Saturday, 30 November 2013

Lost

The results of the ISBA elections have come out and unfortunately, I've been beaten to the post of programme chair for the Section on Biostatistics and Pharmaceutical Statistics.

I am not sure by how much $-$ I meant to ask for more details, but I've been a bit busy last week and didn't have the time. I suspect that the fact that only current members of the sections were allowed to vote wasn't good for me, as, probably, it increased the incumbent's advantage. [CORRECTION: As per ISBA's official numbers, I actually lost 10-9]

Anyway, I should congratulate Telba Irony, who's been re-elected and hopefully get her to take some of my programme points (starting with sponsoring the next BayesPharma) on board anyway.

My talk at the LSHTM

Yesterday I gave a talk on our RDD project at the Centre for Statistical Methodology of the London School of Hygiene and Tropical Medicine. While presenting me, Karla (the organiser of the seminar) joked that I should go for a hat trick of presentations at the LSHTM, since only last month I gave another talk (on the structural zero problems in health economics $-$ on a related note, the paper, which I also discussed here, was actually accepted by Statistics in Medicine).

The main point of this talk was to try and point out various advantages of including genuine prior knowledge in the RDD framework, to try and get suitable estimates and make the assumptions underlying it more robust. I think we need to clarify a couple of points, but also I got good comments, so it was very helpful!

The slides of the talks are here.

Wednesday, 27 November 2013

PSMR 2014

Registration for the short course on Practical Statistics for Medical Research (PSMR) 2014 are now open. Here is the advert we've published on the BMJ with all the relevant information and details and even more info & details are here $-$ in case you're interested...

Saturday, 16 November 2013

BCEs0 version 1.1 on CRAN

O' scarrafone
As I was responding to the points raised by two referees and the editor on my paper on cost-effectiveness with structural zeros (the preliminary version was here, while I have presenting it in a few talks and discussed it here, here, here and here).

I have to say most of the comments I received made a lot of sense and were extremely helpful. In particular, when I was thinking about how I should address them, I realised that I was much better off by modelling all the prior distributions on the scale of the mean and standard deviation of the cost variable, rather than using the original scale (e.g. rate & shape for the Gamma distribution).

This is true in general, of course, but it is quite helpful in this case, because I want to impose a very informative prior for the subjects for whom a 0 has been observed (so that in the posterior the mean cost is identically 0, a fortiori). I have updated the software webpage, which now reports the full list of inputs required by the main function
bces0.

In particular, I have modified the original code so that:
  1. a treatment-specific threshold for the default Uniform prior on the mean and standard deviation of the costs for the non-null component (previously, I was assuming a single value to be applied to both treatment being compared);
  2. a "robust" option, which by default is set to TRUE, which implies that "minimally informative" Cauchy priors are specified on the coefficients for the pattern model for the zero cost indicator. If robust is set to FALSE, then BCEs0 will use a vague Normal prior instead;
  3. a "model.file" option, which allows you to specify the name of the .txt file to which the JAGS model code is saved. This is not quite fundamental, but as I was testing the package I kind of got annoyed that every time I run it, it would overwrite previous versions of the model file, which I may need for future tests. And so I changed this.
I think the paper in its current (hopefully final!) version looks much better and the more I think about the overall problem and how the model deals with it, the more I kind of like it. But then again, as we say in Italian: "ogni scarrafone e' bello a mamma sua", which poorly translates into English as "every cockroach is beatiful to its own mother's eyes"...

Thursday, 14 November 2013

Loophole

I think I should thank Marta (again!) for this post, as she made me think about it while we were riding together to the Stan workshop, in one of our now ("A XY", that is, as opposed to "B XY" when we used to do so all the time) rare joint outings on the Vespa.

Lately, quite a few London Buses advertise electronic cigarettes, which we found peculiar, given the ban on tobacco advertising. Now, of course, technically, electronic cigarettes have nothing to do with tobacco, so, I'm guessing, they are perfectly within the law in advertising them.

However (and I must say I don't really know enough about this!), it appears that some evidence is present to hint at potential risks to health due to e-cigarette consumption. So, one may wonder, why are these allowed to advertise without formal investigations on their safety at least planned? Again: I may be completely ignorant of government-commissioned studies into this matter (in which case, well done UK Gro├če Koalition!). But I may also be guessing well, right?...

Monday, 11 November 2013

Imperialstan

Despite the map here, I'm not going to talk about yet another fraction of the former Soviet Empire which is taken the form of a people's republic, possibly with witty British Ambassadors.

In fact, I'm going to talk about the Stan workshop that I have be to, earlier today, which was held at Imperial College. My friend Lea organised it and Mike Betancourt (who's actually in my department at UCL) run the show (brilliantly, it has to be said).

In the morning, Mike gave a brief overview of MCMC and introduced the basics of Hamiltonian Monte Carlo (I think this by Radford Neal is just a great introduction to the topic). Then in the afternoon he concentrated on Stan and rstan in particular (which, unsurprisingly, is the R interface to the actual HMC engine).

I think this was kind of the first of a potential series of similar talks/workshops and I found it very useful. Of course it's always difficult to strike a balance between how in depth you want to go with the theory and the examples, so for instance, I think a little more on the actual NUTS algorithm would have been helpful $-$ but as I said, I know full well how hard it is to do this, so well done, Mike!

Saturday, 9 November 2013

Keynote speaker

Earlier today, I was trying to finish preparing the poster for the Clinical Trials Methodology Conference $-$ I'll have both the poster presentation (on the Expected Value of Information under mixed strategies) and my talk on the Stepped Wedge design on the Monday, so by 3pm I'll be just wandering around the sessions having done my duty.

Luckily, XY slept a couple of hours, so I could actually do some work. But then he woke up and while he was playing in the living room, he found my badge from the Chemometrics Workshop and the latest copy of Significance

I did put the badge around his neck the first time, but he quickly learned to do it himself; at which point he kept putting it on, while carefully reading the magazine. I think he quite looks the part, doesn't he?

Thursday, 7 November 2013

Rescue remedy

Interesting day, today. I woke up really early (3.45am) to catch my flight to Amsterdam to give my talk at the Chemometrics Workshop. The cab got me to the airport early enough so that I could clear security, have a coffee and slowly make my way to the gate. 

But when I arrived there, I realised that before leaving home, on the spur of the moment, I decided to take a different jacket $-$ you know, just to stir things up a little. Too bad that I had left my passport in the jacket that was at home... But, no matter; after all I still have my Italian ID card $-$ I don't often use it, but surely that would come to the rescue and allow me to board my flight. Except that it was kind of expired (well $-$ "kind of" meaning expired two years ago). And so they kindly escorted me outside the departures area.

At which point (it was about 6am), I decided it was time for desperate measures and called home. Thankfully, my sister-in-law Sara is visiting, so, I thought, if I can get Marta, she could come and bring me my passport and XY won't be alone at home. So all will be fine. Except that, of course, at that point I had missed my flight. But they assured me that the next one would still get me to Amsterdam on time. So I just needed to pay a reasonable "recovery fee" and get the passport in time to re-do the check in, re-clear security (and possibly re-take a coffee).

I can't really blame her, but it was kind of difficult to get hold of Marta and I had to ring quite a few times before she actually picked up the phone. And of course, she was quite upset too! (You know the kind of sleepy voice that basically sounds like: "I would probably kill you and then leave you if you were here"). But again, I don't think I can really blame her... Anyway, thankfully, enter super-wife to the rescue! She drove the 45 minutes from our house to the airport and managed to get me my passport on time.

Oh, did I mention that the flight they told me would get me to Amsterdam on time was actually full, so they couldn't rebook me on that one? Yeah $-$ that happened too... Luckily, just when I was about to give up, I thought I'd check with British Airways; I was half expecting they would ask charge £100,000 but in fact I only had to pay just a little more than the "recovery fee" would have been, so I bought a one-way ticket. 

In the end, I did manage to get to Utrecht on time. The talk was scheduled for 11.15 and I got to the conference centre with well over 10 minutes to spare! Because I didn't want to miss on any of the possible excitement of the day, I also witnessed a robbery on the train from Schipol $-$ an American guy got his backpack stolen by a lovely-looking (but clearly evil-acting) lady when the train stopped at one of the stations along the way.

By the way, the talk went well, I thought. It was probably a bit too long and I had to cut one of the examples short, but people seem to have liked it and asked me quite a few questions. I'm at the airport now, waiting to board my flight back home $-$ assuming I still have a home, that is. I did buy chocolate in the hope of placating my lovely, forgiving other half...

Tuesday, 5 November 2013

Bayesian Biostatistics 2014

This has to do with the ISBA Biostats section (I suppose it will be even more, if I am elected to the post of Program Chair, but I'll try and be involved even if I don't win!): the next Bayesian Biostatistics Conference has just been announced and will be held at MD Anderson (Houston, TX) this coming February (12-14).

I went to the 2009 edition, which was good. Most of the emphasis, as is obvious given the research interest of the organisers, was on clinical trials, in particular early phase. At that time I wasn't really working on that topic, so it was good for the academic experience, but it didn't have immediate impact on my personal work.


Now I am doing some work that is related to this, so this would probably be even more interesting (although it does happen in the middle of the teaching term, so I'm not sure I'll be able to go...). And in any case, the topics are quite diverse:
  • Imaging analysis
  • NGS data analysis
  • Subgroup analysis
  • Enrichment designs
  • Integrative genomics
  • Deconvolving tumor heterogeneity
  • Biomarker-driven adaptive designs
  • Drawing inferences from large databases
  • Anti-infectives and other non-cancer therapeutic areas
so it wouldn't necessarily be just about clinical trials!

Typos in BMHE



No matter how many times you check and no matter how good the publishers are, I'm guessing there's no way out of getting typos in a publication, especially if it's a relatively long one, such as a book.

I've just discovered a couple in BMHE, which I thought I should try and correct (or at least point out) here.


  1. Page 45, figure 2.5: the bottom part of the decision tree shows the possible outcomes when the operation does not go well. However, the headings for the branch out of the "Patient lives" random node are both "No". The top one should read "Yes" (much as in the top half of the tree).
  2. Because of the changes in the R2jags package, the code in chapter 4 and 5 should be slightly modified to say attach.jags() instead of attach.bugs() $-$ I've already explained this in more details here.
  3. Page 186: I don't really like that the transition matrix overflows to the very bottom of the page $-$ but that's not my fault... My original file didn't have that.
I'm sure there are more $-$ I'll post them when I catch them (or, more likely, when people make me notice them: I have to thank my student Shabai for noticing the mistake in the decision tree).

Monday, 4 November 2013

My talk @ the Dutch Chemometrics Symposium

For same reason, Paul Eilers really liked the talk I gave on INLA at the BayesPharma workshop earlier this year and so he invited me to talk at the Dutch Chemometrics Symposium.

Now: you may ask what have I got to do with chemometrics. And you would be right in doing that $-$ in fact, such is the extent of my ignorance on the subject, that I had to actually look "chemometrics" up... But Paul asked me to talk about Bayesian statistics in general, so that was very much up my street, which is why I gladly agreed.

The workshop is this coming Thursday (7th November) in Utrecht. I've put the slides of my talk: "Come to the dark side: we got cookies! An introduction to Bayesian statistics" here.