617

Postby zico » June 5th, 2020, 5:13 pm

ONS sample is random, but only from the 'community' , i.e. not including hospitals and care homes.

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Re: Coronavirus - Modelling Aspects Only

#315619

Postby vrdiver » June 5th, 2020, 5:17 pm

zico wrote:ONS sample is random, but only from the 'community' , i.e. not including hospitals and care homes.

So where did they get their "random" sample data from back in April and how were subjects selected?

Genuine question, considering the coverage at the time re lack of testing for NHS staff.

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Re: Coronavirus - Modelling Aspects Only

#315620

Postby fca2019 » June 5th, 2020, 5:18 pm

Deaths per million population an important stat for comparison between countries. Excl tiny countries like Andorra, the UK is second behind Belgium with 593 deaths per 1M pop. We're ahead of Spain and Italy. Do think Boris has to take a large degree of blame, as when we should taken action in March he was ignoring expert advice and bragging about shaking hands with covid-19 patients. Explicitly ignoring advice and going out of his way to shake hands with as many as possible. Whilst other countries were planning strict lockdowns and social distancing. Then the uk lockdown was a week later than France and not as strict. They had a similar starting situation to us but have fared better due to an earlier and stricter lockdown. France has 29k deaths compared to 40k here. These decisions and complacency early on cost us 11,000 lives.

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Re: Coronavirus - Modelling Aspects Only

#315622

Postby zico » June 5th, 2020, 5:23 pm

Please can we stick to modelling, statistics and discussions about them, leaving political views for Polite Discussions board?

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Re: Coronavirus - Modelling Aspects Only

#315624

Postby jfgw » June 5th, 2020, 5:56 pm

It is too early to compare the effects of different levels of lockdown. Countries that have had a more relaxed lockdown may get the whole thing over and done with a lot sooner than other countries, and it is possible that countries with a stricter lockdown may experience a second wave where we do not. It will be interesting to see what happens in the next few weeks in the UK now that the lockdown has been partly relaxed.

Julian F. G. W.

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Re: Coronavirus - Modelling Aspects Only

#315659

Postby zico » June 5th, 2020, 9:29 pm

A separate estimate of the R-value by London School of Tropical Medicine.
Puts England's R-value at 0.9 (Confidence intervals 0.9-1) with some regional breakdowns.

Based on Tropical Medicine's paper and the other one from Cambridge, it looks a very big stretch indeed to say the R-value is between 0.7-0.9 as the government is claiming.
(Note- SAGE minutes give latest estimate as 0.7-0.9) but they also say the following - which to my eyes, isn't the same statement.
SAGE is confident that overall the R is not above 1. This means that the number of infections is not increasing, and is very likely to be decreasing.


https://epiforecasts.io/covid/posts/nat ... d-kingdom/

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Re: Coronavirus - Modelling Aspects Only

#315661

Postby zico » June 5th, 2020, 9:37 pm

jfgw wrote:It is too early to compare the effects of different levels of lockdown. Countries that have had a more relaxed lockdown may get the whole thing over and done with a lot sooner than other countries, and it is possible that countries with a stricter lockdown may experience a second wave where we do not. It will be interesting to see what happens in the next few weeks in the UK now that the lockdown has been partly relaxed.

Julian F. G. W.


I see what you're saying but I don't entirely agree. The first wave was the crucial time when deaths increased at a very fast rate, and hospitals might be overwhelmed (as happened in Italy) or care homes might be overwhelmed (as has happened in the majority of countries).
From now on, the pace of infection will depend on lockdown measures, track'n'trace and other measures, and countries have had time to look, learn and improve their responses. There won't be any sudden increases in infection and deaths, and everyone's attention is now focused on Covid-19.

The crucial point about squashing the first wave as much as possible is that -

a) If you do it really effectively, then you stop the virus taking hold or alternatively quickly eradicate it from your country, saving lives and the economy. New Zealand did this really well, as did a few other countries.

b) If you don't do a) above but then lockdown early enough, you can reduce the first wave numbers, have far fewer deaths initially, and a vaccine may well arrive before most of the population become infected, and there may be other medical developments and treatments to reduce fatalities. Most European countries reacted in this way.

c) If you have a big first wave (like UK, Brazil, Italy,Spain), then you have a lot of people (sadly) dead, and you also need a longer lockdown to get infection numbers down to a point where you have a decent chance of being able to contain the virus whilst also opening up the economy. If you rush coming out of lockdown, you risk wasting all the economic pain of the lockdown and putting yourself back to square one.

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Re: Coronavirus - Modelling Aspects Only

#315685

Postby servodude » June 6th, 2020, 2:13 am

zico wrote:
jfgw wrote:It is too early to compare the effects of different levels of lockdown. Countries that have had a more relaxed lockdown may get the whole thing over and done with a lot sooner than other countries, and it is possible that countries with a stricter lockdown may experience a second wave where we do not. It will be interesting to see what happens in the next few weeks in the UK now that the lockdown has been partly relaxed.

Julian F. G. W.


I see what you're saying but I don't entirely agree. The first wave was the crucial time when deaths increased at a very fast rate, and hospitals might be overwhelmed (as happened in Italy) or care homes might be overwhelmed (as has happened in the majority of countries).
From now on, the pace of infection will depend on lockdown measures, track'n'trace and other measures, and countries have had time to look, learn and improve their responses. There won't be any sudden increases in infection and deaths, and everyone's attention is now focused on Covid-19.

The crucial point about squashing the first wave as much as possible is that -

a) If you do it really effectively, then you stop the virus taking hold or alternatively quickly eradicate it from your country, saving lives and the economy. New Zealand did this really well, as did a few other countries.

b) If you don't do a) above but then lockdown early enough, you can reduce the first wave numbers, have far fewer deaths initially, and a vaccine may well arrive before most of the population become infected, and there may be other medical developments and treatments to reduce fatalities. Most European countries reacted in this way.

c) If you have a big first wave (like UK, Brazil, Italy,Spain), then you have a lot of people (sadly) dead, and you also need a longer lockdown to get infection numbers down to a point where you have a decent chance of being able to contain the virus whilst also opening up the economy. If you rush coming out of lockdown, you risk wasting all the economic pain of the lockdown and putting yourself back to square one.


Which is pretty much what was suggested by the analysis of the Spanish Flu measures:

https://www.nbcnews.com/politics/politi ... y-n1202111
https://www.nationalgeographic.com/hist ... ronavirus/

-sd

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Re: Coronavirus - Modelling Aspects Only

#315901

Postby Sorcery » June 6th, 2020, 7:52 pm

Looks like Nic Lewis's model or more accurately Gabriela Gomes whose paper Nic cites has gone mainstream. Mat Ridley talks about it here :
https://www.telegraph.co.uk/news/2020/0 ... r-history/

If you tell the models there is thus a correlation between susceptibility and infectiousness you get much lower forecasts of cases and deaths. Add that we now know that cross-immunity from common colds probably allows 40-60pc of the population to resist Covid-19, and the result is – as the work of Gabriela Gomes at the Liverpool School of Tropical Medicine indicates -- that herd immunity is probably reached when as little as 15pc of the population is infected, rather than the 50-60pc implied by Imperial’s model. Hence the epidemic is petering out in London despite crowded streets.

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Re: Coronavirus - Modelling Aspects Only

#315981

Postby GoSeigen » June 7th, 2020, 8:09 am

I think there's a new acceleration happening now... looking at 12000 deaths pd within two to three weeks time IMO.

GS

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Re: Coronavirus - Modelling Aspects Only

#315987

Postby swill453 » June 7th, 2020, 8:32 am

GoSeigen wrote:I think there's a new acceleration happening now... looking at 12000 deaths pd within two to three weeks time IMO.

Where?

Scott.

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Re: Coronavirus - Modelling Aspects Only

#315990

Postby Mike4 » June 7th, 2020, 8:36 am

GoSeigen wrote:I think there's a new acceleration happening now... looking at 12000 deaths pd within two to three weeks time IMO.

GS


Worldwide you mean, presumably? (And your "pd" = per day?)

Moving on, something about this pandemic is puzzling me. Normally in an epidemic, huge effort is put into tracing 'Patient Zero'. Identifying Patient Zero tells us buckloads apparently, about the progress of the infection and all manner of other things.

But with SARS-CoV-2, nada. I've not seen or heard a single mention of any attempt to find and identify Patient Zero since this thing first caught my attention back around Christmas. Why is that?

Could it be that there is no need because all the guvverments know already exactly where and it came from and when, and are keeping it a collective secret for political reasons? Is that a great conspiracy theory or what?

But seriously, why does Patient Zero never get mentioned? Or is it such common knowledge that it doesn't need mentioning, in which case who were they, and where and when and how did they catch it, exactly?


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