I almost didn’t share these HarleMCMC videos, but how long could I resist, really?
We’ll see how this holds up to repeated viewing…
Here is a math/dance video for the ages:
Math and Dance
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Filed under MCMC, Uncategorized
Stan in IPython: reproducing 8 schools
Continuing my experiment using Stan in IPython, here is a notebook to do a bit of the eight schools example from the RStan Getting Started Guide.
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Filed under software engineering
Stan in IPython: getting starting
There has been a low murmur about new MCMC package bouncing through my email inbox for a while now. Stan, it is. The project has reached the point where the developers are soliciting Python integration volunteers, so I decided it is time to check it out.
Good news, it installed and ran the example without frustration! I don’t take that for granted with research software.
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Filed under software engineering
Journal Club: Garbage code redistribution
This week brings another locally grown reading to our journal club, Algorithms for enhancing public health utility of national causes-of-death data. As they say in the text:
While some practitioners may object to the term “garbage code” as pejorative, alternative terms have not yet caught on in the literature. We follow this practice and use the term garbage code (GC) to refer to all deaths assigned to codes that should be redistributed to enhance the validity of public health analysis.
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Filed under global health
GBD Country-level Visualizations
Very cool new visualizations of the GBD2010 results are now on-line: http://viz.healthmetricsandevaluation.org/gbd-compare/
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Filed under global health
Journal club: Performance of Health Workers in the Management of Seriously Sick Children at a Kenyan Tertiary Hospital
This week’s journal club selection is Performance of Health Workers in the Management of Seriously Sick Children at a Kenyan Tertiary Hospital: Before and after a Training Intervention by Irimu et al. That sounds hard to quantify, so I wonder how they did it.
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Filed under global health
Software carpentry at UW
I’m spending yesterday and today helping out with a two day software carpentry workshop at UW.
Software Carpentry helps researchers be more productive by teaching them basic computing skills. We run boot camps at dozens of sites around the world, and also provide open access material online for self-paced instruction. The benefits are more reliable results and higher productivity: a day a week is common, and a ten-fold improvement isn’t rare.
I am impressed by the curriculum and by the attention to evaluation, not an easy task in any educational setting. The 20% productivity increase is an interesting claim. From what I observed yesterday, I would expect huge heterogeneity based on past experience, and I would expect this heterogeneity to be hard to predict.
Extra Journal Club: Cd exposure and neurodevelopment
I’m sure reading a lot lately. That is good. This week, I’m filling in for the PBF journal club, too, and today we’ll be discussing Ciesielski et al’s paper Cadmium Exposure and Neurodevelopmental Outcomes in U.S. Children, which uses 6 years of NHANES data to weigh the evidence that low levels of cadmium cause learning disabilities in children.
All the data is available on the CDC’s website, so I thought I’d take a look at it. Here is an interesting little plot that popped out: prevalence of parent-reported learning disabilities in 6-15 year olds as a function of income-to-poverty-line ratio.
Would you have expected that?
Filed under global health, Mysteries
Journal Club: GBD 2010
I wonder how we’ll tear holes in the arguments of this week’s journal club papers, since they are locally produced:
- Murray et al, GBD 2010: design, definitions, and metrics, The Lancet, Volume 380, Issue 9859, Pages 2063 – 2066, 15 December 2012.
- Murray et al, Disability-adjusted life years (DALYs) for 291 diseases and injuries in 21 regions, 1990—2010: a systematic analysis for the Global Burden of Disease Study 2010, The Lancet, Volume 380, Issue 9859, Pages 2197 – 2223, 15 December 2012.
Also have a look at the accompanying visualizations.
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Filed under global health
Contests and links
There are a couple of Kaggle contests that I call your attention to, now that I have been convinced contests are fun, not tacky: Whale Detection Challenge and
Predicting Parkinson’s Disease Progression. The are both the kind of thing that someone might call “Big Data”, but in two different dimensions.
The whales have 23 teams entered at the time of writing, while PD has zero. I bet that is because there is a way to score interim results on whale detection, but the PD contest is judged based on a 5 page report.
Filed under machine learning
Healthy Algorithms 