Using R in research education

I’m at the UserR! 2010 conference at NIST in Gaithersburg, Maryland. This is the main annual event for R users. there have been whole series of presentations on using R in education. The full program lists the Pedagogic talks (3 sessions, and 9 talks, on the first day).
What I’ve seen so far is great work on training people in data analysis, in statistics and (to some extent) in probability, The work is really good, and I have lots of new ideas. What’s been lacking, and what I need to think about more, is the other part. There are at least three other elements,

  1. asking intelligent questions, that is questions that are well enough specified to be answered, and well enough considered to actually matter.
  2. using research information, and clinical information, to support good clinical decisions
  3. data cleaning, data exploration,

Any thoughts?

Abolishing Fas?

Deputy Ruairi Quinn has called for Fas to be abolished and its budget diverted to the IT sector. While I share his frustration with the running of Fas, it is, I believe, a serious mistake to think that it can easily be replaced.

Just as the IT’s and the universities have different and complementary roles, so Fas fills a vital slot in the educational landscape. No-one else has the same combination of guidance, staged training, and
technical options. We need it, we need it to work well, accountably and efficiently, and we need it more than ever now as the economy crumbles. The only chance for many people to get the skills they need is Fas, or something very like it.

TD’s need to hold Fas, and the rest of the Education sector, accountable for delivery, and efficiency. Soundbite policies got us into the present mess, but will not suffice to get us out of it.
(Irish Times Saturday Sept 4th)

John Nelder has died

Prof. John Nelder, one of the more remarkable British statisticians, has died, at the age of 85.

I never had the good fortune to meet him, but his work had a great influence on me. McCullagh and Nelder, Generalized Linear Models, was my first technical statistics book, as an epidemiology PhD student, and I used Genstat, which he originated, throughout my PhD. His clear explanations have stayed with me, and I am proud to recycle them to my own students (with attribution!). Genstat also showed me a way past the more ‘black box’ approach of SPSS and SAS, to the interactive data analysis, exemplified by R. I’d like to thank him, and offer my condolences to his family.

Impact of health expenditure on health outcomes in Ireland

    Situation
    There have been major improvement in the health of the Irish population over the last 20 years, (e.g. McDaid, 2009 p228), with a rise in life expectancy overall of 5 years from 1990 to 2006. The rate of increase seems to have risen in about 1999, and while Irish life expectancy is still a little low by EU standards, there has been substantial improvement, especially for men. The health care system has many weaknesses, notably very poorly developed primary care, giving us, for example, strikingly low immunization rates (McDaid, 2009, p156). However public health care expenditure has risen substantially as the economy grew from 1995 onwards, form about €3 billion to about €15 billion in 2009. Overall health care expenditure has risen from 8.8% of GNP in 1995 to approximately 10.7% in 2007. What has been the impact of this substantial change, and how much of the improved health outcomes are attributable to the increased expenditure?

    Conclusions
    The existing evidence strongly suggests that :-

    1. Mortality has fallen sharply over the last thirty years
    2. Healthcare expenditure has made a modest contribution to this, substantially less than one third of the total, and possibly only a few percentage points.
    3. Development of primary care, and the more effective delivery of prevention measures will likely lead to the greatest declines in mortality.

    Continue reading →

UK Election – even less democratic than I thought.

I got the UK election results from the BBC just now, and the figures are amazing.

UK election results

PartySeatPercentage of votes castChange in vote since last timeVotes per seatFair number of seats
Conservative30636.13.834,889234
Labour25829-6.233,350188
Liberal Democrats57231119,788149
DUP80.6-0.321,0274
SNP61.70.181,89811
SF50,6-0.134,3884
Plaid Cymru30.6-0.155,1314
SDLP30,4-0.136,9902
Green11-0.1285,6166
Alliance10.1042,7621

This is embarrassing… No wonder Labour and the Tories oppose PR.

Google webmaster tools and wordpress

I wanted to set my site up on Google webmaster’s tools. Google offer two choices, one is to put a meta tag, with defined content, in the header of the index page. This would require programming with PHP which is a little beyond my scope. The alternative to is to download a html page, provided by Google, and put it in your website. The page is actually 1 line of text, so it’s not really html.

The obvious way to do this is to add a page with WordPress, as advised, for example, on Jalal P. Jha’s blog. Obvious, but wrong. Jalal’s advice applies, as he says, to sites hosted on WordPress.com, not to self-hosted sites, such as this. It’s possible to create a WordPress page with the correct title, but WordPress adds in a lot of invisible bits and pieces, which alter the contents of the file, which is what Google checks.

So, the solution is very simple, use ftp, to add the page provided by Google, to the right directory on your web host, in my case the root directory of this website, (/website/httpdocs/astaines) and you are done.

WordPress difficulties- wp-config.php [SOLVED]

I installed WordPress, which you are now reading, from my hosting provider’s Application Vault, and it worked beautifully, but, I wanted to use nice permalinks, which is not possible, if you have installed in this way. This was confirmed, impressively quickly, by Blacknight technical support guru Nils.

So, I installed it manually, and made a daft error, which I recount here, for the instruction or amusement of others.

WordPress configuration, from the users perspective, is done through the file ‘wp-config.php’ file, which you must create when installing manually, by editing the supplied wp-config-sample.php file. The pertinent bit is :-
/** The name of the database for WordPress */
define('DB_NAME', 'dbname');

/** MySQL database username */
define(‘DB_USER’, ‘user’);

/** MySQL database password */
define(‘DB_PASSWORD’, ‘password’); [[This isn’t my password..]]

/** MySQL hostname */
define(‘DB_HOST’, ‘localhost’);

which doesn’t work.

The error is the last line
/** MySQL hostname */
define('DB_HOST', 'localhost');

This is is in the sample file, and several bits of WordPress documentation say things like – ”leave this as ‘localhost’ for 99% of hosting suppliers out there”. However, Blacknight, and many other hosting providers keep their MySQL databases on a different server to the webservers, and so provide an internal hostname, which is what needs to go in the DB_HOST line.

In my case it is :-
Internal hostname: mysql496int.cp.blacknight.com

So the lines in wp-config.php should read

/** MySQL hostname */
define('DB_HOST', 'mysql496int.cp.blacknight.com');

which does work.

Simple when you know how…

Foul-up in cancer services – so what else is new?

Confusion reigns in the Irish health services. The Minister has been asked to resign, because of a very serious foul-up in breast cancer care in the Midlands, but has declined. The Taoiseach (prime minister if you only speak English) has promised her his full support, which is normally a prelude to walking the plank. The opposition (full disclosure – I support them) are rubbing their hands with glee. The night is hideous with the sound of chickens coming home to roost.

So, what happened?

Well, like most stories it depends when you start. If you start recently, it seems that a substantial number of women who had mammography (breast x-rays) , and a rather larger number who had ultrasound breast examinations, in Portlaoise hospital, have needed to have them re-done, and at least 6 of these women have breast cancer. At least 80 require a full re-assessment. Three consultants spent all day (Saturday 23rd) today in Portlaoise running an emergency surgical clinic to look after he first batch of these women.

Going back a bit, queries were raised about one radiologist in the hospital, and her work, both in mammography, and ultrasound, is being re-investigated. There seem to be two investigations going on, and I’m not clear how, or indeed if, they relate. I may not be alone in this, as the minister found out about the second investigation while attending an Oireachtas (parliament) committee meeting three days ago.

Going back quite a bit, the Midland Heath Board, which no longer exists, rejected a proposal to establish one cancer centre in their area about six years ago, and instead decided that it would be nice to have three. While it might have been nice, it was also completely impossible, but that didn’t stop them. With a lethal combination of chutzpah and ignorance they set up three inadequate centres.

What role this played in the later disaster is not yet clear. It may be that some poor sod is genuinely culpable, but it seems more likely that this represents another system failure.