Posts written by Thomas Lumley (2569)

• Last June, the FDA approved a medication for Alzheimer’s Disease, although a lot of people, including their external advisory committee, thought there wasn’t convincing evidence that it works.  The Centers for Medicare & Medicaid Services, the organisation that would be paying for a lot of this treatment, have decided they need some randomised trials showing that the treatment is safe and effective, so they have said they will only fund the treatment in trials.
• According to Pew Research, “Overall, about half of U.S. adults (48%) say that most things in society can be clearly divided into good and evil, while the other half (50%) say that most things in society are too complicated to be categorized this way.” This is another example of a survey question where only differences or changes are really meaningful and we can’t straightforwardly interpret the absolute value. I mean, how about “eggplant” or (for something more obviously socially constructed) “driving on the left-hand side of the road”.  I would have said a lot of things in society have no particular moral valence, but also it’s not clear how you’d categorise “most” in cases where “good or evil or complicated” is a genuine question. The differences between groups are still potentially interesting, as might be changes over time.
• Not precisely ‘statistics’ or ‘in the media’, but a YouTube video of Adam Savage (Mythbusters) talking about measurement via Graeme Edgeler
• I gave a talk about StatsChat at a conference on undergraduate statistics and maths teaching

The governor of Florida, Ron DeSantis was widely quoted last week as saying

 “Before COVID did anyone go out and seek testing to determine if they were sick? It’s usually you feel like you’re sick and you get tested to determine what you maybe have come down with.” 

As most people will know, the answer is “yes, they did”.  You can’t get near a doctor without having your blood pressure measured, because high blood pressure is common, not obvious without testing, and treatable.  There are tests performed on infants (for genetic disorders such as PKU and cystic fibrosis), on children (vision and hearing screening), and on the middle-aged and old (cholesterol, glycated hemoglobin, cancer screening). There are tests mainly done for high-risk groups (TB, HIV); there are tests done before you get certain medications (liver or kidney function).   Until 1986, Florida required a test to see if you had syphilis in order to get a marriage license.  Governor DeSantis has since said that of course he knew all that, and it was obvious he had specifically meant daily or weekly testing for a viral respiratory infection was unprecedented, not all the normal and routine ways people seek out testing to determine if they are sick. And who knows? Maybe he did mean that.

In some ways there’s surprisingly little population screening.  Screening has traditionally been popular, because people like knowing things and having explanations.  People often argue for more or say they have discovered a way to do more. There are three big barriers in going from a test you take when you feel like you’re sick and one you give to people in advance.

The first barrier is that you have to be able to do something with the result. There’s no point in taking healthy people and finding some illness unless you can do something about it.  In the endemic-Covid testing setting,  you can isolate and not go infect your workmates or your grandparents or the blokes at the pub or whoever.   In the 2004 SARS outbreak we didn’t have rapid antigen tests, but temperature screening was used to find people who might not realise they had SARS or weren’t looking to find out for some other reason.

The second barrier is the base rate problem. The New York Times had a very good story recently about prenatal genetic testing. This looks for very rare genetic disorders, usually as add-ons when testing for Down’s Syndrome. Because those disorders are very rare, most fetuses don’t have them — even most of those who test positive.  The Times reported on a set of tests where a positive test had an 80% or higher chance of being wrong.  In one sense these tests are very accurate — a negative result is very likely to be correct– but just assuming no-one has these conditions is almost as likely to be correct and has no false positives.  The base-rate problem goes together with the problem of what to do; follow-up tests are expensive.

The base rate problem is also an issue for Covid testing here in New Zealand; in contrast to many parts of the world, we currently have very low community prevalence, so a rapid antigen test positive in someone without symptoms or known exposure would very likely be a false positive.  In Victoria, the opposite is true: the base rate is high enough that the only rapid antigen tests where PCR follow-up is recommended are those in asymptomatic people with no known exposure.

The third barrier is Rose’s Prevention Paradox: for a lot of diseases, most of the cases don’t happen in high-risk people. There are people at very high risk of heart attack (what Rose was interested in), but they account for a relatively small fraction of all heart attacks.  There are people at very high risk of premature birth, but they account for a relatively small fraction of all premature births.  Someone with a blood alcohol of 0.2 has a very high risk of getting in a crash, but most car crashes aren’t like that.

Unlike the base-rate problem, Rose’s Prevention Paradox isn’t universal.  Testing for the common CFTR mutations will pick up most cases of cystic fibrosis; the Ishihara plates pick up most cases of deficient colour vision; most lung cancer is in smokers; most liver cancer in Western countries is in heavy drinkers or people with Hepatitis B or C.

The Covid example of the prevention paradox is the recent and controversial CDC announcement that most (vaccinated) people who get seriously ill from Covid have co-morbidities.  On top of the issue of whether that’s actually a cause for rejoicing, there’s the problem that the majority people who don’t get seriously ill from Covid also have co-morbidities. That is, it’s hard to pick out high risk people.  The CDC defined ‘high risk’ very broadly, so that too  many people are ‘high risk’; if they define it too narrowly, they would miss a lot of the serious Covid cases.

Very early in the pandemic, the estimate was that a Covid case gave you roughly a year’s worth of mortality risk — if everyone got Covid over a period of one year, death rates for that year would be double what they normally are, across a wide range of subgroups.  Omicron is worse than the original strain, but the vaccine helps a lot: vaccinated people are much less likely to die or become hospitalised.  Not getting Covid helps even more; masks, ventilation, distancing, testing, etc.

According to a poll published in the Washington Post, a substantial majority of Americans think it is never justified for citizens to take violent action against the government. Given the US reverence for George Washington and others who fought in the Revolutionary War, this seems a bit strange. It’s hard to interpret what any particular percentage would mean.

What’s important about the poll is that the percentage is down compared to previous polls with the same question. It’s hard to interpret the level of agreement, but it seems pretty reasonable that a decrease indicates more willingness to consider violence against the government as an option that might come into play in the foreseeable future.  Or, at least, it would be if the polling approach hadn’t also changed, from phone to online, complicating any interpretation of changes.

Similarly, when the poll finds 30% of people claim to think there is solid evidence of widespread electoral fraud in 2020, it’s a bit hard to tell what that really corresponds to — how much is actual belief and how much is going along with a party line.  The fact that it’s about the same percentage as a year ago is more informative, as is the fact that it’s higher than similar questions about past elections.

Asking the same questions over time is a much better way to pick up changes than asking people if their opinion has changed. As a strategy, it can conflict with asking the best question, and that’s an ongoing tension in public opinion research and official statistics.

(The rugby prediction posts, while popular, are most interesting before the games actually happen: predicting the past is relatively easy)

First, the posts, regardless of year of writing, with most 2021 hits

1.  What’s a Group 1 Carcinogen? (2013) Points out that the IARC classification is not about severity or danger but about the types and amounts of evidence. Sunlight is a Group 1 Carcinogen, so are alcohol and plutonium.
2. A post about a Lotto strategy that doesn’t work(2012), as an argument about the usefulness of abstract theory. See also, the martingale optional stopping theorem
3. A climate change post about graphs that shouldn’t have a zero on the y-axis(2015)
4. From October 2020, but relevant to the news again in March this year, on crime rates in the Cuba/Courtenay area of Wellington and denominators
5. Actually from July this year, one of the StatsChat Dialogues: Q: Did you see that learning maths can affect your brain? A: Well, yes. There wouldn’t be much point otherwise

And the top 2021-vintage posts

1. Number 5 from the previous list
2. From October, on interpreting vaccination percentages
3. From April, why there’s so much fuss about very rare adverse reactions to vaccines (the AZ blood clots)
4. From October, why population structure matters to epidemic control, aka, why we need to vaccinate every subgroup. Has pictures!
5. From June, how a cap-and-trade system for (a subset of) emissions messes up our intuition about other climate interventions.

These are WordPress page views: their relationship to actual readership is complicated; keep in a cool, dry place away from children; may contain nuts.

A gentleman who is Not New Zealand’s Favourite DJ has tested positive for Omicron on his 9th day in NZ, after prior negative tests.  It seems surprising that a positive test could take so long — one theory is that it’s the sort of sporadic positive you can get for a while after recovery.  On the other hand, it’s worth thinking about why it’s surprising.  New Zealand keeps seeing strange Covid occurrences: long incubation period, transmission from very brief contact, and so on. Why us? It’s us because no-one else would be able to tell.

The normal assumption if a London DJ tests positive for Omicron on December 25 is that they got it in London a few days earlier. In this example, ‘a few days earlier’ means Waiheke Island and however he got there from MIQ;  in contrast to almost everywhere else in the world, Omicron isn’t circulating in Auckland.  The week before that he was in MIQ, so the next conclusion is that he got it there; unfortunate but not unprecedented. Without genome sequencing we’d stop there, but his viral genome doesn’t match any of the three he could potentially have picked up in MIQ.  We’re now down to weird possibilities, and the least weird is that he was carrying it all the time. But if he was almost anywhere else in the world, we wouldn’t even be starting to think about the weird possibilities.

It’s fairly easy to estimate the low end of the time-to-positive-test distribution: someone goes to a party; a few days later there are twenty cases; you do the maths. To get the low end you need some cases where you’re sure they couldn’t have been infected before a specific exposure, because they weren’t exposed before then. At the start of an outbreak that’s fairly easy. To get the high end of the distribution you need some cases where you’re sure they couldn’t have been infected after a specific exposure. That’s a much less common scenario, so the data aren’t as good.

• Arithmetic fail by Bloomberg Australia: 126 cases over two days is not ‘more than double’ 62 cases in one day.
  
  They’ve since edited to “N.Z. Adds 126 Cases in 2 Days…New Zealand’s daily toll of new local infections has risen from the 62 reported on Dec. 24.”, which is at least arithmetically correct, since 2×62 is 124, and 126 is larger than 124.  Interestingly, the story now says “(Updates with state case numbers in third paragraph)” but doesn’t mention the correction to the maths

• The Washington Post reports on using convalescent plasma — antibodies from people who’ve recovered — to treat Covid. A new trial has positive results, but the story seriously underplays the previous trials with negative results. The story emphasizes that we’re short of treatments for Omicron so a new treatment would be more valuable, but that’s only true if it works, which is what’s in doubt
• Cruise ships are getting Covid outbreaks. Ok, yes, I’m shocked too.  More seriously, the problem is numbers. There were 3500 people on the ship. If each one is 99.95% sure to be Covid-free, that still comes to more than one expected case. At the sort of Covid prevalences the US has now, symptom screens and pre-departure tests aren’t good enough to get a high probability of a safe cruise.

There are two main sorts of Covid tests available: PCR tests and rapid antigen tests.¹

PCR tests have essentially no false positives and ok-ish false negative rates.  They’re processed in lab; overnight if you’re lucky and the lab isn’t overworked. Rapid antigen tests are less accurate: they have rare but non-negligible false positives and they turn positive later in the infection process than PCR tests.  As it says on the tin, they’re rapid: you don’t need a lab and can get results in minutes. The two test types are useful for different purposes.

In New Zealand until recently, Covid was rare and occurred in limited clusters. In this setting, when the public health system is doing zero-tolerance control, there’s not much use for rapid antigen tests².  If you are symptomatic or a contact you should isolate and get PCR tests; if you are asymptomatic and not a contact then you’re very unlikely to have Covid and any positive test is likely to be a false positive.  Anonymous at-home testing allows someone who has symptoms or is a contact to test positive and keep it quiet — maybe stay away from Nana’s 90th birthday party or drinks at the pub, but still go to work and go to the supermarket. The public health system would like this not to happen.

When Covid is everywhere, as in the US and the UK, quite a lot of people will be exposed and not know about it, so asymptomatic community testing is no longer useless. The problem with PCR is that it’s slow, especially when the labs get overworked: you won’t get the result until at least tomorrow and perhaps a few days later.  Rapid antigen tests are very valuable because they are rapid — they tell you, with imperfect but useful accuracy, whether you are infectious right now.  If you’re planning an in-person party or meeting or movie or flight or date, that’s what you want to know.  In the UK and Europe, the ‘lateral flow test’ type of rapid antigen test have been very useful; they miss some infections, but they catch quite a lot.  In the US they would have been useful, but they’re expensive and availability has been limited. The US government has just moved on making the tests a little more available — they’ve bought half a billion tests, nearly two for each US adult.

In New Zealand at the moment the situation is more complicated.  We’re on the boundary between zero Covid and low-level suppression.  The government is still trying to keep control of test results, which has clear benefits in contact tracing and elimination, but removes the ability for everyone to use rapid tests to reduce their individual risk of spreading Covid.  Whether you think the government is making the right decision here depends a lot on how much you trust the public health system, and on how much you trust other people.

¹ yes, and a whole bunch of other minor options
² except perhaps for border workers or customer service people during an outbreak

There’s a piece in Stuff about a startup using NFTs to do carbon capture.  I’m not going to get into a general discussion of NFTs here¹.  What’s StatsChat-relevant about the story is the general principle that when you have two numbers you should do something with them.

The company in question has a current product and a planned product.  The current product is a subscription that offsets more carbon than you use on Instagram, for $5/month.  The planned product is a set of $1000 NFTs that will offset 1 tonne more carbon than they cost to produce, and will potentially generate royalties on future resales to offset more emissions.

Looking at the Instagram offset subscription, you’re getting about 6kg of offset per dollar, so about $160/ tonne.  The NZ emissions trading scheme price is about $70/tonne. You might be worried about the quality and reliability of the NZ offsets — I haven’t looked into this in any detail, and you probably haven’t either — so you might be willing to pay more for offsets you trusted more and which had the potential to develop new technologies.   Or you could buy for US$15/tonne directly from Tradewater, one of the companies used by Cool Points Club, whose approach is to prevent emissions of used refrigerant gasses by incinerating them. The monthly price does include GST and the cost of running the system; I don’t think it’s great value, but it’s priced transparently and it’s probably capturing money that wouldn’t otherwise be spent on carbon offsets.

The NFTs initially cost about $1000 for one tonne of offset. That’s very expensive.  You can buy 14 tonnes of generic NZ offset for that much, or 66 tonnes directly from Tradewater (give or take any GST liability).  If these are going to be worthwhile, nearly all of the value will have to be in the NFT, not in the offset.

¹ and since I moderate the comments, neither are you

• Pfizer’s vaccine trial in kids 2-5 years old wasn’t successful: the dose (1/10th adult dose, 30% of 5-12yr dose) seems to be too low. They will try a three-dose series.  It did work in 6-24 months kidlets.  Pfizer is also testing third-dose boosters for all child age ranges
• “Why trust and transparency are vital in a pandemic” from the UK Office of Statistics Regulation. They note “It will not always be possible to publish information before it is used publicly. In these cases, it is important that data are published in an accessible form as soon as possible after they have been used, with the context provided and strengths and limitations made clear. “
• Lee Wilkinson, a pioneer in statistical computing and graphics, passed away on December 10.  Among other influential contributions, he developed the statistical package ‘Systat’ and wrote ‘The Grammar of Graphics’
• Florida is a counterexample to correlations between Covid vaccination and politics in the US. That seems to be partly because their data are wrong. “People age 18 and over in the 33122 area code had more than a 2,700% vaccination rate, according to the data….’That’s the airport,’ Gelber said.”
• Via Jenny Nicholls on Twitter, a Washington Post story on injuries from bouncy castles. The story quotes the number of injuries as 82,203 from 2008 to 2013 and as one every 46 minutes in 2013.  You might think about whether these are compatible and which sounds bigger.  It also works out as about 0.2% of the roughly 8 million unintentional injuries in kids leading to emergency department visits. Which I think is more than I’d expect

There’s still discussion about whether the Omicron covid variant is milder than Delta. We don’t really know yet, but this post is about why that’s not even the question.

First, Omicron is still scary: people do end up in hospital; people do die; even a ‘mild’ case can still really suck; and we have literally no idea what proportion of people will get Long Covid. If it’s milder, it’s still very much in the Do Not Want category.

Second, we do know that the proportion of people who get hospitalised will probably be lower than with Delta, and that isn’t the answer to ‘mild or not?’ The primary facts about Omicron are that (a) the vaccine is definitely much less effective at preventing infection, but (b) the vaccine is probably still somewhat effective at preventing severe disease.   Suppose, to give us something to work with, an Omicron infection was exactly as likely to cause hospitalisation for an infection in vaccinated individual as Delta, and was exactly as likely to cause hospitalisation for an infection in an unvaccinated individual as Delta.

If you (Dear Reader) are vaccinated or otherwise immune, you’re more likely to be hospitalised by Omicron because you’re more likely to be infected. The vaccine protection is less, even with a third dose, and the prevalence will be higher so you’re more likely to be exposed. If you aren’t vaccinated, you’re more likely to be hospitalised by Omicron because you’re more likely to be infected: the communal vaccine protection is  less so the prevalence will be higher and you’re more likely to be exposed.  So, in that sense Omicron is worse: you are more likely to get sick, more likely to be hospitalised, probably more likely to die than if Omicron hadn’t come along.

On the other hand, the fraction of cases who end up in hospital is likely to be lower than we were seeing with Delta.  That’s because we will have a larger fraction of cases in vaccinated people, and these are less likely to end up in hospital.  The number in hospital will go up, but by a smaller multiple than the total number of infections.

So, if the question about a milder variant is “will the fraction of people with serious disease go down?” the answer is probably “yes”. If the question is “will the number of people with serious disease go down?” the answer is probably “no”.  If the question is “should I relax because it’s not serious?”, the answer is “holy fuck no”.