The R(0) number

DevilsHaircut

amandstu wrote: »

Are we getting confused between a "natural"R(0)number and a mitigated one?

Exactly, R(0) = unmitigated spread (no measures) in naive (never infected) population.


It is very high in Ireland - between 4 and 5 according to Tony Holohan/Philip Nolan.

bb1234567

Roselyn Nutritious Dwarf wrote: »

Would it be safe to assume the R number might increase for Dublin next week, after 1,000+ covidiots today spent more than 15mins together, in close proximity, on a walkabout with a majority not even wearing facemasks properly?

It just increases the likelihood. Given how few cases there are nationwide it is actually very likely that there were anyone with COVID at the march. But cases will increase as social distancing is not being adhered to nationwide and there are young people have parties and meet ups in groups of dozens , big groups at beaches and parks, etc. That will have more of an impact than the march

4068ac1elhodqr

bb1234567 wrote: »

It just increases the likelihood. Given how few cases there are nationwide it is actually very likely that there were anyone with COVID at the march. But cases will increase as social distancing is not being adhered to nationwide and there are young people have parties and meet ups in groups of dozens , big groups at beaches and parks, etc. That will have more of an impact than the march

Problem is, this silly feckless march will now lead to more (very small in comparision) sized groups seeking to meet up and seek premature normalisation, all while still being under Phase 1.

You can't have one rule for some, and another rule for others.

Btw, more of these large crowds (walking/standing in close proximity for longer than 15mins, shouting, and mostly without masks...) Will be occuring again this Saturday in multiple locations.

No one in authority (outside of health professionals) has spoken out against the previous one, or plans for next ones, thus suggests the lockdown is suddenly over for everyone.
May as well book the Coronas to play at Croke Park, if there's thousands out again on Saturday for their teenage insta-likes again.

amandstu

DevilsHaircut wrote: »

Exactly, R(0) = unmitigated spread (no measures) in naive (never infected) population.


It is very high in Ireland - between 4 and 5 according to Tony Holohan/Philip Nolan.

Is there much difference in this R(0) rate across different countries then?


From the way you put it ,the R(0) in, say Italy or Iran might be fairly different from that in Ireland.

As it is presumably the same virus it seems that there may be different types of populations in different regions of the globe.

amandstu

amandstu wrote: »

Is there much difference in this R(0) rate across different countries then?


From the way you put it ,the R(0) in, say Italy or Iran might be fairly different from that in Ireland.

As it is presumably the same virus it seems that there may be different types of populations in different regions of the globe.

The R(0) should be similar for most populations if we behave in the same manner. In reality, different societies have different norms in terms of social contact and etiquette therefore real rates will vary. The R(0) of 4-5 for Ireland in early March is likely an overestimate however. We do not know how many cases arrived into the country late feb and into March, therefore do not know the seed rate. Big difference in R(0) if it spread from 100 or 200 seed cases

downcow

[Deleted User] wrote: »

The R(0) should be similar for most populations if we behave in the same manner. In reality, different societies have different norms in terms of social contact and etiquette therefore real rates will vary. The R(0) of 4-5 for Ireland in early March is likely an overestimate however. We do not know how many cases arrived into the country late feb and into March, therefore do not know the seed rate. Big difference in R(0) if it spread from 100 or 200 seed cases

I am sorry to keep harping on about this, but there is continuing use of the R number here and on media as if someone somewhere has a rational understanding on how it is calculated. I have yet to hear a clear explanation or calculation. Why is it a secret or mystery?

yosemitesam1

downcow wrote: »

I am sorry to keep harping on about this, but there is continuing use of the R number here and on media as if someone somewhere has a rational understanding on how it is calculated. I have yet to hear a clear explanation or calculation. Why is it a secret or mystery?

It's pure guesswork based on incomplete data that is not representative of the population as a whole and as a result is never going to be accurate no matter how many different ways they try to model it.
Estimating the r0 isn't a decision making tool for active use during a pandemic, it's a theoretical observation that can be used to try and compare different diseases outside of an outbreak

quokula

downcow wrote: »

I am sorry to keep harping on about this, but there is continuing use of the R number here and on media as if someone somewhere has a rational understanding on how it is calculated. I have yet to hear a clear explanation or calculation. Why is it a secret or mystery?

Here's a document on calculating R0

https://bmcmedinformdecismak.biomedcentral.com/articles/10.1186/1472-6947-12-147

And here's a critique of the UK government's calculation early in the pandemic, with some of the maths behind their calculation of R0

https://www.medrxiv.org/content/10.1101/2020.04.07.20052340v1.full.pdf

It's not a secret or mystery, nor is it pure guesswork. It's just the result of a lot of painstaking mathematical modelling that can't be turned into an easy quote for someone to put in a news report. Good luck turning this into a headline:

linearity of log(deaths) is clear in the range 16 – 31 March. A linear fit has Adjusted R2 = 0.992, and the coefficient of growth r = 0.224 with s.e. = 0.005. Adaptive M-H sampling passed the Raftery, Geweke, and Heidelberger tests for convergence. Posterior estimates of the transmission parameters, scaled by population N = 66 million, are b1*N = 0.735 with 90% credible interval (0.576, 0.826) whilst b2*N = 1.112 (0.055 , 3.335) and b3*N = 1.015 (0.052 , 3.071). R0 is estimated as 5.81 with 90%CI (5.08 , 6.98).

You've got a lot of data points, such as how many people test positive each day, how many people enter and leave hospital, the level of testing coverage, the number of contacts found per case in contact tracing.

You've got also got a lot of data missing, like how many people have it that haven't been tested, or haven't shown symptoms yet but will. You may also have different characteristics in different settings like spread in hospitals vs in the community.

From this, data scientists can make a best estimate of the R value. Because the data is incomplete they usually have a range that they have a high confidence in, that's why you often hear figures like "0.7 - 0.9" which is as precise as they can get.

downcow

quokula wrote: »

Here's a document on calculating R0

https://bmcmedinformdecismak.biomedcentral.com/articles/10.1186/1472-6947-12-147

And here's a critique of the UK government's calculation early in the pandemic, with some of the maths behind their calculation of R0

https://www.medrxiv.org/content/10.1101/2020.04.07.20052340v1.full.pdf

It's not a secret or mystery, nor is it pure guesswork. It's just the result of a lot of painstaking mathematical modelling that can't be turned into an easy quote for someone to put in a news report. Good luck turning this into a headline:



You've got a lot of data points, such as how many people test positive each day, how many people enter and leave hospital, the level of testing coverage, the number of contacts found per case in contact tracing.

You've got also got a lot of data missing, like how many people have it that haven't been tested, or haven't shown symptoms yet but will. You may also have different characteristics in different settings like spread in hospitals vs in the community.

From this, data scientists can make a best estimate of the R value. Because the data is incomplete they usually have a range that they have a high confidence in, that's why you often hear figures like "0.7 - 0.9" which is as precise as they can get.

Thanks for all the info, but I am afraid I still think it is a total nonsense.
Without even getting into all the crazy stats outlined in those articles, not to mention the very important stats not available, to suggest an R number for the community, and not break it down for different settings makes zero sense.
I don't know about ROI but in Northern Ireland it was revealed the other day that over 50% of the covid deaths took place within the care home population.
The care home population in Northern Ireland makes up 1.2% of the general population.
So we have a situation where 50% of the deaths will occur within 1.2% of the population and the authorities want to ignore that and roll this figure over everyone. I don't have the stats for the percentage of deaths which took place within the hospital environment but I think it will also be fairly stark.

I know a few people who have had Covid and I do not know one single person for whom it did not emanate from a care home or hospital. I have even had it myself brought home by my wife who is a nurse.

It is a farcical situation for governments to quote general community R number in these circumstances.
We have a situation where the real R number (whatever that is) amongst school age children, is to all intent and purpose, zero, and yet their return to contact is being governed by what is happening in care homes.

millb

downcow wrote: »

Thanks for all the info, but I am afraid I still think it is a total nonsense.
Without even getting into all the crazy stats outlined in those articles, not to mention the very important stats not available, to suggest an R number for the community, and not break it down for different settings makes zero sense.
I don't know about ROI but in Northern Ireland it was revealed the other day that over 50% of the covid deaths took place within the care home population.
The care home population in Northern Ireland makes up 1.2% of the general population.
So we have a situation where 50% of the deaths will occur within 1.2% of the population and the authorities want to ignore that and roll this figure over everyone. I don't have the stats for the percentage of deaths which took place within the hospital environment but I think it will also be fairly stark.

I know a few people who have had Covid and I do not know one single person for whom it did not emanate from a care home or hospital. I have even had it myself brought home by my wife who is a nurse.

It is a farcical situation for governments to quote general community R number in these circumstances.
We have a situation where the real R number (whatever that is) amongst school age children, is to all intent and purpose, zero, and yet their return to contact is being governed by what is happening in care homes.

Good point I think folks need to find out the following for the daily new cases:

# from an existing Healthcare or Care-Home Cluster
# from an existing Factory / Retail / Site (nonHelath care centre) cluster
# from a residential / DP or similar setting
# from close family
# from random community transfer (inc unknown)
# from recently arrived persons

these last 2 sources are the real concerns and testing should be focused there..

The real R(0) is the average number of people that those who currently have the virus go on to infect. As simple as that, no magic, voodoo, woo, or anything else. The trouble is, it is impossible to accurately get all the information required to feed into that simple calculation. That's why epidemiologists employ mathematical models to take the information we do know to give an estimate of the R(0), but this will only ever be as good as the data fed into the model.

downcow

Deleted User wrote: »

The real R(0) is the average number of people that those who currently have the virus go on to infect. As simple as that, no magic, voodoo, woo, or anything else. The trouble is, it is impossible to accurately get all the information required to feed into that simple calculation. That's why epidemiologists employ mathematical models to take the information we do know to give an estimate of the R(0), but this will only ever be as good as the data fed into the model.

Agreed.
That leaves us with two possibilities
1)it is a number that does not change an has no relationship to lockdown, behaviour, etc
or
2)It is affected by above and therefore is dramatically different in different settings eh care homes and young people partying on a beach. If this is the case then we deserve to be told. Young people need need people speaking out for them. They are clearly very little at risk from covid but are highly at risk from emotional and mental health.
we need to get real and honest about this as a society

millb

Deleted User wrote: »

The real R(0) is the average number of people that those who currently have the virus go on to infect. As simple as that, no magic, voodoo, woo, or anything else. The trouble is, it is impossible to accurately get all the information required to feed into that simple calculation. That's why epidemiologists employ mathematical models to take the information we do know to give an estimate of the R(0), but this will only ever be as good as the data fed into the model.

The reality is that by good contact tracing & testing you can estimate many R(0) or R(e) values for specific populations / cohorts. Especially at this stage, one of these model operators could give R values (samples or ranges) for say a "meat factory" or "nursing home" in April or May. But that would be too much information to share with the stupid public / media / non-experts etc etc

millb

millb wrote: »

The reality is that by good contact tracing & testing you can estimate many R(0) or R(e) values for specific populations / cohorts. Especially at this stage, one of these model operators could give R values (samples or ranges) for say a "meat factory" or "nursing home" in April or May. But that would be too much information to share with the stupid public / media / non-experts etc etc

If R was done for the general public who have isolated now it will be 0 or thereabouts.

ShineOn7

Numbers, and therefore the R0, seriously on the rise again in Arizona

That's now Arizona, Singapore, Dubai and elsewhere where the numbers rose again sharply when things re-opened. And yet many Irish want the phases rushed up

We should learn from the mistakes of other countries and American states. Not repeat them

https://news.yahoo.com/arizona-calls-emergency-plan-covid-010249888.html?guccounter=1&guce_referrer=aHR0cHM6Ly93d3cuYm9hcmRzLmllL3ZidWxsZXRpbi9zaG93dGhyZWFkLnBocD9wPTExMzY5MTU5Ng&guce_referrer_sig=AQAAAK3J2EZavb74LE5HFVoCX8k9W7f0xX7dkpdkcPrOF9SafrJMjhTjC5xMLmwddW4-Te9mHgjaxXGIBMLH6rVrJ-J5BToTDQCFJbMx0WDdEOGQDNcjW3PEMeRr2zk0k08kuuIgy5aMpPCgp2tSzBLADjefwZg12mWyzPne8hYGojyZ

Arizona again told hospitals to activate the coronavirus emergency plans after cases spiked following reopening, turning it into a U.S. virus hotspot along with neighboring Southwest states.

The state's stay-at-home order ended on May 15, and its cases have increased 115 percent since then, leading a former state health chief to warn Arizona may need new social distancing measures or field hospitals.
State health director Cara Christ on Saturday told hospitals to "fully activate" emergency plans - a message she last sent on March 25 - after Arizona's largest medical network Banner Health warned it was reaching its capacity in intensive care unit beds.


"Since May 15, ventilated COVID-19 patients have quadrupled," Banner Health tweeted on Monday, adding it had hit capacity for some patients needing cardiac and respiratory care.


The alert came after Arizona, New Mexico and Utah each posted rises of 40% or higher in new cases for the week ended June 7 compared with the prior seven days, joining hotpots in the South like Florida and Arkansas, according to a Reuters analysis.

micks_address

In terms of the US you'd probably need to think about each state being a country. I don't think they peaked at all outside of new york.

ShineOn7 wrote: »

Numbers, and therefore the R0, seriously on the rise again in Arizona

That's now Arizona, Singapore, Dubai and elsewhere where the numbers rose again sharply when things re-opened. And yet many Irish want the phases rushed up

We should learn from the mistakes of other countries and American states. Not repeat them

https://news.yahoo.com/arizona-calls-emergency-plan-covid-010249888.html?guccounter=1&guce_referrer=aHR0cHM6Ly93d3cuYm9hcmRzLmllL3ZidWxsZXRpbi9zaG93dGhyZWFkLnBocD9wPTExMzY5MTU5Ng&guce_referrer_sig=AQAAAK3J2EZavb74LE5HFVoCX8k9W7f0xX7dkpdkcPrOF9SafrJMjhTjC5xMLmwddW4-Te9mHgjaxXGIBMLH6rVrJ-J5BToTDQCFJbMx0WDdEOGQDNcjW3PEMeRr2zk0k08kuuIgy5aMpPCgp2tSzBLADjefwZg12mWyzPne8hYGojyZ

Hmmzis

ShineOn7 wrote: »

Numbers, and therefore the R0, seriously on the rise again in Arizona

That's now Arizona, Singapore, Dubai and elsewhere where the numbers rose again sharply when things re-opened. And yet many Irish want the phases rushed up

We should learn from the mistakes of other countries and American states. Not repeat them

https://news.yahoo.com/arizona-calls-emergency-plan-covid-010249888.html?guccounter=1&guce_referrer=aHR0cHM6Ly93d3cuYm9hcmRzLmllL3ZidWxsZXRpbi9zaG93dGhyZWFkLnBocD9wPTExMzY5MTU5Ng&guce_referrer_sig=AQAAAK3J2EZavb74LE5HFVoCX8k9W7f0xX7dkpdkcPrOF9SafrJMjhTjC5xMLmwddW4-Te9mHgjaxXGIBMLH6rVrJ-J5BToTDQCFJbMx0WDdEOGQDNcjW3PEMeRr2zk0k08kuuIgy5aMpPCgp2tSzBLADjefwZg12mWyzPne8hYGojyZ

While bad news for the people getting sick, it's good news for vaccine developers, they now have a prime ground for their phase III trials.

JP Liz V1

It is still low here yes?

ShineOn7

JP Liz V1 wrote: »

It is still low here yes?

It's estimated to be 0.4 to 0.8

Anything below 1 = good

Anything above 1 - bad

micks_address

ShineOn7 wrote: »

It's estimated to be 0.4 to 0.8

Anything below 1 = good

Anything above 1 - bad

When do we stop having new cases?

ShineOn7

micks_address wrote: »

When do we stop having new cases?

That I don't know, but some researchers believe it's getting weaker. I mean, it's a virus, it has to weaken eventually


This thread may interest you

downcow

ShineOn7 wrote: »

That I don't know, but some researchers believe it's getting weaker. I mean, it's a virus, it has to weaken eventually


This thread may interest you

I continue to be a bit bamboozled by the approach to Covid.

We had one covid death reported Thursday - first for four days I think.
I know the situation intimately and I just do not get.

This was a 91 year old woman who was admitted to hospital terminally ill and in the very final stages (days) of cancer. She had not had a bowel movement in almost 4 weeks. All tests for covid were negative, but after examination she was described as 'clinically Covid' - a term used when they think a person has symptoms but are continuing to test negative.

This woman inevitably died and became the latest 'Covid death' in Northern Ireland.

I just can't see the point in the statistics any more? And where do things like the cancer stats sit now?

And this is certainly not an unusual story, from my experience this is the norm.

yosemitesam1

downcow wrote: »

I continue to be a bit bamboozled by the approach to Covid.

We had one covid death reported Thursday - first for four days I think.
I know the situation intimately and I just do not get.

This was a 91 year old woman who was admitted to hospital terminally ill and in the very final stages (days) of cancer. She had not had a bowel movement in almost 4 weeks. All tests for covid were negative, but after examination she was described as 'clinically Covid' - a term used when they think a person has symptoms but are continuing to test negative.

This woman inevitably died and became the latest 'Covid death' in Northern Ireland.

I just can't see the point in the statistics any more? And where do things like the cancer stats sit now?

And this is certainly not an unusual story, from my experience this is the norm.

The average age of covid deaths is also very similar to average life expectancy.

downcow

yosemitesam1 wrote: »

The average age of covid deaths is also very similar to average life expectancy.

interesting point, i hadn't considered

downcow

yosemitesam1 wrote: »

The average age of covid deaths is also very similar to average life expectancy.

Very interesting stat, would you have a link?

yosemitesam1

downcow wrote: »

Very interesting stat, would you have a link?

https://www.gov.ie/en/publication/72d92-updates-on-covid-19-coronavirus-from-april-june-2020/#june

5th of may, over 1,300 deaths average age 82, median 84
I think average life expectancy is 82ish

FishOnABike

ShineOn7 wrote: »

That I don't know, but some researchers believe it's getting weaker. I mean, it's a virus, it has to weaken eventually


This thread may interest you

Why does it have to weaken? Has a virus like measles gotten any weaker in the last thousand years or so?

ShineOn7

FishOnABike wrote: »

Why does it have to weaken? Has a virus like measles gotten any weaker in the last thousand years or so?

You're comparing a worldwide pandemic to ... the Measles?

When did the Measles last cause a global economic shutdown?

Hmmzis

FishOnABike wrote: »

Why does it have to weaken? Has a virus like measles gotten any weaker in the last thousand years or so?

Sure has:

https://www.sciencedirect.com/topics/immunology-and-microbiology/morbillivirus

In part by attenuating the hosts as well.

FishOnABike

Hmmzis wrote: »

Sure has:

https://www.sciencedirect.com/topics/immunology-and-microbiology/morbillivirus

In part by attenuating the hosts as well.

Can you highlight / quote / reference where in the ten or so articles from your link it shows that a virus has to weaken? It's a bit like looking for a, possibly non-existant, needle in a haystack.