COVID-19

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

Post by Herainestold » Thu May 20, 2021 5:21 pm

headshot wrote:
Thu May 20, 2021 5:06 pm
tom p wrote:
Wed May 19, 2021 3:40 pm
bolo wrote:
Thu May 13, 2021 6:21 pm

Your house, your rules, whatever Johnson announces. If they refuse, there are other contractors and removal companies.
I don't know how many removal companies there are in the DC area that have staff just sitting around waiting for a call at a moment's notice, but there aren't any in London or South Holland, that's for sure.
If you have to move house today, you can't wait 3 weeks for your worldly goods to be moved.
Yeah. Don't piss off your removal folk whilst they're moving your entire belongings...is one of my life lessons.
And keep an eye on your stuff. Friends had two vacs that disappeared during a move. They had them out as they were doing some cleaning as boxes were being shifted. Both never made it.
Double dose. Double mask. Double distance

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jdc
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Re: COVID-19

Post by jdc » Thu May 20, 2021 7:28 pm

bob sterman wrote:
Thu May 20, 2021 4:55 pm
Lew Dolby wrote:
Thu May 20, 2021 4:23 pm
Sorry if this has already been asked and answered . . .

once again the media are throwing around "stats" like 2 doses of AZ vac gives 85-90% protection. What exactly is that supposed to mean ?? Is it that 10-15% can still get CoViD; 10-15% will die ?? Or something else ??
I think it means for "90% protection" - if you have 10,000 people and you'd expect 1000 to get symptomatic COVID-19 over a time period, vaccinating the 10,000 will reduce the number of symptomatic cases to 100.

i.e. it prevents 90% of the symptomatic cases you expect.
Yeah. When I've seen discussion of protection via vaccines it's tended to mean prevention of cases (and if they want to say something about prevention of hospitalisation or death people usually specify 'protection against x').

If they're saying 85-90% I'm guessing this is some real world data someone's looking at? I don't recognise those figures from the original list of possible efficacy figures that AZ provided from their trial. I think it was something like 64, 72, and 90.

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bob sterman
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Re: COVID-19

Post by bob sterman » Thu May 20, 2021 7:34 pm

jdc wrote:
Thu May 20, 2021 7:28 pm
If they're saying 85-90% I'm guessing this is some real world data someone's looking at? I don't recognise those figures from the original list of possible efficacy figures that AZ provided from their trial. I think it was something like 64, 72, and 90.
Yes - it's "real world data" in the new PHE surveillance report...

https://www.gov.uk/government/news/covi ... -published

Millennie Al
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Re: COVID-19

Post by Millennie Al » Fri May 21, 2021 1:03 am

Herainestold wrote:
Thu May 20, 2021 5:21 pm
Friends had two vacs that disappeared during a move.
Stolen by anti-vacsers?
Covid-19 - Don't catch it: don't spread it.

Herainestold
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Re: COVID-19

Post by Herainestold » Fri May 21, 2021 2:43 am

Millennie Al wrote:
Fri May 21, 2021 1:03 am
Herainestold wrote:
Thu May 20, 2021 5:21 pm
Friends had two vacs that disappeared during a move.
Stolen by anti-vacsers?
They muse be pro-vacsers if they wanted them.
Double dose. Double mask. Double distance

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Woodchopper
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Re: COVID-19

Post by Woodchopper » Sat May 22, 2021 7:40 am

WHO estimates suggest excess mortality of at least 3 000 000.
https://www.who.int/data/stories/the-tr ... -mortality

OffTheRock
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Re: COVID-19

Post by OffTheRock » Mon May 24, 2021 11:01 pm

https://www.bbc.co.uk/news/uk-england-57232728

Not sure if this is the right thread or whether it should go in the variants or reunreunlockdown thread. Government updated the guidance for people living in areas with rapid Indian variant spread. Including advice to meet outside where possible and not to travel in & out of the area unless essential. Then didn’t tell anyone, including local public health officials it seems.

The important thing to remember is at least they tried. They issued guidance to prevent the spread of the variant and it isn’t their fault nobody followed the advice they didn’t know existed.

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wilsontown
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Re: COVID-19

Post by wilsontown » Tue May 25, 2021 9:32 am

If it wasn't already comprehensively priced in you'd find that level of incompetence astounding.
"All models are wrong but some are useful" - George Box

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wilsontown
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Re: COVID-19

Post by wilsontown » Tue May 25, 2021 11:46 am

The UK 7 day case average has been increasing fairly consistently since May 3rd. But hospital admissions and deaths look to be falling or flat, with deaths now at such low levels that the plot is very spiky.
cases_24052021.png
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admissions_24052021.png
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deaths_24052021.png
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"All models are wrong but some are useful" - George Box

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lpm
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Re: COVID-19

Post by lpm » Tue May 25, 2021 12:05 pm

Looking back at your previous charts... your Y-axis going up to +4 compares to previous months when +10 was needed for Aug 2020 to Jan 2021 (with a couple of spikes way above that).

viewtopic.php?p=71820#p71820

I don't think a wave is building at the current rates. Doubling every two weeks is a pretty different story to doubling every month.

But it's so regional now maybe there's no point to UK numbers?
What ever happened to that Trump guy, you know, the one who was president for a bit?

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Bird on a Fire
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Re: COVID-19

Post by Bird on a Fire » Tue May 25, 2021 12:12 pm

Quick screenshot from the Portuguese dashboard:
Screenshot_2021-05-25_13-02-22.png
Screenshot_2021-05-25_13-02-22.png (126.45 KiB) Viewed 419 times
Cases still low, even though we've basically unlocked - centres of education are allowed to go back (though generally with blended learning, masks, distance, sanitiser, etc), all shops and cafés etc. are open (but with masks, distancing, sanitiser, etc). No recorded increase among any age group.

Reasonable progress being made with vaccinations (population is 10m, which makes the maths easy).

The national map shows are couple of places have localised outbreaks. I'm not sure of the specific reasons, but they're mostly away from major population centres and skipped the first waves. I've got a serious case of covid-fatigue so haven't bothered following every council's outbreak any more.

So yeah, ready for 5000 UK tourists every day (in the Algarve alone) bringing their dodgy variants and unfamiliarity with masks, distancing and sanitiser use. Thank god I don't live anywhere a tourist would want to visit.
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wilsontown
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Re: COVID-19

Post by wilsontown » Tue May 25, 2021 1:30 pm

lpm wrote:
Tue May 25, 2021 12:05 pm
But it's so regional now maybe there's no point to UK numbers?
Yes, I think there's probably something in that. Cases in most of the country are still low and falling so I think the rise in national numbers is probably being driven by a few hotspots. But this can change...
"All models are wrong but some are useful" - George Box

OffTheRock
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Re: COVID-19

Post by OffTheRock » Tue May 25, 2021 4:20 pm

The dashboard map is a sea of white down here and cases still falling. We’ll see what happens when hoardes arrive for half term next week.

If strong winds and torrential rain is their thing, obviously. They might not turn up. I’m not sure I’d be paying eye watering prices for this weather.

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Ladysavage
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Re: COVID-19

Post by Ladysavage » Tue May 25, 2021 4:45 pm

Just had to get Boobshark swabbed, get test results in 24-48 hours. It wasn't nice having to stick that up his wee nosey!

KAJ
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Re: COVID-19

Post by KAJ » Tue May 25, 2021 5:35 pm

wilsontown wrote:
Tue May 25, 2021 1:30 pm
lpm wrote:
Tue May 25, 2021 12:05 pm
But it's so regional now maybe there's no point to UK numbers?
Yes, I think there's probably something in that. Cases in most of the country are still low and falling so I think the rise in national numbers is probably being driven by a few hotspots. But this can change...
I'd be happy if anyone could convince me that the stall in the decline in "Patients in mechanical ventilation beds" (data from coronavirus.data.gov.uk) wasn't both real and a cause for concern; plot with log y axis.
MVBeds.png
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lpm
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Re: COVID-19

Post by lpm » Tue May 25, 2021 5:53 pm

That's a naughty little chart.

Log scale and a short x-axis hide the fact that it's down from 4,000 to 100. While hospital patients are down from 80,000 to 1,000.

It's inevitable that the date will bounce around when a lot levels, while appearing very smooth at high levels. If a wave starts building there won't be anything to see for a couple of weeks due to the lags.
What ever happened to that Trump guy, you know, the one who was president for a bit?

KAJ
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Re: COVID-19

Post by KAJ » Tue May 25, 2021 7:24 pm

lpm wrote:
Tue May 25, 2021 5:53 pm
That's a naughty little chart.

Log scale and a short x-axis hide the fact that it's down from 4,000 to 100. While hospital patients are down from 80,000 to 1,000.

It's inevitable that the date will bounce around when a lot levels, while appearing very smooth at high levels. If a wave starts building there won't be anything to see for a couple of weeks due to the lags.
Disagree.

The graph was explicitly to demonstrate an apparent 'stall in the decline in "Patients in mechanical ventilation beds"' which is equally apparent on a linear y-scale
MVBeds2.png
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Earlier data is irrelevant to a recent stall, but including it doesn't remove the apparent stall (log y again because that nicely demonstrates the close to exponential decline).
MVBeds3.png
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I don't see the relevance of inpatient numbers to the presence or otherwise of a stall in MV beds. If you're pointing out that the ratio of MVbeds to inpatients has changed, I haven't checked but don't disagree. There may be a stall in the decline of inpatients, but I don't think it's as clear.
InPats.png
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The recent data doesn't "bounce around", here are the last 20 reported values in order:

Code: Select all

 182 163 159 151 144 149 138 136 129 124 121 123 125 124 122 123 124 123 120 121 
My point is that, after a sustained decline, these are remarkably constant - the last 11 are all between 120 and 125

I agree that if a wave starts building there will be a lag between increasing infections and increasing MVBeds. But that is irrelevant to whether there is already a 'stall in the decline in "Patients in mechanical ventilation beds"'.

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lpm
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Re: COVID-19

Post by lpm » Tue May 25, 2021 7:36 pm

Your y-axis needs some numbers, vaguely close to where the current dots are. Having 300 up the top is meaningless. Chart is still a fail, I'm afraid.
What ever happened to that Trump guy, you know, the one who was president for a bit?

KAJ
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Re: COVID-19

Post by KAJ » Tue May 25, 2021 7:56 pm

lpm wrote:
Tue May 25, 2021 7:36 pm
Your y-axis needs some numbers, vaguely close to where the current dots are. Having 300 up the top is meaningless. Chart is still a fail, I'm afraid.
Conceded.
My excuse is that I was seeking opinions on the apparent stall which didn't really depend on detail, I linked to the raw data, and that chart was very easy to produce:

Code: Select all

ggplot(subset(UKDF, date > as.Date("2021-04-12")), aes(x = date, y = MVBeds)) + geom_point() + logy
Improving the y-axis would have been more effort than I considered worth it, then and now.

Any opinions on whether the apparent stall is real and/or cause for concern?

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Sciolus
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Re: COVID-19

Post by Sciolus » Tue May 25, 2021 8:02 pm

If those are log y-axes, why are the gridlines mostly (but not quite always) uniform?

KAJ
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Re: COVID-19

Post by KAJ » Tue May 25, 2021 9:45 pm

Sciolus wrote:
Tue May 25, 2021 8:02 pm
If those are log y-axes, why are the gridlines mostly (but not quite always) uniform?
Because that's how ggplot2 did it (i.e. I don't know!).

As indicated above, the plot used only 3 ggplot2 functions.

Code: Select all

ggplot(subset(UKDF, date > as.Date("2021-04-12")), aes(x = date, y = MVBeds)) + geom_point() + logy
  • ggplot() specified the data as a subset of the dataframe UKDF, and default x and y variables
  • geom_point() added symbols
  • I had earlier defined logy <- scale_y_continuous(trans='log10'). Reviewing the help, I could have used the slightly simpler but equivalent logy <- scale_y_log10(). I'll probably change my code to use that.
All those functions have many available arguments, most of which I left at the defaults.
scale_y_continuous() has an argument `breaks` which I could have specified but left at the default breaks = waiver() which uses "the default breaks computed by the transformation object". If you're really interested ( :ugeek: ) the relevant code may be at https://github.com/r-lib/scales/blob/master/R/breaks-log.R

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lpm
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Re: COVID-19

Post by lpm » Tue May 25, 2021 10:22 pm

The apparent stall doesn't tell us much. I think we need to know turnover rate as well. How many people are very long stayers, a month say? How many are brief stayers, two days say? Michael Rosen was in intensive care 47 days.

Also, if a hospital has zero Covid patients in intensive care, it probably has still allocated several for that purpose - with routine operations still being cancelled to leave space. The NHS is not functioning normally still. It might be, therefore, that the criteria for getting into a bed has been made easier in 75% of hospitals but remains strict for 25%. That would probably reveal itself in very short stays - give MV for a few hours maybe for a level of illness that wouldn't have qualified in Jan?
What ever happened to that Trump guy, you know, the one who was president for a bit?

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Bird on a Fire
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Re: COVID-19

Post by Bird on a Fire » Wed May 26, 2021 9:17 am

KAJ wrote:
Tue May 25, 2021 9:45 pm

All those functions have many available arguments, most of which I left at the defaults.
scale_y_continuous() has an argument `breaks` which I could have specified but left at the default breaks = waiver() which uses "the default breaks computed by the transformation object".
You can use breaks=base_breaks() to get labels at 1, 10, 100 etc, which will put a label close to the current values (which are all close to 100), which might be more similar to other log plots the folk complaining have seen.

Labelling side the stall in the decline in mechanical ventilation is very obvious (and would be without any axis labels at all!)

Unless those are all very long-term patients hanging over from a previous wave it's hard to see why there'd be a floor to the values. But I think ventilation would be the very last indicator to respond to changing case numbers. There also might be people with underlying conditions and "long covid" in the data?
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lpm
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Re: COVID-19

Post by lpm » Wed May 26, 2021 9:35 am

Clearly there's a floor to the values at zero, and real world you'd expect a floor of maybe a couple of dozen from people who are there for many weeks? Which is why the Y-axis labels are so important - an flattening at, say, 50 would be a very different story to flattening at 200.

UK is still averaging about 6 or 7 deaths a day, and presumably nearly always these will go through intensive care first. So perhaps we're at 20 people entering MV beds per day, 6 leaving due to death and 14 leaving back to a general ward, at a 33% fatality rate? Flattening at 20 per day would seem pretty good?
What ever happened to that Trump guy, you know, the one who was president for a bit?

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Bird on a Fire
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Re: COVID-19

Post by Bird on a Fire » Wed May 26, 2021 9:38 am

Well it's flattening at 100 and change at the moment. Not sure what to make of that.
He has the grace of a swan, the wisdom of an owl, and the eye of an eagle—ladies and gentlemen, this man is for the birds!

Triple birds. Triple jokes. Triple Tripel.

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