Tag Archives: healthcare

Dataviz of the week, 17/5/2017

nextstrain.org is a website that offers real-time tracking of pathogens as they evolve (flu, ebola, dengue, all your favourites are here). Data gets pulled in from various monitoring systems worldwide and represented with interactive content in several pretty ways:

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They have their own libraries called fauna, augur and auspice, the last of these doing the dataviz stuff, and as far as I could tell built on D3. I don’t pretend to understand the genetic and genomic work that has to go on to process the raw data but that is clearly substantial.

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How to assess quality in primary care

Jim Parle, of the University of Birmingham, and I have an editorial just out in the BMJ responding to the recent Health Foundation report on quality indicators in primary care. There’s a lot one could say about this subject but we had to be brief and engaging. Hopefully the references serve as a springboard for readers who want to dig in more. In brief:

  • We think it’s great that composite indicators received a strongly worded ‘no’; remember that Jeremy Hunt (and probably Jennifer Dixon too) started this process quite keen on global measures of quality reducing all the complexity of primary care organisation and care to a traffic light.
  • We agree that a single port of call would be invaluable. Too much of this information is scattered about online
    • but along with that, there’s a need for standardised methods of analysis and presentation; this is not talked about much but it causes a lot of confusion. At NAGCAE, my role is to keep banging on about this to make analysts learn from the best in the business and to stop spending taxpayers’ money reinventing wheels via expensive private-sector agencies
    • and interactive online content is ideally suited to this, viz ‘State of Obesity’
  • We think they should have talked about the value of accurate communication of uncertainty, arising from many different sources. Consider Elizabeth Ford’s work on GP coding, or George Leckie and Harvey Goldstein on school league tables (googlez-vous).
  • We also think they should have talked about perverse incentives and gaming. It never hurts to remind politicians of Mr Blair’s uncomfortable appearance on Question Time

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The irresistible lure of secondary analysis

The one thing that particularly worries me about the Department of Health in its various semi-devolved guises making 40% cuts to non-NHS spending is that some of the activities I get involved in or advise on, which rely on accurate data, can appear beguilingly simple to cut by falling back on existing data sources, but the devil is in the detail. It is very hard to draw meaningful conclusions from data that were not collected for that purpose, but when the analytical team or their boss is pressed to give a one-line summary to the politicians, it all sounds hunky dory. The guy holding the purse strings might never know that the simple one-liner is built on flimsy foundations.

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They each wanted to improve education; together, they ruined it

If you have any interest in using data to improve public services like education or healthcare, whether enthusiastic or sceptical, read this article. The story is a familiar one to me but rarely sees the public eye in such careful detail as it does here. The road to hell, as you know, is paved with dashboards, performance indicators and league tables.

Righton Johnson, a lawyer with Balch & Bingham who sat in on interviews, told me that it became clear that most teachers thought they were committing a victimless crime. “They didn’t see the value in the test, so they didn’t see that they were devaluing the kids by cheating,” she said. Unlike recent cheating scandals at Harvard and at Stuyvesant High School, where privileged students were concerned with their own advancement, those who cheated at Parks were never convinced of the importance of the tests; they viewed the cheating as a door they had to pass through in order to focus on issues that seemed more relevant to their students’ lives.

Lewis said, “I know that sometimes when you’re in the fight, and you’re swinging, you want to win so badly that you don’t recognize where your blows land.”

There have been similar stories in the UK news recently, but you can get it all from Parks, so I suggest just reading this and carrying those cautionary ideas around with you.

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Can statistics heal?

(A rather florid headline, I’ll admit.)

I was reading this article on survivors of the 2005 London bombings and was struck by the story of someone who had been involved in two acts of terrorism but found it helpful to learn the stats from a disinterested third party:

One patient – so unlucky as to have also been caught up in a previous terrorist attack – was only reassured after being taken to a bookmakers to see how long the odds were of being in a third.

It makes me wonder how statisticians can help provide this sort of information to clinicians caring for people with PTSD and related problems. It is so easy to construct comparisons that are not quite right (horse-riding=ecstasy, for example, or Sally Clark, or lightning = cricket balls), so it is unfair to expect the doctor or psychologist to put them together as required. Perhaps future generations will have a more advanced grasp of statistics from school, but I wouldn’t count on it being able to overcome pathological distortions of risk perception. There may be a role for the quantified-self sort of data here; consider the popularity of pedometers and GPS for knowing how much exercise you really are doing.

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Extract data from Dementia Care Mapping spreadsheets into Stata

March 2017 edit: I removed chunks of code now that I’m freelancing – if you’re interested in an automated, fast, reliable way of getting LOTS of DCM data into one place, contact me! I can do it for you or provide software to do it. Stata and R are both options and then data can go into SPSS or whatever, or it can be a stand-alone executable program.

I’ve recently been involved in three projects using the Dementia Care Mapping data collection tool. This is a neat way of getting really detailed longitudinal observations on the activity, mood, interactions and wellbeing of people with dementia in group settings. The makers of the DCM provide a spreadsheet which looks like this:

Copied from the Bradford DCM manual. These are not real data (I hope!)

Copied from the Bradford DCM manual. These are not real data (I hope!)

that is, there is a row of BCC behaviour codes and a row of ME quality of life codes for each person, and they are captured typically every five minutes. Date and time and other stuff that might be important are floating above the main body of the data. Subsequent worksheets provide descriptive tables and graphs, but we will ignore those as we want to extract data into Stata for more detailed analysis. (But let me, in passing, point out this work in Bradford, which is moving towards electronic collection.)

The good news is that Stata versions 12 and 13 have improved import commands, with specific support for Excel spreadsheets. You can specify that you want to take only particular cells, so that allows us to pull in the stuff at the top like data and time, and then go back and get the bulk of the data.

In the most recent project, there were several care homes, and each was visited several times, and within each visit there was at least a before, during, and after spreadsheet. Thankfully, my colleague who did the collection had very consistently filed everything away so the file and folder structure was very consistent, and that is crucial if you want to automate the process of extracting and compiling the data.

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Visualising data for clinical audit – videos now online

HQIP held a most enjoyable seminar recently on presenting healthcare quality data to clinicians and the public. It’s all now online on YouTube and I recommend it to anyone working in this field.

It took them hours to do my make-up but it was worth it.

Really, I’d now like to reverse the order of topics in my talk (and a nother version of it popped up at Hertfordshire University Business School), starting with interactivity and trends, then going into chart design and perception a bit more. Stats could appear at the end if there’s time, along with software, if there’s time. I’ve also decided to ditch the silly pictures and have concrete examples, good and bad, at every stage. We live and learn (mostly).

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