COVID-19

Covid-19 discussion, bring your own statistics
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Little waster
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Re: COVID-19

Post by Little waster » Sat Jan 09, 2021 4:26 pm

tenchboy wrote:
Sat Jan 09, 2021 4:20 pm
And below that...

You f.cking Dick Head.png


m'cup of tea has just gone everywhere.
c.nt.
TBF Farage has been told if he can get the tip of his tongue inside Trump's appendix he'll get a paying gig at Trump News.
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Woodchopper
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Re: COVID-19

Post by Woodchopper » Sat Jan 09, 2021 6:59 pm

Another good thread on excess mortality in the UK
https://twitter.com/mike_aka_logiqx/sta ... 86177?s=21

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jimbob
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Re: COVID-19

Post by jimbob » Sun Jan 10, 2021 4:39 pm

Woodchopper wrote:
Sat Jan 09, 2021 6:59 pm
Another good thread on excess mortality in the UK
https://twitter.com/mike_aka_logiqx/sta ... 86177?s=21
Have you seen this thread?

https://twitter.com/NickStripe_ONS/stat ... 32544?s=20
THREAD – Mortality 2020

Today we published England & Wales mortality statistics for the w/e 25 Dec

Nearly a full year’s data for 2020

In the last 52 weeks there were:
c.604k deaths registered across E&W

This is:
c.73k deaths (14%) above the 5-yr avg = excess deaths

1/11
Have you considered stupidity as an explanation

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Re: COVID-19

Post by Millennie Al » Mon Jan 11, 2021 2:46 am

...mask wearing...
Little waster wrote:
Sat Jan 09, 2021 3:29 pm
*My 30 seconds pubmed search chucked up 747 such papers, not all will be relevant, but as a random example Number 3 was this https://pubmed.ncbi.nlm.nih.gov/32335167/
Findings: Within first 100 days (31 December 2019 to 8 April 2020), 961 COVID-19 patients were diagnosed in HKSAR. The COVID-19 incidence in HKSAR (129.0 per million population) was significantly lower (p<0.001) than that of Spain (2983.2), Italy (2250.8), Germany (1241.5), France (1151.6), U.S. (1102.8), U.K. (831.5), Singapore (259.8), and South Korea (200.5). The compliance of face mask usage by HKSAR general public was 96.6% (range: 95.7% to 97.2%). We observed 11 COVID-19 clusters in recreational 'mask-off' settings compared to only 3 in workplace 'mask-on' settings (p = 0.036 by Chi square test of goodness-of-fit).

Conclusion: Community-wide mask wearing may contribute to the control of COVID-19 by reducing the amount of emission of infected saliva and respiratory droplets from individuals with subclinical or mild COVID-19.
That is very feeble evidence. There are confounding factors which are extremely difficult to eliminate - compliance with mask wearing is likely strongly correlated with taking other precautions, and government orders to wear masks are likely strongly correclated with other effective government measures.

For the general public, masks are probably only useful for identifying those who refuse to take a cheap and simple precaution so that others can take special care to avoid them.
Covid-19 - Don't catch it: don't spread it.

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Little waster
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Re: COVID-19

Post by Little waster » Mon Jan 11, 2021 4:24 am

Millennie Al wrote:
Mon Jan 11, 2021 2:46 am
...mask wearing...
Little waster wrote:
Sat Jan 09, 2021 3:29 pm
*My 30 seconds pubmed search chucked up 747 such papers, not all will be relevant, but as a random example Number 3 was this https://pubmed.ncbi.nlm.nih.gov/32335167/
Findings: Within first 100 days (31 December 2019 to 8 April 2020), 961 COVID-19 patients were diagnosed in HKSAR. The COVID-19 incidence in HKSAR (129.0 per million population) was significantly lower (p<0.001) than that of Spain (2983.2), Italy (2250.8), Germany (1241.5), France (1151.6), U.S. (1102.8), U.K. (831.5), Singapore (259.8), and South Korea (200.5). The compliance of face mask usage by HKSAR general public was 96.6% (range: 95.7% to 97.2%). We observed 11 COVID-19 clusters in recreational 'mask-off' settings compared to only 3 in workplace 'mask-on' settings (p = 0.036 by Chi square test of goodness-of-fit).

Conclusion: Community-wide mask wearing may contribute to the control of COVID-19 by reducing the amount of emission of infected saliva and respiratory droplets from individuals with subclinical or mild COVID-19.
That is very feeble evidence. There are confounding factors which are extremely difficult to eliminate - compliance with mask wearing is likely strongly correlated with taking other precautions, and government orders to wear masks are likely strongly correclated with other effective government measures.

For the general public, masks are probably only useful for identifying those who refuse to take a cheap and simple precaution so that others can take special care to avoid them.
Like I said that was merely the most recent of hundreds of such papers that a mere single pubmed search chucked up.

Even if that particular one wasn't the best, how far down the list* do you reckon I would need to go before I found one with a stronger evidence base than one retired chemist's unevidenced opinion, when he doesn't even seem to grasp the very basics of respiratory physiology or viral transmission?

My point was he appears to have made no attempt to do even the most basic literature search to check what published evidence either supports or contradicts his opinion; you know the sort of absolute minimum I'd expect a scientist to do before writing an article in the public sphere which draws heavily on his supposed all-knowing authority. The ease by which I dredged up even a single supporting paper begs** the question why did he not even attempt to do similar, or if he did why he came up blank?

Ultimately why is the onus on me to go to far greater lengths researching a throw-away comment on the 200th page of a thread on an obscure intenet forum then this guy did in writing an entire lengthy article intended to significantly shape the public discourse and change public policy across the globe affecting countless millions of lives?




*Here you go https://pubmed.ncbi.nlm.nih.gov/?term=c ... ectiveness

Without leaving the first page I can see in addition to the OP paper, a small scale RCT, a meta-analysis of 4 larger-scale RCTs, two mathematical modelling papers and one direct test of effectiveness, all supporting to a greater or lesser extent the effectiveness of mask-wearing and not one finding the opposite. If you fancy GISH galloping those there are a further 738 other papers there without even changing the search terms. Even the very weakest of any of those trumps anything produced by Mr Electro-Magnetic Spectrum.
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Re: COVID-19

Post by shpalman » Mon Jan 11, 2021 6:34 pm

lpm wrote:
Sun Jan 03, 2021 12:01 pm
No wait, getting muddled, that article is from a year ago. Phew!
Here's another one which seems to be from about a year ago

Morrisons to ban shoppers who refuse to wear face masks

only it's... haha... it's only just being published now!

Along with that one about the UK thinking about requiring incoming airline passengers have negative covid tests.
molto tricky

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Re: COVID-19

Post by jimbob » Mon Jan 11, 2021 11:43 pm

My plotting of the Our World in data total deaths

ImageImage
ImageImage
Have you considered stupidity as an explanation

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shpalman
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Re: COVID-19

Post by shpalman » Tue Jan 12, 2021 6:53 am

shpalman wrote:
Mon Jan 11, 2021 6:34 pm
lpm wrote:
Sun Jan 03, 2021 12:01 pm
No wait, getting muddled, that article is from a year ago. Phew!
Here's another one which seems to be from about a year ago

Morrisons to ban shoppers who refuse to wear face masks
turns out the police can't be arsed

Maybe they'd rather hang around parks making sure nobody goes for a walk.
molto tricky

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shpalman
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Re: COVID-19

Post by shpalman » Tue Jan 12, 2021 8:51 am

shpalman wrote:
Tue Jan 12, 2021 6:53 am
shpalman wrote:
Mon Jan 11, 2021 6:34 pm
lpm wrote:
Sun Jan 03, 2021 12:01 pm
No wait, getting muddled, that article is from a year ago. Phew!
Here's another one which seems to be from about a year ago

Morrisons to ban shoppers who refuse to wear face masks
turns out the police can't be arsed

Maybe they'd rather hang around parks making sure nobody goes for a walk.
It's a bit old and relies on self-reporting but supermarkets [are the] most common places visited before [a person gets a] positive [for the SARS-CoV-2 virus, the infectious agent causing the CoVid-19 illness, as ascertained by RT-PCR] test.

It doesn't tell you how likely it is that you'll catch the covids from any of those places on the list, since just about everybody is probably going to the supermarket at least once a week. But if it's literally the only thing a person does, and then they test positive, well.

Now you're locked down there are things on that list which aren't allowed anymore, and frankly shouldn't have been allowed in November.
molto tricky

OneOffDave
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Re: COVID-19

Post by OneOffDave » Tue Jan 12, 2021 9:50 am

I've been working on COVID-19 for over a year now! Seems like forever and no time at all at the same time

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lpm
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Re: COVID-19

Post by lpm » Wed Jan 13, 2021 4:29 pm

The second UK wave has now killed more people than the first wave. With a long way to go yet.

Cases have peaked, though?

The lockdown started for much of the country on 26 Dec and schools and workplaces were shut. Official lockdown started 5 Jan (but is actually looser in some ways than 25 Dec to 4 Jan). It make sense for cases to peak at around 10 to 14 days after lockdown.

Possible cases will nudge upwards again for a few days, reflecting the return to work and the mad one day of school last week?
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Re: COVID-19

Post by bagpuss » Wed Jan 13, 2021 4:47 pm

We've been in Tier 4 since Dec 20th and, based on the JoinZoe app estimated numbers, we seem to have just about flattened off, possibly even now showing the start of a fall, although it is a bit up and down so probably too early to say that.
Screenshot_20210113-163611_COVID Symptom Study.jpg
Screenshot_20210113-163611_COVID Symptom Study.jpg (224.95 KiB) Viewed 534 times
With Christmas gatherings banned and most local schools having INSET day on that 1 day of term, it's starting to look like the measures are just working. Where Tier4 didn't kick in until the 26th, I suspect it'll be at least another week, maybe more, before we see the same.

Anecdotally, I know of 1 hospitalised case caused directly by a Christmas gathering. Someone from small village in Warwickshire joined multiple household family gathering in Sheffield and brought Covid home as an extra Christmas gift. I'm cross because their irresponsible behaviour has brought Covid into my elderly mother's village where still no one has any news of when vaccines might be arriving.

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Re: COVID-19

Post by bagpuss » Wed Jan 13, 2021 4:52 pm

Oh, and yes, the x axis labelling on the graph is dynamic and looks sh.t but basically, it was low and flat over the summer, started creeping up through September, a bit more in Oct and Nov and then went through the roof in December, just starting to level off towards the end of the month.

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Re: COVID-19

Post by Gfamily » Wed Jan 13, 2021 5:08 pm

Not so good looking here
IMG_13012021_170717_(592_x_1200_pixel).jpg
IMG_13012021_170717_(592_x_1200_pixel).jpg (53.13 KiB) Viewed 518 times
My avatar was a scientific result that was later found to be 'mistaken' - I rarely claim to be 100% correct
ETA 5/8/20: I've been advised that the result was correct, it was the initial interpretation that needed to be withdrawn
Meta? I'd say so!

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Re: COVID-19

Post by KAJ » Wed Jan 13, 2021 5:23 pm

lpm wrote:
Wed Jan 13, 2021 4:29 pm
Cases have peaked, though?

The lockdown started for much of the country on 26 Dec and schools and workplaces were shut. Official lockdown started 5 Jan (but is actually looser in some ways than 25 Dec to 4 Jan). It make sense for cases to peak at around 10 to 14 days after lockdown.

Possible cases will nudge upwards again for a few days, reflecting the return to work and the mad one day of school last week?
Maybe, but I'm not sure. UK cases by specimen date. Zero-weighting the latest 5 (marked as incomplete by coronavirus.data.gov.uk) and Xmas Day and New Years Day.
SpecCases.png
SpecCases.png (13.87 KiB) Viewed 510 times
Interestingly (to a geek :geek: ) the dependence on day-of-week seems to be weakening.

Code: Select all

Analysis of Variance Table

Response: log(SpecCases)
              Df  Sum Sq Mean Sq F value    Pr(>F)    
poly(date, 2)  2 2.70375 1.35187 55.0275 3.757e-08 ***
day            6 0.48420 0.08070  3.2849   0.02476 *  
Residuals     17 0.41764 0.02457                      
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Coefficients:
               Estimate Std. Error t value Pr(>|t|)    
(Intercept)    10.61298    0.08151 130.197  < 2e-16 ***
poly(date, 2)1  1.77598    0.25579   6.943 2.37e-06 ***
poly(date, 2)2 -0.53400    0.24951  -2.140   0.0471 *  
dayMon          0.23770    0.11091   2.143   0.0469 *  
dayTue          0.29031    0.11113   2.612   0.0182 *  
dayWed          0.17668    0.11150   1.585   0.1315    
dayThu         -0.03299    0.11205  -0.294   0.7720    
dayFri          0.17051    0.14372   1.186   0.2518    
daySat         -0.07320    0.11092  -0.660   0.5181    
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Residual standard error: 0.1567 on 17 degrees of freedom
Multiple R-squared:  0.8842,	Adjusted R-squared:  0.8297 
The apparent slowing down doesn't appear in some smaller areas, e.g. Worcestershire
Worcs.png
Worcs.png (10.75 KiB) Viewed 510 times

Code: Select all

Coefficients:
               Estimate Std. Error t value Pr(>|t|)    
(Intercept)     5.66313    0.05715  99.085  < 2e-16 ***
poly(date, 2)1  3.59291    0.39608   9.071 4.65e-09 ***
poly(date, 2)2  0.04600    0.38772   0.119    0.907    
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Residual standard error: 0.2507 on 23 degrees of freedom
Multiple R-squared:  0.8387,	Adjusted R-squared:  0.8247 

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Brightonian
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Re: COVID-19

Post by Brightonian » Wed Jan 13, 2021 6:24 pm

Based on last couple of days, new cases seem to be going down in Ireland too.

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Woodchopper
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Re: COVID-19

Post by Woodchopper » Wed Jan 13, 2021 6:32 pm

We fitted a model of SARS-CoV-2 transmission in care homes and the community to regional surveillance data for England. Among control measures implemented, only national lockdown brought the reproduction number below 1 consistently; introduced one week earlier it could have reduced first wave deaths from 36,700 to 15,700 (95%CrI: 8,900-26,800). Improved clinical care reduced the infection fatality ratio from 1.25% (95%CrI: 1.18%-1.33%) to 0.77% (95%CrI: 0.71%-0.84%). The infection fatality ratio was higher in the elderly residing in care homes (35.9%, 95%CrI: 29.1%-43.4%) than those residing in the community (10.4%, 95%CrI: 9.1%-11.5%). England is still far from herd immunity, with regional cumulative infection incidence to 1st December 2020 between 4.8% (95%CrI: 4.4%-5.1%) and 15.4% (95%CrI: 14.9%-15.9%) of the population.
https://www.medrxiv.org/content/10.1101 ... 21249564v1

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jimbob
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Re: COVID-19

Post by jimbob » Thu Jan 14, 2021 4:38 pm

Equally relevant:
Little waster wrote:
Thu Jan 14, 2021 3:52 pm
https://www.theguardian.com/education/2 ... -half-term

Do you ever get the feeling of having had dejavu again again again?


I'm guessing there will be a few newscycles of outcry while Government ministers doggedly defend this and cast nasturtiums on anybody who dares complain about it before Johnson's inevitable U-turn, after which the self-same ministers will hail the U-turn as making them very happy and what they actually always wanted.
https://www.theguardian.com/politics/20 ... is-madness
Plan to discharge Covid patients to care homes in England is 'madness'

Yes - I did check the date for that story
Have you considered stupidity as an explanation

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Re: COVID-19

Post by JQH » Thu Jan 14, 2021 4:55 pm

FFS!
And remember that if you botch the exit, the carnival of reaction may be coming to a town near you.

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Re: COVID-19

Post by RoMo » Thu Jan 14, 2021 5:02 pm

If they've done 14 days in isolation and aren't symptomatic then it should be fine to be discharged to a care home, shouldn't it?

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Re: COVID-19

Post by jdc » Thu Jan 14, 2021 5:23 pm

jimbob wrote:
Thu Jan 14, 2021 4:38 pm
Equally relevant:
Little waster wrote:
Thu Jan 14, 2021 3:52 pm
https://www.theguardian.com/education/2 ... -half-term

Do you ever get the feeling of having had dejavu again again again?


I'm guessing there will be a few newscycles of outcry while Government ministers doggedly defend this and cast nasturtiums on anybody who dares complain about it before Johnson's inevitable U-turn, after which the self-same ministers will hail the U-turn as making them very happy and what they actually always wanted.
https://www.theguardian.com/politics/20 ... is-madness
Plan to discharge Covid patients to care homes in England is 'madness'

Yes - I did check the date for that story
tbf, they've been isolating for 14 days so there's no need to retest them. We now know they do not pose an infection risk to other residents in a care home.

https://www.forbes.com/sites/brucelee/2 ... 63ad2032c6 "There are several situations where you may be contagious for longer than the 10 to 20 day period. If your immune system is weaker, consider erring on the conservative side."

https://www.cell.com/cell/fulltext/S009 ... 20)31456-2 "Long-term severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) shedding was observed from the upper respiratory tract of a female immunocompromised individual with chronic lymphocytic leukemia and acquired hypogammaglobulinemia. Shedding of infectious SARS-CoV-2 was observed up to 70 days, and of genomic and subgenomic RNA up to 105 days, after initial diagnosis."

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Re: COVID-19

Post by shpalman » Thu Jan 14, 2021 5:28 pm

jdc wrote:
Thu Jan 14, 2021 5:23 pm
jimbob wrote:
Thu Jan 14, 2021 4:38 pm
Equally relevant:
Little waster wrote:
Thu Jan 14, 2021 3:52 pm
https://www.theguardian.com/education/2 ... -half-term

Do you ever get the feeling of having had dejavu again again again?


I'm guessing there will be a few newscycles of outcry while Government ministers doggedly defend this and cast nasturtiums on anybody who dares complain about it before Johnson's inevitable U-turn, after which the self-same ministers will hail the U-turn as making them very happy and what they actually always wanted.
https://www.theguardian.com/politics/20 ... is-madness
Plan to discharge Covid patients to care homes in England is 'madness'

Yes - I did check the date for that story
tbf, they've been isolating for 14 days so there's no need to retest them. We now know they do not pose an infection risk to other residents in a care home.

https://www.forbes.com/sites/brucelee/2 ... 63ad2032c6 "There are several situations where you may be contagious for longer than the 10 to 20 day period. If your immune system is weaker, consider erring on the conservative side."

https://www.cell.com/cell/fulltext/S009 ... 20)31456-2 "Long-term severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) shedding was observed from the upper respiratory tract of a female immunocompromised individual with chronic lymphocytic leukemia and acquired hypogammaglobulinemia. Shedding of infectious SARS-CoV-2 was observed up to 70 days, and of genomic and subgenomic RNA up to 105 days, after initial diagnosis."
... and a person who's managed to stay ill for a long time is a great way to breed a new variant
molto tricky

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Re: COVID-19

Post by lpm » Fri Jan 15, 2021 11:26 am

In a nice example of international cooperation, we've given Brazil the English variant and Brazil has given us the Brazilian variant.

Or at least we've detected one of the two Brazilian variants.

I think there's a strong case for a complete UK shut down for two weeks. A fire break within the lockdown. No schools, no leaving the house except for food and essential work, no travel etc. Like other countries do. Punch that curve downwards, then resume the current lockdown to continue the progress.

Zero Covid is possible this summer, with track and trace effective plus vaccines leading to near zero deaths each month. We can worry about an autumn wave later - under the assumption that vaccines at the least partially reduce transmission, we should be able to control it pretty easily once the adult vaccination program is nearing completion.
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Re: COVID-19

Post by Bird on a Fire » Fri Jan 15, 2021 11:43 am

Portugal has shut down again (some school classes still running). Two weeks at least, maybe a month.
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lpm
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Re: COVID-19

Post by lpm » Fri Jan 15, 2021 2:04 pm

My God, nearly a year on and Sage is still f.cking up their models. How can they possibly be this bad? Are they locked in a dark room only able to see their models and none of the other data?

We can all see that cases have basically peaked, with the start of the decline beginning in some places. Nowhere are cases still shooting up. R is clearly at around 0.8 or 0.9 or maybe 1.0 or perhaps 1.1 in some places.

What it obviously cannot be is 1.2 to 1.3.

Can anyone explain why these modellers are so bad?
The reproduction number, or R value, of coronavirus transmission in the UK is between 1.2 and 1.3, the Government Office for Science and the Scientific Advisory Group for Emergencies (Sage) has said.
What ever happened to that Trump guy, you know, the one who was president for a bit?

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