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Coronavirus - modelling aspects only please

Scientific discovery and discussion
GoSeigen
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Re: Coronavirus - modelling aspects only please

#311460

Postby GoSeigen » May 23rd, 2020, 3:19 pm

dealtn wrote:
GoSeigen wrote:In #311332 in the Snug:

Mike4 wrote:I'm surprised you cannot see the difference. Heart attacks and ovarian cancers kill people at a broadly steady pace. The number deaths from CV19 left unchecked in a population increases broadly exponentially, until the disease runs out of victims. Or do you not accept that as true?


No, that is not true. The growth of an infections disease approximates the logistic function. This is approximately exponential in the very early stages, but long before the victims have run out the spread slows. Most deaths occur after the exponential stage has ended.

GS


Not saying you're wrong. I haven't researched it. But I suspect the 2 words "left unchecked" have some bearing on that. Presumably there has been an amount of work leading to the conclusion "the growth of an infections disease approximates the logistic function"? So was that work based on observations in the real world (or to some extent a laboratory), and if so were these on infections that were "left unchecked" (easier in a laboratory than the real world I would think), or on those where attempts were made, either through behavioural change, or medical intervention, to "check" it?

It could be you are not in disagreement with each other, just not realising the subtle, but important, difference in what you are claiming.


Yes, I think you may be right. I don't know what the outcome would be "unchecked"; I don't think anyone is suggesting that CV has been or should be allowed to spread unchecked; I would prefer if the restrictions were much less draconian and more targeted; something like the South Korea/Japan approach...

For more on the maths/modelling, John Hussman is a good commentator to follow for both CV itself and the investment consequences.

I find it highly ironic that the same people (my parents for example) who would find it perfectly reasonable to target "black" people for "random" police stops because that is more likely to reduce crime would consider it grossly unfair to target "older" people (themselves) with tighter lockdown rules to try to save their lives!!!

GS

dealtn
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Re: Coronavirus - modelling aspects only please

#311465

Postby dealtn » May 23rd, 2020, 3:24 pm

GoSeigen wrote:
dealtn wrote:
GoSeigen wrote:In #311332 in the Snug:



No, that is not true. The growth of an infections disease approximates the logistic function. This is approximately exponential in the very early stages, but long before the victims have run out the spread slows. Most deaths occur after the exponential stage has ended.

GS


Not saying you're wrong. I haven't researched it. But I suspect the 2 words "left unchecked" have some bearing on that. Presumably there has been an amount of work leading to the conclusion "the growth of an infections disease approximates the logistic function"? So was that work based on observations in the real world (or to some extent a laboratory), and if so were these on infections that were "left unchecked" (easier in a laboratory than the real world I would think), or on those where attempts were made, either through behavioural change, or medical intervention, to "check" it?

It could be you are not in disagreement with each other, just not realising the subtle, but important, difference in what you are claiming.


Yes, I think you may be right. I don't know what the outcome would be "unchecked"; I don't think anyone is suggesting that CV has been or should be allowed to spread unchecked;


I don't think anyone is suggesting it should grow unchecked either.

I just think that with tighter language the argument about whether it is, or not, "exponential" which seems to be going on, could be resolved.

It is probably the case that left unchecked it would be exponential (or close), but because it isn't being left unchecked it isn't. This is a bit "angels on a pinhead".

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Re: Coronavirus - modelling aspects only please

#311471

Postby XFool » May 23rd, 2020, 3:36 pm

Bubblesofearth wrote:
XFool wrote:
It's infectious?

Of course "runs out of victims" can mean many things: Everybody has already been infected, the people still around are mostly immune, a successful vaccination programme. In these cases it presumably ends up being endemic, which it likely will do. But that's a whole new problem.

But why are some people apparently having difficulty with the concept of 'infectious'?

I have no problem with either the concept of infection or that the virus is infectious. I simply asked for evidence for your claim of exponential growth of cases.

I've looked at a lot of the data from different countries and fail to see much evidence of exponential growth. Maybe in the very early stages but the data is noisy there.

It wasn't me who used the term 'exponential' in this case. But anyway, I am seriously not interested in any further pursuit of what is or is not the best fit mathematical function to the spread of this disease - which anyway would likely differ from country to country. It seems to me to be like arguing how many angels can dance on the head of a pin*, not really the substantive point, which is: It's infectious, so it spreads if not checked in some manner. This means that individual, personal 'risk' metrics - such as an individual's chance of a heart attack - by themselves cannot give a full and correct picture. That's what it was about AFAIAC.

* SNAP! - Just noticed. ;)

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Re: Coronavirus - modelling aspects only please

#311476

Postby Itsallaguess » May 23rd, 2020, 3:46 pm

modellingman wrote:
Itsallaguess wrote:
Not sure if this has been posted already, but I've just noticed that the 'Worldometers' site is now showing 'Outcome of cases' data for Italy and Spain, which show interesting and encouraging improvements over time in the Covid recovery-rates in both countries -

Image

Sources for both of the above images -

Italy - https://www.worldometers.info/coronavirus/country/italy/

Spain - https://www.worldometers.info/coronavirus/country/spain/

Given that we're still at a relatively early stage of investigation into this virus, there's a chance that things might get more encouraging still, given the above steady improvements...


I think Zico is right.

The graphs simply show deaths and recovereds as a proportion of deaths+recovereds (and this also explains why they are symmetrical about the 50% horizontal line). They are also based, in the main, on hospitalised cases where, I suspect, the average time to death is less than the average time to recovery. If my suspicion is correct, then in any daily cohort of cases the measured fatality rate will be biassed towards overestimation until sufficient time has elapsed to know the outcome of all cases in that cohort, though the degree of bias decreases with time.

The fatality rate at a point in time as shown in Worldometer's graphs is simply derived from the measured fatality rates at that point in time of all the daily cohorts prior to that point (in fact it is a weighted sum of the measured rates where the weights are the cohort sizes). Older cohorts will have little or no bias but more recent ones will and the result is that the overall fatality rate at the point in time still shows some bias. As time marches on, the proportion of all daily cohorts which are more recent also declines so the overall degree of bias reduces.

So I don't think the graphs are reflective of any steady improvement. Rather they are a consequence of the the lifetime of a case being shorter when death rather than recovery is the outcome.

Eventually, the bias will disappear completely and the graphs will converge to an asymptote representing the true fatality rate. I have had a close look at Spain's data and my estimate is around 11%. This represents the case fatality rate (CFR) which is different from the infection fatality rate (IFR).

If I get some time later today or tomorrow I will post some more details.


Just wanted to come back to the points raised above, because whilst the replies to my original post made sense, I've just read something on the BBC news feed that makes the same point I thought the original charts were showing -

Outcome improving for critically ill patients in UK -

A breakdown of the latest weekly statistics of Covid-19 patients admitted to critical care units in England, Wales and Northern Ireland shows doctors have become more skilled at keeping seriously ill patients alive during the course of the pandemic.

Recent statistics, from the Intensive Care National Audit & Research Centre, show that of the 5,330 patients who needed advanced respiratory support, more than half (54.4%) are still alive.

This marks a significant improvement from the early days of the crisis: figures produced up to Thursday 9 April showed that only a third of patients who needed advanced respiratory support survived.


https://www.bbc.co.uk/news/live/world-52781481

So whilst the charts above were in relation to Italy and Spain, the above text regarding improved outcomes over time in UK hospitals does seem to suggest that the medical profession are generally getting better at simply coping and dealing with the virus for those people that end up in hospitals..

Cheers,

Itsallaguess

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Re: Coronavirus - modelling aspects only please

#311480

Postby dealtn » May 23rd, 2020, 3:55 pm

Itsallaguess wrote:... the above text regarding improved outcomes over time in UK hospitals does seem to suggest that the medical profession are generally getting better at simply coping and dealing with the virus for those people that end up in hospitals..



I can't dig into the text at the moment for some reason.

There are two things possibly going on here.

They have improved the treatment such that more are now surviving than were previously. Or, the outcome is the same but the length of time taken to die is longer.

I am hoping it is the former, but could be the latter. Does it say which?

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Re: Coronavirus - modelling aspects only please

#311481

Postby Bubblesofearth » May 23rd, 2020, 3:57 pm

XFool wrote:It wasn't me who used the term 'exponential' in this case. But anyway, I am seriously not interested in any further pursuit of what is or is not the best fit mathematical function to the spread of this disease - which anyway would likely differ from country to country. It seems to me to be like arguing how many angels can dance on the head of a pin*, not really the substantive point, which is: It's infectious, so it spreads if not checked in some manner. This means that individual, personal 'risk' metrics - such as an individual's chance of a heart attack - by themselves cannot give a full and correct picture. That's what it was about AFAIAC.

* SNAP! - Just noticed. ;)


Mike4 said that if unchecked deaths would increase in a broadly exponential fashion.

I asked for evidence.

You responded with 'it's infectious' and asked (in a rather patronising way) why people had difficulty with that concept. Because you were responding to my post asking for evidence it is IMO logical to assume that, when you supplied a reason (it's infectious) you agreed with Mike4's assertion regarding exponential growth. Otherwise simply saying 'it's infectious' is a statement of what Basil would call 'the bl44ding obvious'.

BoE

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Re: Coronavirus - modelling aspects only please

#311487

Postby XFool » May 23rd, 2020, 4:18 pm

Bubblesofearth wrote:Mike4 said that if unchecked deaths would increase in a broadly exponential fashion.

I asked for evidence.

You responded with 'it's infectious' and asked (in a rather patronising way) why people had difficulty with that concept. Because you were responding to my post asking for evidence it is IMO logical to assume that, when you supplied a reason (it's infectious) you agreed with Mike4's assertion regarding exponential growth. Otherwise simply saying 'it's infectious' is a statement of what Basil would call 'the bl44ding obvious'.

BoE

The full text of Mike4's post you originally quoted was:
Mike4 wrote:I'm surprised you cannot see the difference. Heart attacks and ovarian cancers kill people at a broadly steady pace. The number deaths from CV19 left unchecked in a population increases broadly exponentially, until the disease runs out of victims. Or do you not accept that as true?

In the context of the original thread topic (which is now presumably OT here!) it was, to me, the part underlined that was relevant. He was making the simple point that, left unchecked, it increased in a population - I don't think it matters to the point being made what the precise mathematical shape of that increase is.

I asked why people had apparent 'difficulty' with the concept of 'infectious' because they were comparing COVID-19 risk metrics with heart attacks and ovarian cancers (not my comparator, I used the counter analogy of being hit by a bus in the street) which I and others pointed out, seemed to not make complete sense in the context of 'personal risk metrics' as they, unlike COVID-19, are not (AFAWK) transmitted by infection.

I hope this explains it.

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Re: Coronavirus - modelling aspects only please

#311492

Postby Bubblesofearth » May 23rd, 2020, 4:36 pm

XFool wrote:The full text of Mike4's post you originally quoted was:
Mike4 wrote:I'm surprised you cannot see the difference. Heart attacks and ovarian cancers kill people at a broadly steady pace. The number deaths from CV19 left unchecked in a population increases broadly exponentially, until the disease runs out of victims. Or do you not accept that as true?

In the context of the original thread topic (which is now presumably OT here!) it was, to me, the part underlined that was relevant. He was making the simple point that, left unchecked, it increased in a population - I don't think it matters to the point being made what the precise mathematical shape of that increase is.

I asked why people had apparent 'difficulty' with the concept of 'infectious' because they were comparing COVID-19 risk metrics with heart attacks and ovarian cancers (not my comparator, I used the counter analogy of being hit by a bus in the street) which I and others pointed out, seemed to not make complete sense in the context of 'personal risk metrics' as they, unlike COVID-19, are not (AFAWK) transmitted by infection.

I hope this explains it.


Rubbish. It is crystal clear that the point being made was that the difference was that deaths from the virus would increase broadly exponentially rather than in the steady manner for the other diseases mentioned. How can it not matter what the shape of the increase is when that was the key difference being described? All deaths from all diseases can only increase over time unless you believe in reincarnation or zombies.

BoE

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Re: Coronavirus - modelling aspects only please

#311497

Postby XFool » May 23rd, 2020, 4:42 pm

Bubblesofearth wrote:Rubbish. It is crystal clear that the point being made was that the difference was that deaths from the virus would increase broadly exponentially rather than in the steady manner for the other diseases mentioned. How can it not matter what the shape of the increase is when that was the key difference being described?

If you say so...

Bubblesofearth wrote:All deaths from all diseases can only increase over time unless you believe in reincarnation or zombies.

Really? So how's smallpox doing? Wither The Black Death? Yeah... But that's not what you mean is it?

You see, I think this may be where we have a problem. But, to go further would be to go seriously OT for this thread and even risk possible banishment to PD! :shock:

So I think I'll leave it there.

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Re: Coronavirus - modelling aspects only please

#311532

Postby Bubblesofearth » May 23rd, 2020, 5:48 pm

XFool wrote:Really? So how's smallpox doing? Wither The Black Death? Yeah... But that's not what you mean is it?


1977 for smallpox. Still cases of Black Death most years in the US.

You see, I think this may be where we have a problem. But, to go further would be to go seriously OT for this thread and even risk possible banishment to PD! :shock:

So I think I'll leave it there.


Probably best.

BoE

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Re: Coronavirus - modelling aspects only please

#311557

Postby GrahamPlatt » May 23rd, 2020, 6:38 pm

dealtn wrote:
Itsallaguess wrote:... the above text regarding improved outcomes over time in UK hospitals does seem to suggest that the medical profession are generally getting better at simply coping and dealing with the virus for those people that end up in hospitals..



I can't dig into the text at the moment for some reason.

There are two things possibly going on here.

They have improved the treatment such that more are now surviving than were previously. Or, the outcome is the same but the length of time taken to die is longer.

I am hoping it is the former, but could be the latter. Does it say which?


Another explanation might simply be that with reduction in ICU occupancy, there’s now a better ratio of experienced staff cover/bed.

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Re: Coronavirus - modelling aspects only please

#311562

Postby dealtn » May 23rd, 2020, 6:49 pm

GrahamPlatt wrote:
dealtn wrote:
Itsallaguess wrote:... the above text regarding improved outcomes over time in UK hospitals does seem to suggest that the medical profession are generally getting better at simply coping and dealing with the virus for those people that end up in hospitals..



I can't dig into the text at the moment for some reason.

There are two things possibly going on here.

They have improved the treatment such that more are now surviving than were previously. Or, the outcome is the same but the length of time taken to die is longer.

I am hoping it is the former, but could be the latter. Does it say which?


Another explanation might simply be that with reduction in ICU occupancy, there’s now a better ratio of experienced staff cover/bed.


But that's just another version of 1.

What I'm really asking is do we know if it is fewer dying (more surviving), or a lengthening in the time to die. Both you could argue are good, but the former better, surely?

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Re: Coronavirus - modelling aspects only please

#311563

Postby stockton » May 23rd, 2020, 6:52 pm

As I understand things, at the beginning of the outbreak people were simply being given the wrong treatment - ventilators; they are now being given blood thinners.
The strange thing is that we still do not have an honest assessment of the value of chloroquine.

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Re: Coronavirus - modelling aspects only please

#311583

Postby Mike4 » May 23rd, 2020, 7:44 pm

stockton wrote:The strange thing is that we still do not have an honest assessment of the value of chloroquine.


My theory on this is the same issue is affecting HXQ as happened with PPE. There is not enough of it in the world, so rather than fess up and say yes it would be great to give it to everyone but we don't have enough, the authorities come up with specious reasons not to use it.

HXQ is massively valuable for malaria, lupus and a few other things. Imagine what would happen to supplies and malaria infection rates if 2bn people in the world suddenly realised it was perfect for preventing C-19 too.

So a massive campaign to deny the effectiveness of the stuff and play down the mass of empirical evidence that it works is wheeled out. As Dr Chris Martensen keeps asking on youtube, how come billions of doses of it have been used so far for malaria but there have been NO DEATHS attributed to it? Not one single fatality so far that he can discover. Can anyone here cite a fatality known to have been caused by HXQ?

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Re: Coronavirus - modelling aspects only please

#311595

Postby dealtn » May 23rd, 2020, 8:20 pm

Mike4 wrote: Can anyone here cite a fatality known to have been caused by HXQ?


Isn't that what the Lancet study suggests?

https://www.bbc.co.uk/news/world-52779309

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Re: Coronavirus - modelling aspects only please

#311603

Postby Mike4 » May 23rd, 2020, 8:38 pm

dealtn wrote:
Mike4 wrote: Can anyone here cite a fatality known to have been caused by HXQ?


Isn't that what the Lancet study suggests?

https://www.bbc.co.uk/news/world-52779309


No.

For a start they are only looking at hospitalised cases, by which time it's too late to be administering HXQ. It needs giving early when symptoms first appear, not as a last gasp attempt to save a dying patient. Secondly, there is no mention of zinc being given at the same time, without which we know it's effectiveness is compromised.

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Re: Coronavirus - modelling aspects only please

#311604

Postby dealtn » May 23rd, 2020, 8:42 pm

Mike4 wrote:
dealtn wrote:
Mike4 wrote: Can anyone here cite a fatality known to have been caused by HXQ?


Isn't that what the Lancet study suggests?

https://www.bbc.co.uk/news/world-52779309


No.

For a start they are only looking at hospitalised cases, by which time it's too late to be administering HXQ. It needs giving early when symptoms first appear, not as a last gasp attempt to save a dying patient. Secondly, there is no mention of zinc being given at the same time, without which we know it's effectiveness is compromised.


So why do twice as many die as the control? I thought you asked whether there were fatalities, not whether it worked if given earlier and/or with zinc.

I only tried to answer the question you asked.

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Re: Coronavirus - modelling aspects only please

#311612

Postby Mike4 » May 23rd, 2020, 9:18 pm

dealtn wrote:
Mike4 wrote:
dealtn wrote:
Isn't that what the Lancet study suggests?

https://www.bbc.co.uk/news/world-52779309


No.

For a start they are only looking at hospitalised cases, by which time it's too late to be administering HXQ. It needs giving early when symptoms first appear, not as a last gasp attempt to save a dying patient. Secondly, there is no mention of zinc being given at the same time, without which we know it's effectiveness is compromised.


So why do twice as many die as the control? I thought you asked whether there were fatalities, not whether it worked if given earlier and/or with zinc.

I only tried to answer the question you asked.


I asked if anyone could cite a fatality attributed to HXQ. You haven't cited one, have you? Just put forward some circumstantial evidence suggesting it happens, no actual case(s) cited. You haven't even found one attributed to HXQ being taken for malaria, and there have been billions of doses taken!

The Lancet study is a collection of observational studies as I understand it, not a 'gold standard' placebo controlled double blind trial. Observational studies are helpful but have massive limitstions. Selection of the cohort to study is one major failing. How were the subjects to study selected by the Lancet? For a start, only people ill enough to arrive in hospital, probably. HXQ is most effective when used as a prophylactic or when first infected. There is an Indian study of 10,000 police who were offered HXQ as a prophylactic. Approx half elected to take it, and half declined. Nine deaths from C-19 recorded so far in the cohort declining it, and none in the cohort taking it. why did the Lancet study choose not to look at that I wonder.

We are still waiting for a placebo-controlled double-blind trial to nail this either way, once and for all. Until we get that, all these anecdotal studies are worth Jack.

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Re: Coronavirus - modelling aspects only please

#312355

Postby zico » May 26th, 2020, 2:58 pm

England & Wales ONS coronavirus update for week 20 deaths (w/e 15th May) has just been published.

There's a slight uptick in excess deaths, but this is almost certainly due to VE day bank holiday in previous week, which meant that deaths were under-reported then. Latest week's data confirms we are clearly past the first peak of the epidemic.

53,960 excess deaths since coronavirus deaths first counted in UK compared to 5-year average.
24,000 of these excess deaths have occurred in care homes.

https://www.ons.gov.uk/peoplepopulation ... g15may2020


This link shows, for England only, the comparison between government's published daily deaths, and actual daily deaths.
30,753 deaths on Government daily figures for 15th May.
40,096 deaths occurring by 15th May (registered by 23rd May)

We'd thought on this board that after the peak was passed, the daily figures might be overstating the true deaths, because daily figures include deaths from previous days. It seems clear now the main effect is due to the delay in reporting deaths, so the daily published figure consistently under-reports.


https://www.ons.gov.uk/peoplepopulation ... les/latest

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Re: Coronavirus - modelling aspects only please

#312366

Postby zico » May 26th, 2020, 3:23 pm

Interesting link here to deaths per million head of population, which I've summarised in a rough table below.

https://www.statista.com/statistics/110 ... habitants/

Obviously there are difficulties in comparing countries, such as
- different stages of the epidemic
- different definition of Covid-19 deaths
- countries with more international airport hub links.
- countries where virus hasn't spread to all parts.
- poor reporting in some countries (particularly 3rd world countries)

I've removed countries where I think the statistics are probably very unreliable and patchy.

But even so, some very very significant differences between developed nations.
I've put gaps in the table below, just to show the break points, where there are different groups of countries - e.g. Spain/UK/Italy grouped together and 500-600 deaths/mill, then France/Sweden together around 400, before Netherlands/Ireland at 330.
I've highlighted countries of interest - e.g. UK, Sweden, USA, Brazil, Iran.

A few thoughts.
Belgium has clearly suffered incredibly badly, with 60% more deaths per million than the second country, Spain.
UK deaths/million similar to Spain & Italy, though at an earlier stage in pandemic, so likely to be worse after first wave has passed.
Sweden's "social distancing" policy has done surprisingly well if you compare it to Spain/Italy/UK/France/Netherlands/Ireland.
However, if you compare Sweden (395) to Germany (100)/Denmark(97)/Norway (44)/Finland (55) - it's done very badly.

Amongst the big 5 European countries of UK/Spain/Italy/France/Germany it's very clear that Germany has only 25% of deaths/million of comparable "big" countries, and so have managed the epidemic far more successfully.

Some spectacularly low deaths/million for the countries that have handled coronavirus best. Bulgaria (18), Greece (16), Latvia (11), Japan (7), Slovakia (5), New Zealand (5), Australia (4).

With the glaring exception of Belgium, small European countries have done far better than larger ones. This may well be because larger European countries have far more major international airport hubs, so smaller countries had more time to act.


Of course, if coronavirus inevitably spreads through an entire population, then the countries that look best in the table below have simply delayed their deaths until later rather than "taking it on the chin". However, in many countries, the deaths look so low that it seems reasonable to assume they can contain the virus while returning to close-to-normal-life, thereby minimising deaths, and also minimising harm to their economies.


Table below shows
Deaths - Population in millions - Covid deaths per million

Belgium 9,312 11.42 815.26


Spain 26,834 46.72 574.31
UK 36,914 66.49 555.19
Italy 32,877 60.43 544.04

France 28,421 66.99 424.27
Sweden 4,029 10.18 395.65



Netherlands 5,830 17.23 338.34
Ireland 1,606 4.85 330.89

USA 98,081 327.17 299.79

Switzerland 1,913 8.52 224.62
Canada 6,655 37.06 179.58



Portugal 1,330 10.28 129.36
Peru 3,629 31.99 113.44
Brazil 23,473 209.47 112.06
Germany 8,309 82.93 100.2
Denmark 563 5.8 97.11
Iran 7,451 81.8 91.09



Moldova 261 3.55 73.61
Austria 641 8.85 72.45


Romania 1,207 19.47 61.98
Finland 308 5.52 55.82
North Macedonia 113 2.08 54.25
Turkey 4,369 82.32 53.07
Slovenia 107 2.07 51.76
Hungary 499 9.77 51.08
Estonia 65 1.32 49.21


Norway 235 5.31 44.22
Bosnia and Herzegovina 146 3.32 43.92
Dominican Republic 460 10.63 43.29
Chile 761 18.73 40.63
Puerto Rico 129 3.2 40.37
Kuwait 165 4.14 39.88


Serbia 239 6.98 34.23
Israel 281 8.88 31.63
Armenia 91 2.95 30.83
Czechia 317 10.63 29.83


Poland 1,007 37.98 26.51
United Arab Emirates 248 9.63 25.75
Russia 3,633 144.48 25.15
Croatia 100 4.09 24.45
Lithuania 63 2.79 22.58
Belarus 204 9.49 21.51


Bulgaria 130 7.02 18.51
Kosovo 30 1.85 16.26
Greece 172 10.73 16.03

Latvia 22 1.93 11.42

Japan 830 126.53 6.56

Slovakia 28 5.45 5.14

New Zealand 21 4.89 4.3

Australia 102 24.99 4.08


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