Posts filed under Research (180)

January 25, 2016

Meet Statistics summer scholar Eva Brammen

photo_brammenEvery summer, the Department of Statistics offers scholarships to a number of students so they can work with staff on real-world projects. Eva, right, is working on a sociolinguistic study with Dr Steffen Klaere. Eva, right,  explains:

“How often do you recognise the dialect of a neighbour and start classifying them into a certain category? Sociolinguistics studies patterns and structures in spoken language to identify some of the traits that enable us to do this kind of classification.

“Linguists have known for a long time that this involves recognising relevant signals in speech, and using those signals to differentiate some speakers and group others. Specific theories of language predict that some signals will cluster together, but there are remarkably few studies that seriously explore the patterns that might emerge across a number of signals.

“The study I am working on was carried out on Bequia Island in the Eastern Caribbean. The residents of three villages, Mount Pleasant, Paget Farm and Hamilton, say that they can identify which village people come from by their spoken language. The aim of this study was to detect signals in speech that tied the speaker to a location.

“One major result from this project was that the data are sometimes insufficient to answer the researchers’ questions satisfactorily. So we are tapping into the theory of experimental design to develop sampling protocols for sociolinguistic studies that permit researchers to answer their questions satisfactorily.

“I am 22 and come from Xanten in Germany. I studied Biomathematics at the Ernst-Moritz-Arndt-University in Greifswald, and have just finished my bachelor degree.

“What I like most about statistics is its connection with mathematical theory and its application to many different areas. You can work with people who aren’t necessarily statisticians.

“This is my first time in New Zealand, so with my time off I am looking forward to travelling around the country. During my holidays I will explore Northland and the Bay of Islands. After I have finished my project, I want to travel from Auckland to the far south and back again.”

January 21, 2016

Meet Statistics summer scholar David Chan

David ChanEvery summer, the Department of Statistics offers scholarships to a number of students so they can work with staff on real-world projects. David, right, is working on the New Zealand General Social Survey 2014 with Professor Thomas Lumley and Associate Professor Brian McArdle of Statistics, and  Senior Research Fellow Roy Lay-Yee and Professor Peter Davis from COMPASS, the Centre of Methods and Policy Application in the Social Sciences. David explains:

“My project involves exploring the social network data collected by the New Zealand General Social Survey 2014, which measures well-being and is the country’s biggest social survey outside the five-yearly census. I am essentially profiling each respondent’s social network, and then I’ll investigate the relationships between a person’s social network and their well-being.

“Measurements of well-being include socio-economic status, emotional and physical health, and overall life satisfaction. I intend to explore whether there is a link between social networks and well-being. I’ll then identify what kinds of people make a social network successful and how they influence a respondent’s well-being.

“I have just completed a conjoint Bachelor of Music and Bachelor of Science, majoring in composition and statistics respectively.  When I started my conjoint, I wasn’t too sure why statistics appealed to me. But I know now – statistics appeals to me because of its analytical nature to solving both theoretical and real-life problems.

“This summer, I’m planning to hang out with my friends and family. I’m planning to work on a small music project as well.”



January 19, 2016

Rebooting your immune system?

OneNews had a strange-looking story about multiple sclerosis tonight, with lots of footage of one British guy who’d got much better after treatment, and some mentions of an ongoing trial. With the trial still going on, it wasn’t clear why there was publicity now, or why it mostly involved just one patient.

I Google these things so you don’t have to.

So. It turns out there was a new research paper behind the publicity. There is an international trial of immune stem cell transplant for multiple sclerosis, which plans to follow patients for five years after treatment. The research paper describes what happened for the first three years.

As the OneNews story says, there has been a theory for a long time that if you wipe out someone’s immune system and start over again, the new version wouldn’t attack the nervous system and the disease would be cured. The problem was two-fold. First, wiping out someone’s immune system is an extraordinarily drastic treatment — you give a lethal dose of chemotherapy, and then rescue the patient with a transplanted immune system. Second, it didn’t work reliably.

The researcher behind the current trial believes that the treatment would work reliably if it was done earlier — during one of the characteristic remissions in disease progress, rather than after all else fails. This trial involves 25 patients, and so far the results are reasonably positive, but three years is really to soon to tell whether the benefits are worth the treatment. Even with full follow-up of this uncontrolled study it probably won’t be clear exactly who the treatment is worthwhile for.

Why the one British guy? Well,

The BBC’s Panorama programme was given exclusive access to several patients who have undergone the stem cell transplant.

The news story is clipped from a more in-depth current-affairs programme. That BBC link also shows a slightly worrying paranoid attitude from the lead researcher

He said: “There has been resistance to this in the pharma and academic world. This is not a technology you can patent and we have achieved this without industry backing.”

That might explain pharma, but there’s no real reason for the lack of patents to be a problem for academics. It’s more likely that doctors are reluctant to recommend ultra-high-dose chemotherapy without more concrete evidence. After all, it was supposed to work for breast cancer and didn’t, and it was theorised to work for HIV and doesn’t seem to. And at least in the past it didn’t work reliably for multiple sclerosis.

All in all, I think the OneNews story was too one-sided given the interim nature of the data and lack of availability of the treatment.  It could also have said a bit more about how nasty the treatment is.  I can see it being fine as part of a story in a current affairs programme such as Panorama, but as TV news I think it went too far.

January 11, 2016

Meet Statistics summer scholar Christopher Nottingham

Chris NottinghamEvery summer, the Department of Statistics offers scholarships to a number of students so they can work with staff on real-world projects. Christopher, right, is working with Associate Professor David Scott on All Blacks-related data. Christopher explains:

“My project is aimed at predicting the career lengths of current and future All Blacks based on data from all of the past All Blacks. This project will be useful as it will aid the planning within the All Blacks camp.

“This coming year, I will be studying a research-based MSc in Statistics. My thesis is in the area of quantitative fisheries science and will involve translating ADMB code into STAN code.

“Statistics appeals to me because of its diversity. For example, one day you could be analysing fisheries data, and the next, data relating to the All Blacks.

“In my spare time I enjoying walks along the beach, sailing and cycling around the waterfront with my wife.”



December 8, 2015

Sense of direction

From the Herald:

For a lot of men, the notion that they have a better sense of direction than women was already a fact, now a scientific study proves it.

Researchers from the Norwegian University of Science and Technology conducted a study where volunteers completed a series of navigation based tasks with brain scans taken in the process.

The results show men have a more adept sense of direction because they use a separate part of their brain to find their way.

The press release is here, and it describes the research as coming from two separate experiments. There’s a link to the research paper, but only for the second experiment involving testosterone. No link is given for the claim about men vs women.  I tried the PubMed research database, but the data aren’t in any of the other papers published by the same lead researcher.

The second experiment involved only women, half of whom were given a dose of testosterone. The story says

It was also found when women in the study had a dose of testosterone dropped onto their tongue, their navigational skills improved.

The research paper says

Surprisingly, the specific increase in MTL activity was not accompanied by increased navigation performance in the testosterone group.

That is, they saw changes in brain waves, but no change in navigation. The press release has this right, saying

“We hoped that they would be able to solve more tasks, but they didn’t.”

So, we have two claims. For one of them the evidence isn’t available, for the other it contradicts the story.

November 27, 2015

What should data use agreements look like?

After the news about Jarrod Gilbert being refused access to crime data, it’s worth looking at what data-use agreements should look like. I’m going to just consider agreements to use data for one’s own research — consulting projects and commissioned reports are different.

On Stuff, the police said

“Police reserves the right to discuss research findings with the academic if it misunderstands or misrepresents police data and information,” Evans said. 

Police could prevent further access to police resources if a researcher breached the agreement, he said. 

“Our priority is always to ensure that an appropriate balance is drawn between the privacy of individuals and academic freedom.

That would actually be reasonable if it only went that far: an organisation has confidential data, you get to see the data, they get to check whether you’ve reported anything that would breach their privacy restrictions. They can say “paragraph 2, on page 7, the street name together with the other information is identifying”, and you can agree or disagree, and potentially get an independent opinion from a mediator, ombudsman, arbitrator, or if it comes to that, a court.

The key here is that a breach of the agreement is objectively decidable and isn’t based on whether they like the conclusions. The problem comes with discretionary use of data. If the police have discretion about what analyses can be published, there’s no way to tell whether and to what extent they are misusing it. Even if they have only discretion about who can use the data, it’s hard to tell if they are using the implied threat of exclusion to persuade people to change results.

Medical statistics has a lot of experience with this sort of problem. That’s why the International Committee of Medical Journal Editors says, in their ‘conflict of interest’ recommendations

Authors should avoid entering in to agreements with study sponsors, both for-profit and non-profit, that interfere with authors’ access to all of the study’s data or that interfere with their ability to analyze and interpret the data and to prepare and publish manuscripts independently when and where they choose.

Under the ICMJE rules, I believe the sort of data-use restrictions we heard about for crime data would have to be disclosed as a conflict of interest.  The conflict wouldn’t necessarily lead to a paper being rejected, but it would be something for editors and reviewers to bear in mind as they looked at which results were presented and how they were interpreted.



November 25, 2015

Why we can’t trust crime analyses in New Zealand

Jarrod Gilbert has spent a lot of time hanging out with people in biker gangs.

That’s how he wrote his book, Patched, a history of gangs in New Zealand.  According to the Herald, it’s also the police’s rationale for not letting him have access to crime data. I don’t know whether it would be more charitable to the Police to accept that this is their real reason or not.

Conceivably, you might be concerned about access to these data for people with certain sorts of criminal connections. There might be ways to misuse the data, perhaps for some sort of scam on crime victims. No-one suggests that is  the sort of association with criminals that Dr Gilbert has.

It gets worse. According to Dr Gilbert, also writing in the Herald, the standard data access agreement for the data says police “retain the sole right to veto any findings from release.” Even drug companies don’t get away with those sorts of clauses nowadays.

To the extent these reports are true, we can’t entirely trust any analysis of New Zealand crime data that goes beyond what’s publicly available. There might be a lot of research that hasn’t been affected by censorship and threats to block future work, but we have no way of picking it out.

November 13, 2015

Blood pressure experiments

The two major US medical journals each published  a report this week about an experiment on healthy humans involving blood pressure.

One of these was a serious multi-year, multi-million-dollar clinical trial in over 9000 people, trying to refine the treatment of high blood pressure. The other looks like a borderline-ethical publicity stunt.  Guess which one ended up in Stuff.

In the experiment, 25 people were given an energy drink

We hypothesized that drinking a commercially available energy drink compared with a placebo drink increases blood pressure and heart rate in healthy adults at rest and in response to mental and physical stress (primary outcomes). Furthermore, we hypothesized that these hemodynamic changes are associated with sympathetic activation, which could predispose to increased cardiovascular risk (secondary outcomes).

The result was that consuming caffeine made blood pressure and heart rate go up for a short period,  and that levels of the hormone norepinephrine  in the blood also went up. Oh, and that consuming caffeine led to more caffeine in the bloodstream than consuming no caffeine.

The findings about blood pressure, heart rate, and norepinephrine are about as surprising as the finding about caffeine in the blood. If you do a Google search on “caffeine blood pressure”, the recommendation box at the top of the results is advice from the Mayo Clinic. It begins

Caffeine can cause a short, but dramatic increase in your blood pressure, even if you don’t have high blood pressure.

The Mayo Clinic, incidentally, is where the new experiment was done.

I looked at the PubMed research database for research on caffeine and blood pressure.  The oldest paper in English for which I could get full text was from 1981. It begins

Acute caffeine in subjects who do not normally ingest methylxanthines leads to increases in blood pressure, heart rate, plasma epinephrine, plasma norepinephrine, plasma renin activity, and urinary catecholamines.

This wasn’t news already in 1981.

Now, I don’t actually like energy drinks; I prefer my caffeine hot and bitter.  Since many energy drinks have as much caffeine as good coffee and some have almost as much sugar as apple juice, there’s probably some unsafe level of consumption, especially for kids.

What I don’t like is dressing this up as new science. The acute effects of caffeine on the cardiovascular system have been known for a long time. It seems strange to do a new human experiment just to demonstrate them again. In particular, it seems ethically dubious if you think these effects are dangerous enough to put out a press release about.


November 10, 2015

New blood pressure trial

A big randomised trial comparing strategies for treating high blood pressure has just ended early (paper, paywalled).  There’s good coverage in the New York Times, and there will probably be a lot more over the next week. It’s a relatively complicated story.

The main points:

  • Traditionally, doctors try to get your blood pressure below 140mmHg, but some people always thought lower would be better.
  • The study, funded by the US government, randomly allocated over 9000 people with high blood pressure and some other heart disease risk factor (but not diabetes) to either try to get blood pressure of 140mmHg or try to get 120mmHg.
  • A previous trial with the same targets, but in people with diabetes, had been unimpressive: the results slightly favoured more-intensive treatment, but the difference was small, and well within the variation you’d expect by chance.
  • In the new trial blood pressure targeting worked really well: the average blood pressure in the low group was 122mmHg, and in the normal group was 135.
  • Typically, people in the low group took two or three blood pressure medications, those in the normal group typically took one or two — but in both cases with quite a lot of variation.
  • There were 76 fewer ‘primary outcome events’:  heart attack, stroke, heart failure, or death from heart disease in the low BP group, and 55 fewer deaths from any cause.
  • From the beginning, the plan was to stop whenever the difference in number of ‘primary outcome events’ exceeded a specified threshold, unless there was a good reason based on the data to continue. The difference had been just barely over the threshold at the previous analysis, and they continued. In mid-September it was clearly over the threshold, and they stopped.
  • Stopping early will tend to overestimate the benefit, but the fact that they waited for one more analysis reduces this bias.

I’m surprised the benefit from extreme blood pressure reduction is so large (in a relative sense), but even more surprised that they managed to get so many healthy people to take their treatments that consistently for over three years.  As context for this, data from a US national survey in 2011-12 showed only about two-thirds of those currently taking medications for high blood pressure even get down to 140mmHg.

In an absolute sense the risk reduction is relatively small: for every thousand people on intensive blood pressure reduction — healthy people taking multiple pills, multiple times per day — they saw 12 fewer deaths and 16 fewer ‘events’.   On the other hand, the treatments are cheap and most people can find a combination without much in the way of side effects. If intensive treatment becomes standard, there will probably be more use of combination pills to make multiple drugs easier to take.

There’s one moderately worrying factor: a higher rate of kidney impairment in the low BP group (higher by a couple of percentage points). The researchers indicate that they don’t know if this is real, permanent  damage, and that more follow-up and testing of those people is needed. If it is a real problem it could be more serious in ordinary medical practice than in the obsessively-monitored trial.  This may well explain why the trial didn’t stop even earlier:  the monitoring committee would have wanted to be sure the benefits were real given the possibility of adverse effects — the sort of difficult decision that is why you have experienced, independent monitoring committees. 

November 9, 2015

To each according to his needs

There’s a fairly overblown story in the Guardian about religion and altruism

“Overall, our findings … contradict the commonsense and popular assumption that children from religious households are more altruistic and kind towards others,” said the authors of The Negative Association Between Religiousness and Children’s Altruism Across the World, published this week in Current Biology.

“More generally, they call into question whether religion is vital for moral development, supporting the idea that secularisation of moral discourse will not reduce human kindness – in fact, it will do just the opposite.”

The research found that kindergarten (update: and primary school) children from religious families scored lower on an altruism test (a version of the Dictator game).  Given ten stickers, non-religious children would give about one more away on average than religious children.


While it’s obviously true that this sort of simple moral behaviour doesn’t require religion, the cause-and-effect conclusion the story is trying to draw is stronger than the data. I’m pretty confident the people quoted approvingly wouldn’t have been as convinced by the same sort of research if it had found the opposite result.

The research does provide convincing evidence on another point, though: three-dimensional graphics are a Bad Idea.