Colin Angus @VictimOfMaths Twitter profile

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Colin Angus

4 years

I've taken the various bits of analysis and visualisation I've done with #RStats in relation to COVID-19 data, tidied the code up a bit, updated it using the latest data and put it all in one place:

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Colin Angus

@VictimOfMaths

2 years

France's population is arranged in an extremely satisfying way. Well done France.

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Colin Angus

@VictimOfMaths

3 years

I still can't get over how stark the divide in COVID-19 cases between Northern Ireland and the Republic of Ireland is. It's been like this for *months*.

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Colin Angus

@VictimOfMaths

2 years

I've seen a few people recently shouting about how new ONS data shows that the "true" death toll from COVID in England & Wales is only 17,371, rather than the ONS figure of 157,816. This is obviously nonsense, but evidently still needs debunking, so here goes...

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Colin Angus

@VictimOfMaths

2 years

Oh boy, cancelling the COVID Infection Survey is such a bad idea.

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Colin Angus

@VictimOfMaths

2 years

So this is not good. Both new COVID cases and hospital admissions are rising again in England. Just how bad this is remains to be seen. But trying to work out how worried we should be (if at all) requires some understanding of *why* it's happening, and honestly🤷 /THREAD

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Colin Angus

@VictimOfMaths

2 years

This is one of the stupidest things I have ever read in the name of science. No, red wine does not ward off COVID. Not being poor (which is strongly correlated with red wine consumption) does though.

Red wine wards off coronavirus but not beer, according to new research

People who drink more than five glasses of red wine a week had a 17 per cent lower risk of catching Covid-19, according to new research at China's Shenzhen Kangning Hospital.

www.dailymail.co.uk

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Colin Angus

@VictimOfMaths

3 years

Woah, the layout of this graphic in the FT is 😍💥🤯

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Colin Angus

@VictimOfMaths

2 years

I accidentally made a map comparing rainfall and sunshine hours across the UK in 2021. Conclusive proof that Yorkshire>Lancashire (among other things). High-res version here:

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Colin Angus

@VictimOfMaths

2 years

Since @ONS now publish experimental inflation indices showing how different population groups experience inflation rates differently (thanks to @BootstrapCook ) we can see how inflation rates differ by income, and it isn't pretty.

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Colin Angus

@VictimOfMaths

3 years

I try and share the R code that produces all of the graphs that I post on here alongside each graph. I was wary at first, but it's turned out to be an *excellent* decision. Here's why and why I think you should do the same:

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Colin Angus

@VictimOfMaths

3 years

Reasons to be (cautiously) optimistic: COVID cases in Scotland have been rising steadily for 6+ weeks, but the number of patients in hospital with COVID has barely risen over that time. This is very different to how things looked at a similar stage in October.

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Colin Angus

@VictimOfMaths

2 years

Hong Kong is currently experiencing a horrifying COVID-19 outbreak. The mortality rate is approaching the UK's peak in January 2021. Why, if Omicron is so much milder? Most of that mildness is really due to vaccination and Hong Kong has hugely failed to vaccinate older people.

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Colin Angus

@VictimOfMaths

10 months

Playing around with ONS' data on prices and this is something I hadn't realised before. The variation in the price of a pint across England has increased *massively* in the last decade or so.

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Colin Angus

@VictimOfMaths

3 years

More good news for Scotland - cases have been falling for a couple of weeks and now the number of people in hospital with a positive COVID diagnosis looks to have started to fall too.

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Colin Angus

@VictimOfMaths

2 years

Not counting deaths with pre-existing conditions is saying to people with these conditions that their lives don't matter. The argument being made is that only the lives of people with no pre-existing health conditions count.

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Colin Angus

@VictimOfMaths

2 years

People with pre-existing conditions are real people. Their lives matter. They are your parents, your grandparents, your friends, your children. Very possibly you.

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Colin Angus

@VictimOfMaths

4 years

A map of Great Britain drawn using only the pubs.

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Colin Angus

@VictimOfMaths

2 years

It seems extremely bizarre to claim that this means the person died from asthma and not from COVID. Perhaps they wouldn't have died if they didn't have asthma, but they *definitely* wouldn't have died if they didn't have COVID.

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Colin Angus

@VictimOfMaths

2 years

This is obviously repugnant. It's the even nastier cousin of the 'they were old and would have died soon anyway' argument that we've heard trotted out many times, in spite of the fact that the average years of lost life per COVID death is ~10.

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Colin Angus

@VictimOfMaths

2 years

But I think it says a lot about the kind of person making these arguments that rather than go and look for the data to answer a question, their first resort of just to send an FOI request demanding somebody provide it to them on a plate.

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Colin Angus

@VictimOfMaths

2 years

#30DayMapChallenge Day 7 - Raster I normally make a new map each day, but I'm quite proud of this one that I made a few months ago - annual sunshine hours vs. rainfall across the UK on a bivariate map. #RStats code here:

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Colin Angus

@VictimOfMaths

2 years

If you are seriously making the argument that only 17,371 people have *really* died from COVID then you are saying that the ~140,000 people who died with pre-existing conditions were expendible and didn't matter.

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Colin Angus

@VictimOfMaths

2 years

Well this is exciting. I *finally* managed to get something to work that I've been trying to do for *ages*. Now to have a play...

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Colin Angus

@VictimOfMaths

2 years

A propos of nothing in particular, I made a weird graph of COVID case numbers in the UK.

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Colin Angus

@VictimOfMaths

1 year

After a year off (because, you know, stuff happened), the Health Survey for England ran again in 2021 and we now have some data from it via @NHSDigital The increase in the proportion of young people who don't drink alcohol is *astonishing*.

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Colin Angus

@VictimOfMaths

2 years

I hope it's obvious that that is an utterly repulsive and morally indefensible position. Don't even *think* about trying to make that argument to me.

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Colin Angus

@VictimOfMaths

3 years

Recent analysis from AP found that 99.2% of COVID deaths in the US in May were in those not fully vaccinated. In England, PHE data shows the figure is more like 57%. This sounds bad, but actually, this is *good* news for the UK 🧵

Nearly all COVID deaths in US are now among unvaccinated

Nearly all COVID-19 deaths in the United States now are in people who weren’t vaccinated, a staggering demonstration of how effective the vaccines have been and an indication that daily deaths — now...

apnews.com

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Colin Angus

@VictimOfMaths

2 years

I made a graph.

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Colin Angus

@VictimOfMaths

2 years

This also looks like good news - the recent increase in people in English hospitals with positive COVID tests is mostly driven by patients who are being treated for something else, *not* COVID.

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Colin Angus

@VictimOfMaths

3 years

The more I think about this map, the more interesting I think it is. So I thought I would do a little thread on it...

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Colin Angus

@VictimOfMaths

2 years

Once you get past your mid-50s, chances are you have a long-term health condition. By the time you reach your 70s, you have to be extremely lucky not to.

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Colin Angus

@VictimOfMaths

2 years

English local councillors by party affiliation and deprivation. One of these parties is not like the others...

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Colin Angus

@VictimOfMaths

2 years

As a final comment, there was absolutely no need for anyone to have FOIed this data. It was already in the public domain, published quarterly here:

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Colin Angus

@VictimOfMaths

2 years

Data from ICNARC shows that the vast majority of people being admitted to critical care were happily living without any support prior to admission. These are not people who were already at death's door.

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Colin Angus

@VictimOfMaths

3 years

I've been looking at vaccination rates in the USA and England a bit more. The US has vaccinated 10m+ teenagers, but has lower vaccination rates in older age groups compared to England, where vaccine rollout was much more strictly tied to age.

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Colin Angus

@VictimOfMaths

3 years

How has the failure of the Immensa lab in Wolverhampton affected hospital admissions in the areas that saw the most incorrect test results returned? The government line is "not at all". I beg to disagree. 🧵

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Colin Angus

@VictimOfMaths

2 years

Something like a third of the population have high blood pressure (hypertension), ~5 million people in the UK have diabetes, just under a third are obese etc. etc.

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Colin Angus

@VictimOfMaths

2 years

I posted this graph yesterday as part of the #30DayChartChallenge and a few people have asked some reasonable questions about why I chose to present this data in this way. So I thought I'd write a thread to explain my thought process...

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Colin Angus

@VictimOfMaths

2 years

When it comes to COVID, we already know that the vast majority of deaths where COVID is mentioned on the death certificate list COVID itself as the underlying cause.

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Colin Angus

@VictimOfMaths

2 years

So what is in this list of pre-existing conditions that denote somebody who is already at death's door? Here's the list. It is, well, pretty broad.

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Colin Angus

@VictimOfMaths

2 years

If we look at cases, and specifically the rate at which they are changing relative to 7 days previously, then it's really striking how *every* age group has suddenly changed direction at the same time.

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Colin Angus

@VictimOfMaths

3 years

Dear rude people of the internet, Before you hit send on that oh so clever tweet saying “this analysis is shit, you should look at x instead”, how about finding out if there is actually any data on x to analyse first? Yours, someone who is tired of your shit x

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Colin Angus

@VictimOfMaths

2 years

So this, I think, strongly suggests one of two possibilities: - some population-level shift in behaviour has suddenly increased the number of people getting COVID - BA.2

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Colin Angus

@VictimOfMaths

2 years

And prevalence of these conditions is strongly linked to age. Slightly different definition (though similar), but here's a great study from Scotland on the prevalence of long-term health conditions by age.

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Colin Angus

@VictimOfMaths

2 years

COVID is a respiratory virus. Many of the people who get severely ill have trouble breathing and need ventilation. It is hopefully obvious that having asthma will potentially exacerbate these difficulties and will therefore be listed as a contributory cause if they sadly die.

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Colin Angus

@VictimOfMaths

4 years

ONS have just published new weekly all-cause deaths data up to 17th April. Here's what it looks like (spoiler, it's not pretty):

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Colin Angus

@VictimOfMaths

2 years

So that is a *lot* of people with pre-existing conditions. If any of them were unlucky enough to have caught COVID, get severely ill and die, all it takes is for these conditions to have *some* impact for it to end up as a contributory cause on the death certificate.

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Colin Angus

@VictimOfMaths

2 years

So much of what we observe in the COVID data is driven by age dynamics - cases rising and falling in different age groups at different times. Here's the full tapestry of the pandemic in England (for cases at least). So many different stories written into this plot.

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Colin Angus

@VictimOfMaths

3 years

To everyone saying ‘but population density’ - here’s a map of population density across Ireland. The border isn’t *that* stark.

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Colin Angus

@VictimOfMaths

3 years

I was a bit sceptical at first, but I'm increasingly convinced that the gender gap that has emerged in COVID cases in 20-39 year-olds in England is a direct consequence of the football. And it's too early to expect any effects from the semi-final or final to show in this data...

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Colin Angus

@VictimOfMaths

2 years

The claim comes from an FOI request that some genius sent to the ONS asking them for the number of deaths where *only* COVID was listed on the death certificate without any other pre-existing conditions listed.

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Colin Angus

@VictimOfMaths

2 years

But this new claim is that *any* deaths where there is a pre-existing condition listed on the death certificate alongside COVID aren't really COVID deaths. Because obviously these people are sick and were just about to die anyway before they caught COVID.

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Colin Angus

@VictimOfMaths

2 years

To illustrate how stupid this whole argument is, let's take an example - asthma. The ICD-10 code for asthma is J45, so it's on the list of pre-existing conditions.

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Colin Angus

@VictimOfMaths

2 years

But what does it mean to die with both COVID and a pre-existing condition on the death certificate? Death certificates list an "underlying cause" and can list several "contributory causes".

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Colin Angus

@VictimOfMaths

2 years

Omicron has really taken hold in the US, how worried should we be? The US hasn't seen the nice decoupling of cases from admissions and deaths that we have in the UK. Partly because of lower testing (I believe), but also lower and less well targeted vaccination uptake.

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Colin Angus

@VictimOfMaths

2 years

Whooooooosh. Can't get enough of this sort of thing.

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Colin Angus

@VictimOfMaths

2 years

So that's a long-winded way of saying that I don't know what's going on, and I haven't seen anyone else come up with a compelling theory yet. I'm sceptical about it being waning vaccine effectiveness though.

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Colin Angus

@VictimOfMaths

3 years

Oh, this *is* a good way of visualising the impact of vaccinations on deaths.

Alison Buttenheim

@abuttenheim

3 years

This picture paints about 3000 words.

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Colin Angus

@VictimOfMaths

2 years

I'm a little surprised at the number of high profile data visualisation people on here that I've seen dunking on this chart from the NYT. We've seen (and I've made) a million boring line/area charts of COVID cases. It's refreshing to see somebody trying something new.

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Colin Angus

@VictimOfMaths

3 years

One of these waves is not like the others.

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Colin Angus

@VictimOfMaths

3 years

At the national level, the number of COVID patients in hospital is rising, but things still look very different from previous waves.

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Colin Angus

@VictimOfMaths

2 years

Well, no. The number of people being admitted to hospital with COVID, or testing positive in a hospital setting, has started rising *at the same time* in all age groups.

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Colin Angus

@VictimOfMaths

3 years

Here is some *much* better news. Rates of COVID-19 vaccination have picked up *massively* in the last week. Yesterday, we reported vaccinating over a quarter of a million people. In a day. That's pretty amazing.

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Colin Angus

@VictimOfMaths

2 years

This pushes us away from any explanations that might be age-specific, for example the (entirely plausible) idea that the protective benefits of boosters are starting to wear off. Because the booster rollout was very staggered with age.

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Colin Angus

@VictimOfMaths

2 years

Here's another way of looking at recent patterns in COVID case rates. Cases still falling, but much more slowly, in all age groups except for primary school kids and their parents age bracket where cases are rising again.

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Colin Angus

@VictimOfMaths

2 years

@ledredman @HalseyJane Sadly the kind of people making these arguments are also the kind of people who will just claim that all excess deaths are "lockdown deaths" caused by the response to COVID. It's like reasoning with treacle.

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Colin Angus

@VictimOfMaths

2 years

It really is *such* interesting data though...

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Colin Angus

@VictimOfMaths

3 years

Turned a heatmap of COVID case rates by age in England into a contour plot. I like this a lot.

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Colin Angus

@VictimOfMaths

2 years

Good news: COVID admissions now starting to fall in London (and maybe, *maybe*, plateau a little elsewhere)

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Colin Angus

@VictimOfMaths

4 years

This chart from @TheEconomist is outstanding, so I thought I'd have a go at replicating it for every election in my lifetime. #ge2019data

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Colin Angus

@VictimOfMaths

4 years

Here's some good news - we're finally starting to see some blue reappear on the right hand side of these figures.

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Colin Angus

@VictimOfMaths

2 years

Comparing COVID admissions now with 12 months ago, it's impressive how well vaccines have kept adults protected from severe disease. For under 18s, it's a rather different picture, both during Delta and now Omicron waves.

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Colin Angus

@VictimOfMaths

2 years

NHS England have just published their weekly breakdown of patients in hospital 'with' or 'for' COVID. In London, both numbers have really shot up in the last 2 weeks, but two thirds of patients in acute hospitals who have COVID are there *because* of COVID.

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Colin Angus

@VictimOfMaths

3 years

The areas in Great Britain which currently have the highest rates of COVID-19 cases are generally areas where fewer people work from home. Lots of other factors at play, but the prevalence of red (high cases, low WFH) and turquoise (low cases, high WFH) is clear.

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Colin Angus

@VictimOfMaths

2 years

There is always a bit of a lag on genomic surveillance, but as of 26th February, the BA.2 variant of Omicron was dominant almost everywhere in England.

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Colin Angus

@VictimOfMaths

1 year

Our new paper looking at alcohol, drug and suicide mortality during the first 2 years of the pandemic in the USA and the UK nations has just been published in @RSPH_PUHE Lots of attention on these deaths early in the pandemic, so what actually happened?

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Colin Angus

@VictimOfMaths

3 years

This graph looks pretty remarkable - in mid September, COVID case rates suddenly became highest in the least deprived areas, a sharp reversal of the prevous trend. So what's going on here? 🧵

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Colin Angus

@VictimOfMaths

2 years

And pretty much at the same time in all regions, although there is a little bit of variation - admissions have already exceeded their Omicron peak in the South East and South West in the oldest age groups.

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Colin Angus

@VictimOfMaths

2 years

Three things that I think will be interesting to look out for tomorrow: - New data from NHS England on the with/for COVID breakdown of admissions - New data from NHS England with amore detailed age breakdown of admissions - A new @UKHSA surveillance report

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Colin Angus

@VictimOfMaths

1 year

How to make something that’s getting worse look like it’s getting better? Reverse the x-axis. @GraphCrimes

Peter Rice

@peterricev2

1 year

@MrTrevMcCarthy @felly500 Here's Drinkaware's graph of the mortality trends. Notice anything unusual about the layout? It took me a couple of minutes.

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Colin Angus

@VictimOfMaths

3 years

Why is it so hard to work out what's going on with this new wave of COVID cases in the UK? The answer lies in the fact that a *lot* of things have changed in comparison to previous waves, and it's *really* hard to parse out the specific impact of each contributing factor...

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Colin Angus

@VictimOfMaths

3 years

I've seen a few sources talking about the new COVID-19 variant being more transmissible among younger children. I've no reason to doubt this, but it's hard to look at this graph and infer that young children have been driving the recent rise in case numbers.

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Colin Angus

@VictimOfMaths

2 years

Genuinely amazed at the number of tedious COVID chumps who seem to think that pointing out that the average age of a COVID death being close to life expectancy demonstrates anything other than their own ignorance of how life expectancy works.

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Colin Angus

@VictimOfMaths

2 years

Still lots of reasons to be very cautious about interpreting this (day of the week effects, changes in ability to get tests, changes in test processing times etc etc) but this looks pretty good I'd say.

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Colin Angus

@VictimOfMaths

3 years

To put this another way: When nobody is vaccinated, 100% of deaths are in unvaccinated people. When everyone is vaccinated, 100% of deaths are in vaccinated people.

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Colin Angus

@VictimOfMaths

17 days

There's some amazing data hidden away in ONS's user requested data section. Last year they quietly published death data by age, deprivation decile and cause, which means we can look at age patterns in alcohol deaths by IMD, with sadly predictably grim results:

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Colin Angus

@VictimOfMaths

2 years

I've been meaning to make a plot like this for a while, after seeing @jburnmurdoch do something similar. This is COVID case rates by age, relative to their peak level last winter, coloured by booster coverage. As the lines turn green, they go down 👍

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Colin Angus

@VictimOfMaths

3 years

COVID vaccination rates by age in the US (in blue) compared to England (in red) - double jabbed in darker colours. The US has better coverage in the youngest age groups, but much worse coverage in older ages. As COVID risks vary so much with age, this is bad news for the US.

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Colin Angus

@VictimOfMaths

2 years

But nor am I convinced that the timing of relaxing restrictions entirely fits with what we're currently seeing. And there is the oddity that admissions started rising *before* cases, even though admissions should lag cases.

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Colin Angus

@VictimOfMaths

3 years

Every single person I know working in Public Health, be that PHE/W/S, local PH teams or other organisations, has been working incredibly hard in this past year and achieved some *incredible* things. If your worldview involves them being the baddies, then you’re very wrong.

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Colin Angus

@VictimOfMaths

2 years

There really is a lot going on in the recent COVID case numbers in England. Cases back to being highest (and rising fastest) in primary age children. Cases starting to rise again in their parents' age group. Falls stalling in other ages. Let's do some graphs...

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Colin Angus

@VictimOfMaths

2 years

One for the 'but they are all incidental admissions crowd here'. In every English region, the majority of patients in hospital with COVID are being treated *for* COVID. In many areas, it's a substantial majority. And the numbers are rising *everywhere*.

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Colin Angus

@VictimOfMaths

2 years

This is great. Everything you ever wanted to know (and plenty you probably didn't know you ought to know) about choosing and using fonts from the always excellent @lisacmuth

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Colin Angus

@VictimOfMaths

2 years

So I think both of these explanations are *plausible*, but I'm not totally convinced about the timing of either of them. BA.2 has been growing since early January, so that doesn't really fit (IMO) with a sudden, simultaneous change in cases and admissions.

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Colin Angus

@VictimOfMaths

3 years

Hmm. This looks, kind of, surprisingly, sort of ok. Maybe? Lots of areas seeing the rise in case rates decelerating in the last couple of days.

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Colin Angus

@VictimOfMaths

2 years

The number of patients in English hospitals being treated for COVID keeps on falling and is now smaller than the number of patients 'with' COVID but being primarily treated for something else.

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Colin Angus

@VictimOfMaths

2 years

BA.2 clearly has a growth advantage over OG Omicron, but UKHSA analysis doesn't suggest it leads to more severe outcomes, or is any better at overcoming vaccinations.