Data, Stats and Daily Numbers started 5 December 2021

[JanglyBeads]

Welcome to the DATA thread.

Our preference is for actual, data driven and analytical contributions.
Please try to keep discussion focused on these

Our links below probably need a refresh ready for the festive season,. so all reasonable suggestions welcome.

UK govt press conferences slides & data www.gov.uk/government/collections/slides-and-datasets-to-accompany-coronavirus-press-conferences#history
PHE Variants of Concern Technical Briefings www.gov.uk/government/publications/investigation-of-novel-sars-cov-2-variant-variant-of-concern-20201201
PHE Vaccine efficacy www.gov.uk/government/publications/phe-monitoring-of-the-effectiveness-of-covid-19-vaccination
SAGE : Minutes and Models www.gov.uk/government/collections/scientific-evidence-supporting-the-government-response-to-coronavirus-covid-19
Data Dashboard coronavirus.data.gov.uk/ includes R estimates
PHE Weekly Flu & Covid Surveiilance Reports 2021-22 Season www.gov.uk/government/statistics/national-flu-and-covid-19-surveillance-reports-2021-to-2022-season
Dashboard Vaccine Map to MSOA level coronavirus.data.gov.uk/details/interactive-map/vaccinations
Covid 19 Genomics www.cogconsortium.uk/tools-analysis/public-data-analysis-2/
Sanger Genome Maps & Data covid19.sanger.ac.uk/lineages/raw
UCL Virus Watch ucl-virus-watch.net/
NHS Vaccination data www.england.nhs.uk/statistics/statistical-work-areas/covid-19-vaccinations/
Sewage www.gov.uk/government/publications/wastewater-testing-coverage-data-for-19-may-2021-emhp-programme/wastewater-testing-coverage-data-for-the-environmental-monitoring-for-health-protection-emhp-programme.
Sewage reports www.gov.uk/government/publications/monitoring-of-sars-cov-2-rna-in-england-wastewater-monthly-statistics-june-2021
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 MSOA Map English deaths www.england.nhs.uk/statistics/statistical-work-areas/covid-19-daily-deaths/

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/

With regards to NHS expanding data collection, when I looked at booking a PCR yesterday (I didn't need one, just looking at availability), I almost gave up as the number of pages of information they are now collecting has increased immensely. Off the top of my head, they now also ask vaccination status, one or two and boosted, and previous infection (I think), and lots of other random questions.

Oh I'm glad they are now asking about booster status. I filled in details after my PCR result came back on 14th and it was only asking one vax or 2.

I get that the info is useful but can absolutely see that anyone with eg, poor literacy or limited data, is going to give up before actually booking a test (or registering a test from walking into a test site).l

news.sky.com/story/covid-uk-latest-news-omicron-coronavirus-skynews-12469075

Shows Chris Whitty now very informative

I think that sums up the issues nicely @quartz
But do wonder why we don't question this notion of "NHS capacity" a bit more? If we now have a new virus around that means some people require hospital care when they catch it, we need to increase hospital capacity so that that can be provided, including plans to cope with fluctuations in numbers. It's now two years since covid appeared and at least 18 months since it should have been obvious that we couldn't eliminate it, so why is the government not being held to account a bit more around the "crisis" in the NHS which is not a crisis at all, but a lack of adaptation to a new set of circumstances. Masks, wfh, covid passports, ventilation, etc are none of them going to do more than slow things down a little bit, which doesn't fix the problem of inadequate NHS capacity.

Just what I was saying the other day Fire! Make covid-specific hospitals (funded by a tax which is waived for the vaccinated) (just kidding....)(...)

Tbf the NHS should already be a top top priority for govt but no-one is demanding it (well, obviously we are, but it's not translating into votes etc)

@Firefliess

I think that sums up the issues nicely *@quartz* But do wonder why we don't question this notion of "NHS capacity" a bit more? If we now have a new virus around that means some people require hospital care when they catch it, we need to increase hospital capacity so that that can be provided, including plans to cope with fluctuations in numbers. It's now two years since covid appeared and at least 18 months since it should have been obvious that we couldn't eliminate it, so why is the government not being held to account a bit more around the "crisis" in the NHS which is not a crisis at all, but a lack of adaptation to a new set of circumstances. Masks, wfh, covid passports, ventilation, etc are none of them going to do more than slow things down a little bit, which doesn't fix the problem of inadequate NHS capacity.

I agree but I think the biggest issue with NHS capacity is a lack of qualified staff (I think the nightingale hospitals highlighted that quite well).

Bottom line is that the NHS needs more drs/nurses/healthcare assistants etc. So we need to really be looking at how we encourage people to train for and enter those roles and, even more crucially, stay in those roles.

I think it would be very useful if the number of people in hospital could be expressed as a percentage of total capacity as well as raw numbers. 8k from a 180k capacity is a lot less concerning than 8k from a 80k capacity.

London Healthcare
to 2nd Dec 726 "admissions" 54 more patients in hospital.
to 9th Dec 883 "admissions" 80 more patients in hospital.
to 16th Dec 1127 "admissions" 297 more paitents in hospital.

There's certainly not evidence for admissions in London hospitals being less severe there with omicron, but that is very noisy data and it's not really linked up in exactly that way.

Ventilation not yet increased though.

@Bordois

I think it would be very useful if the number of people in hospital could be expressed as a percentage of total capacity as well as raw numbers. 8k from a 180k capacity is a lot less concerning than 8k from a 80k capacity.

Currently about 5% - but that obviously could change dramatically in the next week or so.

Would anyone happen to know off the top of their head at what level the daily PCR testing capacity maxes out and also where we can find % of positive PCRs tracked?

Or is the Zoe symptom tracker app going to be a better indicator in forthcoming weeks.

88 thousand cases. Bloody hell.

@Lelivre

Would anyone happen to know off the top of their head at what level the daily PCR testing capacity maxes out and also where we can find % of positive PCRs tracked?

Or is the Zoe symptom tracker app going to be a better indicator in forthcoming weeks.

I just read that the capacity is one million PCR tests per day. The Zoe App does not appear to be keeping pace with the current rise - still around 88,000 per day which it has been for ages.

Since we know Omicron is circulating widely it's not surprising that hospital numbers are rising. What we don't know is how many are being treated for other ailments and happen to have covid vs those whose sole reason for admission is covid.

The real kicker for the NHS is going to be staff absenteeism. Lots of D&V/Noro usually at this time of year but isolation requirements can be as little as 48 hours ad opposed to 10 days for covid.

@lelivre is this the kind of thing you mean? (Second graph down in particular)

coronavirus.data.gov.uk/details/testing?areaType=overview&areaName=United%20Kingdom

For some reason Positivity is not available for UK, if you go to a smaller region it is, you can see that e.g. London is at 10.7% which is still not at all indicative of missed cases etc.
coronavirus.data.gov.uk/details/testing?areaType=region&areaName=London

What we don't know is how many are being treated for other ailments and happen to have covid vs those whose sole reason for admission is covid

On admissions, no that's not published, but on beds, that number is available from one of the links in the thread opener.
www.england.nhs.uk/statistics/wp-content/uploads/sites/2/2021/12/Primary-Diagnosis-Supplement-20211216.xlsx

For London on the 14th 963 of the 1248 beds were primarily covid, this is slightly lower than the historical average, and does appear to be dropping (it's mostly been over 80%), but it is still obviously a very high percentage.

Hello data people, I’ve got a question which might be a bit daft but I’ll ask it anyway

I’ve been looking at the handily colour coded map that they put on the daily stats page pretty much since it started. At some points over the whole pandemic some areas have been the darkest possible blue. Now when there are over 88k cases, they’re all just purple (Plymouth was dark blue yesterday, haven’t noticed today). Can someone put it in really simple terms how we can have had darker blue with lower cases in the past, and now we’re at the highest cases ever the map has hardly any dark areas?

Thanks in advance - yours sincerely, a non-data person who has found these threads very interesting

Some reinfection data for Denmark, not severity though:
mobile.twitter.com/JadeKhalife/status/1471395439131955206

@TweezerMay

Hello data people, I’ve got a question which might be a bit daft but I’ll ask it anyway

I’ve been looking at the handily colour coded map that they put on the daily stats page pretty much since it started. At some points over the whole pandemic some areas have been the darkest possible blue. Now when there are over 88k cases, they’re all just purple (Plymouth was dark blue yesterday, haven’t noticed today). Can someone put it in really simple terms how we can have had darker blue with lower cases in the past, and now we’re at the highest cases ever the map has hardly any dark areas?

Thanks in advance - yours sincerely, a non-data person who has found these threads very interesting

It's dynamic and changes as number rise.

There are only so many shades so it adjusts to create room to darken as the numbers rise.

Areas are lighter now because capacity to move up through the darker shades is about to be needed.

[quote sirfredfredgeorge]For some reason Positivity is not available for UK, if you go to a smaller region it is, you can see that e.g. London is at 10.7% which is still not at all indicative of missed cases etc.
coronavirus.data.gov.uk/details/testing?areaType=region&areaName=London[/quote]
Pillar 2 positivity for London looks much higher than 10.7% on the UKHSA surveillance report.

Yes - the 10.7 is combined, and you'd obviously expect pillar 2 to be higher than pillar unless things were badly going wrong in hospitals with our general availability of tests. The increase (of people who should have symptoms or be close contacts) is certainly not disproportionate to the number of people getting tested still, just means that now the symptoms are more likely, and close contact with omicron more likely to be infected.

It's still not high enough to indicate cases not being caught because of it if you see what I mean?

Thankyou! That makes sense.

Areas are lighter now because capacity to move up through the darker shades is about to be needed.

I don't understand this. The case rate range and corresponding colour code have remained unchanged.

Can someone put it in really simple terms how we can have had darker blue with lower cases in the past, and now we’re at the highest cases ever the map has hardly any dark areas?

I've noticed this too. I think distribution of cases is one factor. If you have many areas at he lower end of the dark blue range, 200-220 cases per 100k for example, then all of those areas could increase to 399 cases per 100k before the colour changes but at the same time many of the areas in purple could be nearer the upper limit of the case rate range, which would account for the high number of recorded cases. I also think the 7 day rolling average can be a bit misleading. In my area I have noticed days when the case rate is higher than the day before but the map shows numbers trending down. Also if you zoom in there are pockets of black even in the blue areas.

The map is still a few days old, delta really is falling in lots of places, the post half term wave that remixed delta into new schools/communities is gone, hence lots of areas now have falling cases.

On top of that, there's an Omicron wave, that's still confined to fewer areas, but going up very fast, how many other areas it's already in but not yet noticeable is the next question and will show how quickly things will really start to go up.