August 21, 2017

Effective treatment is effective

There’s a story in New Scientist, and in the NY Daily News, based on this research paper, saying that choosing alternative treatment instead of conventional treatment for cancer is bad for you.

The research is well done: they looked at the most common cancers in the US and found a small set of people who turned down all conventional treatment in favour of ‘alternative’ medicine.  They matched these people on cancer type, age, clinical group stage, what other disease they had, insurance type, race, and year of diagnosis, to a set who did get conventional treatment.   Even after all that matching, there was a big difference in survival.

There are two caveats to the story. First, this is people who turned down all conventional treatment, even surgery. That’s rare. In the database they used, 99.98% of patients received some conventional treatment. It’s much more common for people to receive some or all of the recommended conventional treatment, plus other things — not ‘alternative’ but ‘complementary’ or ‘integrative’ medicine.

Second, the numbers are being misinterpreted.  For example, New Scientist says

Among those with breast cancer, people taking alternative remedies were 5.68 times more likely to die within five years.

The actual figures were 42% and 13%, so about 3.1 times more likely. Here’s the graph
breastcancer

Similarly, the New Scientist story says

They found that people who took alternative medicine were two and half times more likely to die within five years of diagnosis.

The actual figures were 45% and 26%; 1.75 times more likely.

What’s happening is a confusion of rate ratios and actual risks of death; these aren’t the same.  The rate (or hazard) is measured in % per year; the risk is measured in %.  The risk is capped at 100%; the rate doesn’t have an upper limit.   Because of the cap at 100%, risk ratios are mathematically less convenient to model than rate ratios. As a tradeoff, it’s harder to explain your results using rate ratios. The Yale publicity punted on the issue, not mentioning the numbers and leaving reporters to get it wrong.  When this happens, it’s the scientists’ fault, not the reporters’.

 

Stat of the Week Competition: August 19 – 25 2017

Each week, we would like to invite readers of Stats Chat to submit nominations for our Stat of the Week competition and be in with the chance to win an iTunes voucher.

Here’s how it works:

  • Anyone may add a comment on this post to nominate their Stat of the Week candidate before midday Friday August 25 2017.
  • Statistics can be bad, exemplary or fascinating.
  • The statistic must be in the NZ media during the period of August 19 – 25 2017 inclusive.
  • Quote the statistic, when and where it was published and tell us why it should be our Stat of the Week.

Next Monday at midday we’ll announce the winner of this week’s Stat of the Week competition, and start a new one.

(more…)

August 19, 2017

Sampling bias

Via GeoNet, a magnitude 4.5 quake south of Dannevirke (blue box)

quake

The squares are reports of shaking. The big cluster is Palmerston North, with secondary clusters in Feilding and Ashhurst: there are more people who felt the quake there because there are more people there.  See also XKCD

August 18, 2017

Green and full of terrors

Q: Did you see avocado gives you breast cancer?

A: Me?

Q: Well, women with mutations in the BRCA genes, such as Angelina Jolie

A: 🙄

Q: “Women with the faulty ‘Angelina Jolie’ gene should cut back on trendy avocado-based breakfasts to slash their chances of cancer.

A: No.

Q: So the study wasn’t in women?

A: No. Or avocados.

Q: Mice

A: Not even. Cells in a lab. (press release)

Q: And the avocados?

A: The cells were given extra folate.

Q: And they got cancer?

A: No, they died.

Q: Then why is there a cancer story?

A: The researchers speculated that folate could be part of a future treatment for BRCA-damaged tumours.

Q: That’s kind of not what the Herald says

A: No, but they did get the story from the Daily Mail.

Q: So what do the researchers say about avocados?

A: They don’t mention avocados

Q: Ok, what do they say about folate, then?

A: “The authors caution that no conclusions should be drawn about whether there is any overall effect in a living animal consuming folate.”

Q: So it wasn’t the press release this time

A: No, this looks like it’s down to the Daily Mail.

 

August 16, 2017

Briefly

  • “Is it legal for me to violate Terms of Service in order to collect data for a research project?” (in the US). Casey Fiesler on law and ethics of scraping
  • My first boss as a statistician. John Simes, has won the University of Sydney Vice-Chancellor’s Award for Excellence. Among other things, he was one of the early proponents of universal clinical trial registration. In 1986 he wrote about the impact of publication bias on treatment choice in cancer.
  • A teaching example based on a baseball/brain cancer ‘cluster’ that didn’t hold up.  Much smaller numbers than the brain injury problems in US football or even rugby, and less prior plausibility.
  • It’s not just New Zealanders who have order of magnitude-and-units problems. From The New Yorker, via Felix Salmon
    nyfeet

Seatbelts save (some) lives

It’s pretty standard that headlines (and often politicians) overstate the likely effect of road safety precautions — eg, the claim that lowering the blood alcohol limit would prevent all deaths in which drivers were over the limit, which it obviously won’t.

This is from the Herald’s front page.

belt

On the left, the number 94 is the number of people who died in crashes while not wearing seatbelts. On the right (and in the story), the we find that this is about a third of all the deaths. It’s quite possible to wear a seatbelt and still die in a crash.

Looking for research, I found this summary from a UK organisation that does independent reviews on road safety issues. They say seatbelts in front seats prevent about 45% of fatal injuries in front seat passengers. For rear-seat passengers the data are less clear.

So, last year probably about 45 people died on our roads because they weren’t wearing seatbelts. That’s a big enough number to worry about: we don’t need to double it.

August 15, 2017

Emoji backlash?

Q: Did you see that using emoji in work-related emails could hurt your career?

A:😕

Q: Yes, it’s apparently a common email mistake

A: 😯

Q: The 549 study participants from 29 countries “were asked to read a work-related email from an unknown person, and were asked to evaluate the competence and warmth of the sender”

A:🤔 💻 🇹🇷

Q: Yes, they were from Amazon’s Mechanical Turk (paper)

A: 😕

Q: Ok, so they weren’t really work-related emails from someone they’d never met, in another country. But the participants were told to pretend they were.

A: 🙁

Q: And it undermined information sharing

A: 😕 👥 💻 🤐 ?

Q: The email replies to messages with emoji had fewer words in them on average

A: 🤔 🙂

Q: Ok, yes, that’s not necessarily a bad thing.

A: 👩‍💼👨🏽‍💼🗣 😀 ?

Q: Is it really common to use emoji in business email? Yes, they say nearly 20% of emails in one previous sample included emoji.

A: 🙄 🇬🇸🇸🇱🇸🇬🇸🇳🇸🇦 👩‍💼👨🏽‍💼🗣 😀 ?

Q: No, I suppose that wasn’t international emails between people who had never met or corresponded before.

A: 🙄

Q: So using emoji in formal emails to a complete stranger could be a bad idea?

A: 😴

 

NRL Predictions for Round 24

Team Ratings for Round 24

The basic method is described on my Department home page.

Here are the team ratings prior to this week’s games, along with the ratings at the start of the season.

Current Rating Rating at Season Start Difference
Storm 10.10 8.49 1.60
Broncos 8.52 4.36 4.20
Raiders 5.81 9.94 -4.10
Cowboys 3.91 6.90 -3.00
Panthers 3.40 6.08 -2.70
Roosters 1.71 -1.17 2.90
Sharks 1.44 5.84 -4.40
Sea Eagles -0.35 -2.98 2.60
Dragons -0.69 -7.74 7.00
Eels -0.83 -0.81 -0.00
Rabbitohs -1.77 -1.82 0.00
Wests Tigers -4.19 -3.89 -0.30
Warriors -6.01 -6.02 0.00
Bulldogs -6.99 -1.34 -5.70
Knights -7.19 -16.94 9.70
Titans -8.92 -0.98 -7.90

 

Performance So Far

So far there have been 168 matches played, 102 of which were correctly predicted, a success rate of 60.7%.
Here are the predictions for last week’s games

Game Date Score Prediction Correct
1 Rabbitohs vs. Bulldogs Aug 10 28 – 14 7.70 TRUE
2 Eels vs. Knights Aug 11 10 – 29 15.00 FALSE
3 Broncos vs. Sharks Aug 11 32 – 10 8.40 TRUE
4 Dragons vs. Titans Aug 12 42 – 16 9.10 TRUE
5 Storm vs. Roosters Aug 12 16 – 13 13.60 TRUE
6 Panthers vs. Cowboys Aug 12 24 – 16 2.00 TRUE
7 Warriors vs. Raiders Aug 13 16 – 36 -5.50 TRUE
8 Wests Tigers vs. Sea Eagles Aug 13 30 – 26 -1.20 FALSE

 

Predictions for Round 24

Here are the predictions for Round 24. The prediction is my estimated expected points difference with a positive margin being a win to the home team, and a negative margin a win to the away team.

Game Date Winner Prediction
1 Eels vs. Titans Aug 17 Eels 11.60
2 Rabbitohs vs. Warriors Aug 18 Rabbitohs 8.20
3 Broncos vs. Dragons Aug 18 Broncos 12.70
4 Knights vs. Storm Aug 19 Storm -13.80
5 Roosters vs. Wests Tigers Aug 19 Roosters 9.40
6 Cowboys vs. Sharks Aug 19 Cowboys 6.00
7 Raiders vs. Panthers Aug 20 Raiders 5.90
8 Bulldogs vs. Sea Eagles Aug 20 Sea Eagles -3.10

 

Currie Cup Predictions for Round 6

Team Ratings for Round 6

The basic method is described on my Department home page.

Here are the team ratings prior to this week’s games, along with the ratings at the start of the season.

Current Rating Rating at Season Start Difference
Cheetahs 4.88 4.33 0.50
Lions 4.54 7.41 -2.90
Sharks 3.67 2.15 1.50
Western Province 2.47 3.30 -0.80
Blue Bulls 1.90 2.32 -0.40
Griquas -10.00 -11.62 1.60
Pumas -10.20 -10.63 0.40

 

Performance So Far

So far there have been 15 matches played, 10 of which were correctly predicted, a success rate of 66.7%.
Here are the predictions for last week’s games.

Game Date Score Prediction Correct
1 Lions vs. Sharks Aug 12 31 – 47 6.80 FALSE
2 Western Province vs. Blue Bulls Aug 12 45 – 34 3.90 TRUE
3 Cheetahs vs. Griquas Aug 12 25 – 30 20.90 FALSE

 

Predictions for Round 6

Here are the predictions for Round 6. The prediction is my estimated expected points difference with a positive margin being a win to the home team, and a negative margin a win to the away team.

Game Date Winner Prediction
1 Western Province vs. Lions Aug 18 Western Province 2.40
2 Blue Bulls vs. Cheetahs Aug 19 Blue Bulls 1.50
3 Griquas vs. Pumas Aug 20 Griquas 4.70

 

August 14, 2017

Meters and litres

There have been a surprisingly large number of order-of-magnitude errors by people you’d expect to know better when commenting on Labour’s proposed water policy.  The Greens, last month, proposed a 10c/litre charge on water for bottling.  Labour are proposing a variable charge from one or two cents per cubic metre on irrigation up to “cents per litre, not ten cents” for bottled water not taken from a mains supply.

The conversion is fairly simple: 10c per litre is $100 per cubic metre, 1c per litre is $10 per cubic metre, one-one thousandth of a cent per litre is 1c per cubic metre.

How much does that come to for a cabbage or a carton of milk? According to Daniel Collins, the water taken from rivers or aquifers to produce a litre of milk varies from about 1L in the Waikato to about 250L in the Canterbury plains (you’ll see figures of 1000L, but these include needs met from local rainfall) .  So a 1c or 2c per cubic metre water charge would come out to less than a cent per litre of milk.

On the other hand, most of our milk isn’t produced for local consumption but for export as milk solids, at a bit more than 11 L of milk per kilogram.  At Canterbury water consumption, a 2c charge works out as about 6 cents per kg of milk solids. One Canterbury dairy farmer on Twitter estimated about twice that based on his production and consumption, so we’re at the right order of magnitude. Fonterra is currently paying $6.75 per kilogram of milk solids.

Horticulture is the other use that’s been in the news.  I found an estimate that, it takes 237L of water to produce 1kg of cabbage, ie, less than a quarter of a cubic metre, so less than 1 cent. Maybe NZ horticulture is less water-efficient than the average for the world, but that estimate, again, counts rainfall.

It’s hard to get up-to-date data, but in 2010 the total water use consented for horticulture, orchards, and viticulture was about 800 million cubic metres (PDF, table C-21), which would cost $8 million at 1c/cubic metre or $16 million at 2c/cubic metre; the amount actually used was lower.  In 2010, Horticulture NZ said the total production of the sector was worth $6 billion.

According to StatsNZ, total water for irrigation, other farming uses,  and industrial uses was consented at a maximum of about 8.5 billion cubic metres last year.  At 2c per cubic metre that would be 17 billion cents, or $170 million, if all the consented volume was taken and if there was no reduction in use as a result of charging.  Some fraction of the water would be priced a lot higher, and Labour is saying “less than $500 milllion“, which looks plausible.  That’s a fair sum of money, but it’s about two-thirds of one percent of Crown Revenue.

The cost to the water-using industries of a water charge isn’t trivial;  they’re going to notice the increase in their costs; this isn’t free money for the government or the taxpayer. I’m not going to comment on whether this is a good policy; that’s outside my expertise. But, some of the claims about costs have been off by huge factors, and people should be able to do basic maths better than that.