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Re: COVID-19

Posted: Fri Jan 01, 2021 4:16 pm
by shpalman
Another day, another 50,000 new covids in the UK. Well, not 50,000: 53,285. And not the UK: England and Scotland. Northern Ireland and Wales haven't reported anything today so there's probably about 4,000 cases missing.

613 deaths taking the total to 74125, and that's only England because none of NI, Scotland, and Wales report today. So there could be 50-100 deaths missing and since it's nearly the weekend it'll probably be Tuesday before we've caught up there.

Re: COVID-19

Posted: Fri Jan 01, 2021 5:25 pm
by shpalman
Meanwhile, Italy has 22,211 new covids today but when 14.1% of the day's swabs are positive it's probably the case that this is somewhat of an underestimate. The 7-day average is about 12% and rising while the UK is at about 11% and rising.

Re: COVID-19

Posted: Fri Jan 01, 2021 7:11 pm
by shpalman
James Annan has added the effect of the vaccination program to his model in terms of a reduction of the IFR over the next few months:

https://twitter.com/jamesannan/status/1 ... 6747096064

He hasn't explicitly accounted for the immunity itself "which will have relatively little effect on transmission over this time scale". The model suggests we will be through to herd immunity soon anyway unless there's a very strong lockdown.

Re: COVID-19

Posted: Fri Jan 01, 2021 7:20 pm
by KAJ
KAJ wrote:
Thu Dec 31, 2020 5:48 pm
I'm not convinced, see below. Models don't fit well, but there really isn't much evidence (even visual) of a consistent increase.
By date of death (last 5 zero weighted, day-of-week doesn't help fit)
<snip>

By date of publication
<snip>

That has to change soon, look at
Patients in mechanical ventilation beds, where the R-sq is 99%
<snip>
Well that didn't take long!
Deaths by date of death
OK, the fit isn't very good ( ~ 40%) but I think the evidence for an upwards trend is becoming clear, even zero-weighting the last 5 points.
DateDeaths.png
DateDeaths.png (10.39 KiB) Viewed 550 times

Code: Select all

At 30/12 fit = 566.7 with doubling time = 34.2 days. That time halving in 13.3 days 

Coefficients:
               Estimate Std. Error t value Pr(>|t|)    
(Intercept)     6.14114    0.01460 420.644  < 2e-16 ***
poly(date, 2)1  0.46396    0.10199   4.549  0.00012 ***
poly(date, 2)2  0.17702    0.09885   1.791  0.08544 .  
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Residual standard error: 0.06549 on 25 degrees of freedom
Multiple R-squared:  0.464,	Adjusted R-squared:  0.4212 

Re: COVID-19

Posted: Fri Jan 01, 2021 9:01 pm
by shpalman
sTeamTraen wrote:
Thu Dec 24, 2020 4:31 pm
bob sterman wrote:
Thu Dec 24, 2020 2:46 pm
plodder wrote:
Thu Dec 24, 2020 2:34 pm
It’s gone.

https://mobile.twitter.com/TiceRichard/ ... 2773159936
Maybe it has - but I wouldn't believe a word that guy Richard Tice says. He's the Brexit Party chair - known as "Farage's sidekick" and is one of these folk who thinks most cases are PCR false positives.
I think the point here is that the government's handling of this has been so incompetent that even a conspiracist tw.t like Tice can make hay and a lto of sensible people will be nodding along. Apart from one brief moment in that clip where he lets slips that the real point of his story is to show that there is no problem in London ("because they've taken the Nightingale down, so that proves it") and so everyone should get back in the pub immediately, it could equally well have been made by a principled opposition party to show that the whole idea of the Nightingales was flawed from day one because there are no doctors or nurses to staff them. For example, Tice has fooled the otherwise admirable Gary Neville into thinking it was about resources.

Indeed, the same question could have been asked back when the government was about to order 30,000 ventilators or however many it was; it turns out that you can't just get a bloke from Kwik-Fit, or even a regular nurse, to just stand by it and press button B when it goes "beep".
... the Nightingale hospital built in London’s ExCeL centre is expected to take Covid patients next week, for the first time since the spring.

Not that there will be anyone to staff them.

Re: COVID-19

Posted: Sat Jan 02, 2021 4:09 pm
by KAJ
Today's coronavirus.data.gov.uk data is out. Cases by specimen date (excluding Christmas Day = 14,150) shows almost pure exponential growth with doubling time = 14.7 days (with day of week factor), R-sq ~95%
SpecCases.png
SpecCases.png (14.32 KiB) Viewed 467 times

Code: Select all

Analysis of Variance Table

Response: log(SpecCases)
              Df Sum Sq Mean Sq F value    Pr(>F)    
poly(date, 2)  2 4.1394 2.06970 188.260 2.986e-13 ***
day            6 0.6836 0.11394  10.364 3.826e-05 ***
Residuals     19 0.2089 0.01099                      
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Coefficients:
               Estimate Std. Error t value Pr(>|t|)    
(Intercept)     9.96505    0.05494 181.391  < 2e-16 ***
poly(date, 2)1  2.59545    0.18063  14.369 1.17e-11 ***
poly(date, 2)2  0.01161    0.17037   0.068 0.946401    
dayMon          0.40533    0.07419   5.464 2.85e-05 ***
dayTue          0.31398    0.07431   4.225 0.000458 ***
dayWed          0.26584    0.07454   3.567 0.002059 ** 
dayThu          0.13923    0.07488   1.859 0.078525 .  
dayFri          0.24910    0.07436   3.350 0.003366 ** 
daySat         -0.05936    0.07419  -0.800 0.433524    
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Residual standard error: 0.1049 on 19 degrees of freedom
Multiple R-squared:  0.9585,	Adjusted R-squared:  0.941 

Re: COVID-19

Posted: Sat Jan 02, 2021 4:30 pm
by OffTheRock
To much to hope that the 74,510 cases with a specimen date of the 29/12 is some kind of mistake? Apart from the obvious mistake of allowing households to mix 4 days previously.

Re: COVID-19

Posted: Sat Jan 02, 2021 4:48 pm
by lpm
OffTheRock wrote:
Sat Jan 02, 2021 4:30 pm
To much to hope that the 74,510 cases with a specimen date of the 29/12 is some kind of mistake? Apart from the obvious mistake of allowing households to mix 4 days previously.
29 Dec was the first day back at work after the bank holidays. So likely that many people delayed getting themselves tested until that day?

Re: COVID-19

Posted: Sat Jan 02, 2021 5:32 pm
by OffTheRock
That might explain some of it, but I don't think all of it. I'm still trying to get my head round the positive cases vs tests processed data and how they do or don't match up.

Re: COVID-19

Posted: Sat Jan 02, 2021 6:00 pm
by KAJ
OffTheRock wrote:
Sat Jan 02, 2021 4:30 pm
To much to hope that the 74,510 cases with a specimen date of the 29/12 is some kind of mistake? Apart from the obvious mistake of allowing households to mix 4 days previously.
See the graph. 29/12 agrees very closely with the model based on the previous month's data. 29/12 was not considered when fitting that model (weight = zero).

Re: COVID-19

Posted: Sat Jan 02, 2021 6:20 pm
by Opti
There we are then. Gibraltar is f.cked. Incredibly fast acceleration of cases. All the adjoining ayuntamientos in Cadiz province are now locked down as well.
Covid don't give a sh.t about anyone taking control of are borders.
Only a day or so ago, you could fly from UK to Gib without a prior PCR test. Tested only on arrival. By then, you were Gib's problem.

Re: COVID-19

Posted: Sat Jan 02, 2021 6:30 pm
by shpalman
OffTheRock wrote:
Sat Jan 02, 2021 4:30 pm
To much to hope that the 74,510 cases with a specimen date of the 29/12 is some kind of mistake? Apart from the obvious mistake of allowing households to mix 4 days previously.
shpalman wrote:
Thu Dec 24, 2020 8:12 pm
.... It seems ridiculous that we might be seeing 80,000 on one of the days next week but maybe we will.
Italy only has 11,831 new covids today (and 364 deaths) but that's 17.6% of the days tests; it clearly relates to less testing on New Year's Day.

Not sure if it relates to saving up a few cases and deaths so that a higher number gets reported on Wednesday or Thursday next week when the new "colours" get announced...

Re: COVID-19

Posted: Sat Jan 02, 2021 7:04 pm
by KAJ
OffTheRock wrote:
Sat Jan 02, 2021 5:32 pm
That might explain some of it, but I don't think all of it. I'm still trying to get my head round the positive cases vs tests processed data and how they do or don't match up.
When trying to understand the day-of-week dependence of cases by specimen date I tried looking at the relation to test numbers. I was stymied, in part, by different sources and types of tests ("pillars" see link, inter alia) and different meanings of "date".
Finally I gave up trying to understand the day-of-week dependence and settled for being able to model it, so that I could better characterise the underlying trends.

Re: COVID-19

Posted: Sat Jan 02, 2021 7:05 pm
by Brightonian
Big jump in the number of new cases in Ireland: 3394 today. Over the previous week it ranged from 744 to 1754. Here's hoping it's just an artefact of the Christmas period, but I'm pessimistic.

Re: COVID-19

Posted: Sat Jan 02, 2021 7:21 pm
by Bird on a Fire
Portugal slightly relaxed its covid restrictions - including compulsory work-from-home, closing shops at 1:00 and a curfew - during the weekends around Christmas and New Years, which had been in place since early November.

The slight relaxation in covid restrictions looked like this:
scrot.png
scrot.png (166.39 KiB) Viewed 378 times
The peak in reports was 31 December, though I'm not sure if there were delays because of the holidays.

Hospitalisations are still trending downwards, thankfully. I hope we don't see a big spike next week.

Re: COVID-19

Posted: Sat Jan 02, 2021 8:10 pm
by OffTheRock
KAJ wrote:
Sat Jan 02, 2021 7:04 pm
OffTheRock wrote:
Sat Jan 02, 2021 5:32 pm
That might explain some of it, but I don't think all of it. I'm still trying to get my head round the positive cases vs tests processed data and how they do or don't match up.
When trying to understand the day-of-week dependence of cases by specimen date I tried looking at the relation to test numbers. I was stymied, in part, by different sources and types of tests ("pillars" see link, inter alia) and different meanings of "date".
Finally I gave up trying to understand the day-of-week dependence and settled for being able to model it, so that I could better characterise the underlying trends.
I think the pillars are less of an issue. The problem is the dates and perhaps to a lesser extent the fact we don’t count the number of people tested, but the number of tests. I assume it’s because the number of cases is about how many new cases there are on a given day whereas the testing data is all about how many tests our world beating testing system can process not how those tests relate to the number of positive cases.

Re: COVID-19

Posted: Sat Jan 02, 2021 8:25 pm
by shpalman
Number of people tested was being given, but the last data I have is the 22nd of May. They lost track of it after that.

It's not always entirely clear what date is used for postal tests.

This is why I tend to just 7-day average everything.

Re: COVID-19

Posted: Sat Jan 02, 2021 10:29 pm
by jimbob
shpalman wrote:
Sat Jan 02, 2021 8:25 pm
Number of people tested was being given, but the last data I have is the 22nd of May. They lost track of it after that.

It's not always entirely clear what date is used for postal tests.

This is why I tend to just 7-day average everything.
A similar reason for doing this for most data connected to this.

Re: COVID-19

Posted: Sun Jan 03, 2021 1:01 am
by sTeamTraen
Opti wrote:
Sat Jan 02, 2021 6:20 pm
There we are then. Gibraltar is f.cked. Incredibly fast acceleration of cases. All the adjoining ayuntamientos in Cadiz province are now locked down as well.
Covid don't give a sh.t about anyone taking control of are borders.
Only a day or so ago, you could fly from UK to Gib without a prior PCR test. Tested only on arrival. By then, you were Gib's problem.
Fark. 686 cases in the last 7 days. That's 2% of the population in a week.

On the plus side, the hospital has 210 beds, which is about twice the per-1,000 population number of GB.

Re: COVID-19

Posted: Sun Jan 03, 2021 1:06 am
by Brightonian
Brightonian wrote:
Sat Jan 02, 2021 7:05 pm
Big jump in the number of new cases in Ireland: 3394 today. Over the previous week it ranged from 744 to 1754. Here's hoping it's just an artefact of the Christmas period, but I'm pessimistic.
Seems there's a massive backlog in reporting.

Re: COVID-19

Posted: Sun Jan 03, 2021 12:00 pm
by lpm
Woah, this can't be good.
Chinese authorities have launched an investigation into a mysterious viral pneumonia which has infected dozens of people in the central city of Wuhan.

A total of 44 cases have been confirmed so far, 11 of which are considered "severe", officials said on Friday.

The Wuhan health commission said on Friday it was investigating the cause of the outbreak.

In a statement on its website, it said it had already ruled out a number of infection sources - including influenza, avian influenza and common respiratory diseases.
https://www.bbc.co.uk/news/world-asia-china-50984025

Re: COVID-19

Posted: Sun Jan 03, 2021 12:01 pm
by lpm
No wait, getting muddled, that article is from a year ago. Phew!

Re: COVID-19

Posted: Sun Jan 03, 2021 12:05 pm
by shpalman
Yeah whatever happened to that anyway?

Re: COVID-19

Posted: Sun Jan 03, 2021 4:08 pm
by Sciolus
Don't worry, I'm sure the authorities won't allow the Chinese New Year, that great national celebration in which large swathes of the population travel across the country to see their families, to spread and entrench the disease.

Re: COVID-19

Posted: Sun Jan 03, 2021 4:18 pm
by OffTheRock
We can always apply border control here and ensure people travelling from affected areas quarantine. Being an island should give us an advantage.