Fraud in Medical Research

Already in September last year, Der Spiegel published an interview with Peter Wilmshurst, a British medical doctor and whistleblower who made fraudulent practices in medical research public:

In the course of the 66-year-old’s career, he conducted studies for pharmaceutical and medical devices companies, and unlike many of his colleagues, never hesitated to publish negative results. He’s been the subject of multiple cases of legal action and risked bankruptcy and his reputation to expose misconduct in the pharmaceutical industry.

A very interesting article that’s worth reading. Fact is, that companies who have a strong economic interest in the scientific process will have an impact on the quality of the research. It is, again and again, horrible to learn how far companies try to go – and often successfully do. While medical companies has always been an obvious target (and perpetrator), the problem runs deeper than the narrative of “Big Pharma”.  Continue reading Fraud in Medical Research

The Vanual: Customizing a Van for a Mobile Lifestyle

While sitting in one of my three offices, dreaming of beautiful, exotic and serene places is just natural. Zach Both does not dream about these places, he just goes there. But he is not a travel-a-my-life type of guy, but a film maker and designer who happens to life mobile: He customized a van to have a bed and a kitchen to live where likes to while still doing his day-to-day business (more or less):

Zach Both is a young filmmaker who in a past life worked as a designer and art director. His passion for telling unique and unusual stories through filmmaking has lead him to travel the country in a van that doubles as his mobile production company.

Thankfully, he made a website explaining how he re-worked the van. He also posted a lot of pictures of the process and the result.

I really like his project and would love to make something similar for holiday travels. But after reading all the “vanual”, I might need to learn how to do stuff first. Being all thumbs does not really make this process much easier, I guess.

Euro Cup predictions through Stan

After I calculated the probabilities of Germany dropping out of the world cup two years ago, I always wanted to do some Bayesian modeling for the Bundesliga or the Euro Cup that started yesterday. Unfortunately, I never came to it. But Andrew Gelman posted some model by Leonardo Egidi today on his blog:

Leonardo Egidi writes:

Inspired by your world cup model I fitted in Stan a model for the Euro Cup which start today, with two Poisson distributions for the goals scored at every match by the two teams (perfect prediction for the first match!).

The available PDF contains the results and the description for the model. Really interesting and already a perfectly predicted first match! But the model will not fit very well at the semi-finals… Germany losing to Italy? Again? Can’t be!

Choosing Cut-Offs in Tests

My last blog post was on the difference between Sensitivity, Specificity and the Positive Predictive Value. While showing that a positive test result can represent a low probability of actually having a trait or a disease, this example used the values of Sensitivity and Specificity as pre-known input. For established tests and measures they indeed are often available in literature together with recommended cut-off values.1

In this post, I would like to show how the choice of a cut-off value influences quality criteria such as Sensitivity, Specificity and the like. If you just want a tool to play with, see my Shiny web application here.

Continue reading Choosing Cut-Offs in Tests

Visualizing Sensitivity and Specificity of a Test

In my university course on Psychological Assessment, I recently explained the different quality criteria of a test used for dichotomous decisions (yes/no, positive/negative, healthy/sick, …). A quite popular example in textbooks is the case of cancer screenings, where an untrained reader might be surprised by the low predictive value of a test. I created a small Shiny app to visualize different scenarios of this example. Read on for an explanation or go directly to the app here.

Continue reading Visualizing Sensitivity and Specificity of a Test

Vagrant VM for starting a Rails project

This is something off-topic for this blog, but after spending several hours setting up an environment for developing and testing a Ruby on Rails project, I’d like to share my solution.

I recently had an idea for a small web-project, for that I’d like to use Ruby on Rails. From previous attempts of using Rails, I knew that Ruby and Rails are updated regularly and that the setup of the environment might be tricky. And using my Mac not only for web-development, I did not want to have many versions of Ruby, Python, whatnot, in parallel on it. And as I read about Vagrant some weeks ago, I wanted to give it a try.

It took quite some time to set-up the provisioning script properly. I tried using Chef, but it made things more complex and I appreciated the simplicity of a shell script. Continue reading Vagrant VM for starting a Rails project