Data, Stats Thread June 11

[PatriciaHolm]

UK govt pressers Slides & data

www.gov.uk/government/collections/slides-and-datasets-to-accompany-coronavirus-press-conferences#history

Data Dashboard coronavirus.data.gov.uk/
Covid 19 Genomics www.cogconsortium.uk/tools-analysis/public-data-analysis-2/
Covid 19 Variant Mapping Sanger Institute covid19.sanger.ac.uk/lineages/raw
NHS Vaccination data www.england.nhs.uk/statistics/statistical-work-areas/covid-19-vaccinations/
Global vaccination data ourworldindata.org/covid-vaccinations
R estimates UK & English regions www.gov.uk/guidance/the-r-number-in-the-uk
Imperial UK weekly LAs, cases / 100k, table, map, hotspots statistics imperialcollegelondon.github.io/covid19local/#map
NHS England Hospital activity www.england.nhs.uk/statistics/statistical-work-areas/covid-19-hospital-activity/
NHs England Daily deaths www.england.nhs.uk/statistics/statistical-work-areas/covid-19-daily-deaths/
Cases Tracker England Local Government lginform.local.gov.uk/reports/view/lga-research/covid-19-case-tracker
ONS MSAO Map English deaths www.england.nhs.uk/statistics/statistical-work-areas/covid-19-daily-deaths/
CovidMessenger live update by council area in England www.covidmessenger.com/
Scot gov Daily data www.gov.scot/publications/coronavirus-covid-19-daily-data-for-scotland/
Scotland TravellingTabby LAs, care homes, hospitals, tests, t&t www.travellingtabby.com/scotland-coronavirus-tracker/
PH Wales LAs, cases, tests, deaths Dashboard public.tableau.com/profile/public.health.wales.health.protection#!/vizhome/RapidCOVID-19virology-Public/Headlinesummary
ICNRC Intensive Care National Audit & Research reports www.icnarc.org/Our-Audit/Audits/Cmp/Reports
NHS t&t England & UK testing Weekly stats www.gov.uk/government/collections/nhs-test-and-trace-statistics-england-weekly-reports
PHE Surveillance reports & LA Local Watchlist Maps by LSOA (from last summer) www.gov.uk/government/collections/nhs-test-and-trace-statistics-england-weekly-reports
ONS England infection surveillance report each Friday www.ons.gov.uk/peoplepopulationandcommunity/healthandsocialcare/conditionsanddiseases/bulletins/coronaviruscovid19infectionsurveypilot/previousReleases
Datasets for ONS surveillance reports www.ons.gov.uk/peoplepopulationandcommunity/healthandsocialcare/conditionsanddiseases/datasets/coronaviruscovid19infectionsurveydata/2020
ONS Roundup deaths, infections & economic reports www.ons.gov.uk/peoplepopulationandcommunity/healthandsocialcare/conditionsanddiseases/articles/coronaviruscovid19roundup/2020-03-26
Zoe UK data covid.joinzoe.com/data#interactive-map
ECDC (European Centre for Disease Control rolling 14-day incidence EEA & UK www.ecdc.europa.eu/en/cases-2019-ncov-eueea
Worldometer UK page www.worldometers.info/coronavirus/country/uk/
Our World in Data GB test positivity etc, DIY country graphs ourworldindata.org/coronavirus/country/united-kingdom?country=~GBR
FT DIY graphs compare deaths, cases, raw / million pop ig.ft.com/coronavirus-chart/?areas=eur&areas=usa&areas=bra&areas=gbr&areas=cze&areas=hun&areasRegional=usny&areasRegional=usnj&areasRegional=usaz&areasRegional=usca&areasRegional=usnd&areasRegional=ussd&cumulative=0&logScale=0&per100K=1&startDate=2020-09-01&values=deaths
PHE local health data fingertips.phe.org.uk/profile/health-profiles
Alama Personal COVID risk assessment alama.org.uk/covid-19-medical-risk-assessment/
Local Mobility Reports for countries www.google.com/covid19/mobility/
UK Highstreet Tracker for cities & large towns Footfall, spend index, workers, visitors, economic recovery www.centreforcities.org/data/high-streets-recovery-tracker/

⏭ Our STUDIES Corner ⏮ www.mumsnet.com/Talk/coronavirus/3869571-Studies-corner?msgid=99913434

We welcome factual, data driven and analytical contributions
Please try to keep discussion focused on these

more than a year? Where did that claim come from? I find no mention of it in the SE report

There's loads of papers on it, see e.g. a review with this conclusion

"the conservative estimate of the net increase in life expectancy with physical activity is about 2–4 years but presumably even greater because of the positive influence of physical activity on major risk factors for mortality."
www.hindawi.com/journals/jar/2012/243958/

I don't think it's controversial to suggest moving people to inactive has caused a reduction in QALYs - inactivity is very pronounced in vulnerable populations too (which is why shielding was such a disaster for this)

As you say, it's reversible, as is the weight gain you mention, however we also know from many studies that people do not lose the weight, or get more active in even the majority of cases.

And remember I am not saying this is an argument for no restrictions - I'm suggesting that restrictions that enable dozens of people in a pub should not be prioritised over say parkrun. And mostly I'm arguing that Whitty needs to update his actual guidance on exercise that he's neglected for the entire covid era - and has pretended that the restrictions are harmless in health terms.

@wintertravel1980

Firstly, they aren't averages!

I was referring to the "blended"/"average" efficacy estimates produced by James Ward (80%/95% across Pfizer and AZ), not the central points in the PHE modelled results.

The reality is it was possible to come up with a pretty good model for vaccine effectiveness without having all the data inputs. Some information (e.g .vaccination profile of the UK population and pre-vaccine CFR by age group) is much more important than other (e.g. exact age distribution of Delta cases).

James Ward's analysis produced numbers that ended up very close to the PHE results.

I am aware the confidence intervals are quite wide but they will narrow as we have more data. In the mean time, most people (including scientists) will be using modelled central points/means as the best available proxies.

In the mean time, most people (including scientists) will be using modelled central points/means as the best available proxies.

Any person using a figure without factoring in the margin of error is not a good scientist!

If you look at the PHE release you'll see that when they quote the OR figures, they incorporate the error margins from the paper they were sourced from. Those margins of error are then incorporated into their final figures.

It's a common (rookie) mistake to simply look at central points - if that's what you do, any conclusions you attempt to draw are automatically invalid.

Secondly one of the values used to calculate the Vaccine efficacy was itself subject to margins of error - the protection against symptomatic disease determined in a separate paper.
Multiplying together two numbers each with a significant margin of error gives rise to these huge ranges in the final figure!
Yeah, that's where I felt they ran a bit of a con. I'd like them to have made their own assumptions using the case data they can see, instead of piling assumptions on assumptions. An actuary doesn't get away with saying "my assumptions have margin for error, so losses might be 10% to 50%, FINISHED". They run stochastic models and narrow the range.

@sirfredfredgeorge

more than a year? Where did that claim come from? I find no mention of it in the SE report

There's loads of papers on it, see e.g. a review with this conclusion

"the conservative estimate of the net increase in life expectancy with physical activity is about 2–4 years but presumably even greater because of the positive influence of physical activity on major risk factors for mortality."
www.hindawi.com/journals/jar/2012/243958/

I don't think it's controversial to suggest moving people to inactive has caused a reduction in QALYs - inactivity is very pronounced in vulnerable populations too (which is why shielding was such a disaster for this)

As you say, it's reversible, as is the weight gain you mention, however we also know from many studies that people do not lose the weight, or get more active in even the majority of cases.

And remember I am not saying this is an argument for no restrictions - I'm suggesting that restrictions that enable dozens of people in a pub should not be prioritised over say parkrun. And mostly I'm arguing that Whitty needs to update his actual guidance on exercise that he's neglected for the entire covid era - and has pretended that the restrictions are harmless in health terms.

But you basically made up the figure based on studies that suggest a physically active life is associated with a longer life expectancy?

Note - I agree with your general point, I'm just taking issue with presenting hard numbers when they're non-evidenced.

What is undeniable is that covid and how we chose to deal with it will have had LOTS of nefarious consequences beyond those caused directly by the virus and bad habits developed as a result of restrictions will certainly form part of this.

Completely agree on Parkrun btw - I think this is the consequences of safety measures becoming a box ticking exercise. The way in which covid-safe strategies are drawn up by businesses and organisations doesn't need to make sense - it just needs to tick all the boxes.

If you look at the PHE release you'll see that when they quote the OR figures, they incorporate the error margins from the paper they were sourced from.

As I have mentioned, yes, I am aware the confidence levels are wide. It does not change the fact that the mean estimates are the most pragmatic proxy to use until more detailed information becomes available.

Generally, I think it is pretty safe to assume that everyone in this thread has got some degree of familiarity with interpreting research and understanding means, odd ratios and confidence intervals. So why don't we focus interpreting on data and stats?

And - to clarify - there is a difference between blindly "using the numbers" and "using as a proxy".

In my line of work, we use a lot of proxies and "guestimates" for high level modelling. Later on, when we are able to refine our assumptions and calculations, the end result usually comes pretty close to the preliminary estimate. Unlike Covid, it is not the matter of life and death but it shows why back of the envelope calculations can be very useful.

"In the mean time, most people (including scientists) will be using modelled central points/means as the best available proxies.

Any person using a figure without factoring in the margin of error is not a good scientist!

If you look at the PHE release you'll see that when they quote the OR figures, they incorporate the error margins from the paper they were sourced from. Those margins of error are then incorporated into their final figures.

It's a common (rookie) mistake to simply look at central points - if that's what you do, any conclusions you attempt to draw are automatically invalid."

Isn't there a problem, though, that people in various media take hold of the figure that catches their attention and broadcast it widely without any of the caveats that a scientist would add? Then that figure gets into the mainstream and is quoted in any discussion, amplifying the 'common (rookie) mistake'. You see it all the time on Mumsnet that, no matter how often the inaccuracies are explained, the same old numbers are repeated again and again as if they were gospel and more and more people think they are.

Sorry, there must be a better word than 'gospel' - I've just been in a church WhatsApp discussion!

@MRex

no other boundary condition has changed Vaccine immunity quite literally grows daily.

& possibly also wanes daily in people jabbed in December or early January

I've seen a few people on mumsnet recently suggesting that people vaccinated in December/ January have waning immunity; what I haven't seen is any real life evidence of that, have you? There isn't even evidence of waning immunity from natural infection. www.scientificamerican.com/article/concerns-about-waning-covid-19-immunity-are-likely-overblown/

We'll need to wait and see, but it's been good news so far.

Don't have the link to hand but the ONS antibodies surveys have seemed to suggest a bit of a dip in antibodies in the age groups who were single jabbed and due their second. No sign as yet of them waning after two jabs

Scientist interviewed on R4 this morning (can’t remember who, sorry, but on SAGE) pointing out that there could still be 100s of deaths per day again even without proceeding to Step 4 yet.

@JanFebAnyMonth

Scientist interviewed on R4 this morning (can’t remember who, sorry, but on SAGE) pointing out that there could still be 100s of deaths per day again even without proceeding to Step 4 yet.

With hospitalisations set to eclipse those seen in the Second Wave, this was obvious.

And the government will do jack all until it is too late.

Leading scientists commenting on the data and models presented yesterday, ties in with what’s been said here I think:

www.sciencemediacentre.org/expert-reaction-to-modelling-papers-in-the-sage-documents-published-today/?fbclid=IwAR2MedqXwQCJMjX-oi6SIGavrTwm3RmLJtzteLGMHbyLKQV40kA09EFDWyI

I like this quote:

“I think it can be hard to understand how the modelling can suggest we may be facing a third wave of a comparable magnitude to previous waves, when so many people have been vaccinated. Surely, we would expect a smaller wave this time around because of vaccines?

The crucial difference is that wave 1 in April 2020, and wave 2 in January 2021, were both stopped short by lockdowns, which prevented either peak from reaching their full heights. For this third wave, we are returning to almost-normal behaviour, and the projections are showing what would happen if no further action was taken by policymakers to attenuate any resulting third wave. So these waves are reaching their full height rather than being cut short by any lockdowns.

Another important difference is the increase in transmissibility, lower efficacy of vaccination, and increase in severity for the Delta variant relative to previous variants.”

We really need to reintroduce some restrictions if we want to avoid another lockdown.

@NannyAndJohn

We really need to reintroduce some restrictions if we want to avoid another lockdown.

Very unlikely

I take it you didn't read the quote?

Just out of curiousity, NancyAndJohn, is there a specific reason why you have edited the last sentence from the quote?

Another important difference is the increase in transmissibility, lower efficacy of vaccines and (in some scenarios we prepared) increase in severity for the Delta variant relative to previous variants.

@NannyAndJohn

I take it you didn't read the quote?

We won’t re introduce restrictions. I know you’re very keen though.

And I doubt lockdown too. It talks about a wave. Too vague, that’s cases. How does it translate to hospitalisation figures?

Yes, @NannyAndJohn, that quote (from Dr Nick Davies, Assistant Professor of Mathematical Modelling, London School of Hygiene and Tropical Medicine), is a very basic point really.

@JanFebAnyMonth

Yes, *@NannyAndJohn*, that quote (from Dr Nick Davies, Assistant Professor of Mathematical Modelling, London School of Hygiene and Tropical Medicine), is a very basic point really.

Wouldn’t you like to know about how it converts to hospitalisation?

I can see how this thread will go same as the others. Shame, I appreciate its difference to rest of mn.

agree with you @MarshaBradyo, I ike this thread that provides good data and analysed by many PPs. If it turns into another "good news vs catastrophic news" thread then we'll lose a good source of info

I think the interesting thing about the third wave is that the number of cases required to get hospital admissions up to high levels is going to be very much higher than we've ever seen before - because they'll be mainly in the young, and because vaccines help reduce the severity of Covid. But I've seen very little discussion about how these high case rates will affect things - everyone seems entirely focused on hospital admissions, but case rates in schools that are 10 fold higher than present are going to lead to massive disruption for children and parents. Also in workplaces they'll be huge numbers off because they've been in contact with a Covid case, as even vaccinated people have to isolate for 10 days every time. And more social mixing will mean everyone has more contacts. By focusing only on hospital admissions and deaths I think we're failing to think about the impact these high case rates are going to have - staff shortages (including in the NHS), holidays cancelled, schools closed. There has been no talk about these and no changes planned for the 10 day isolations for all contacts. I'd like to at least see the projected case rates by age group that the modellers are expecting, and some analysis of what that'll mean for the education sector in particular.

@MarshaBradyo This is the Data and Stats thread. I gave a quote by someone who works with the government on Data and Stats.