Everyday R: tips and tricks for data science with R

Having your work published is always a great honor and satisfaction, even though your results are not so optimistic. If, by accident, you follow my blog for a while, you may have noticed a post concerning the CovILD project - an observation cohort study, I've been curating as a data scientist. Quite recently, we've managed to publish the follow-up quite prominently in eLife ( Sonnweber et al. ) and develop a toolbox which may help us to assess the risk of complicated recovery from COVID-19, at least when it comes to lung injury and functional deficits. Lung injury following COVID-19 tends to be chronic and symptom-independent As a reminder, at the onset of the SARS-CoV-2 pandemic in Tyrol, a cohort of 145 patients was recruited, including those suffering from mild COVID-19 managed by home isolation and individuals requiring hospitalization, including mechanical oxygen supply and intensive care. The intention of the study was to establish a long-term observation collective to mo...

 I had a lot of ideas for the next post... I really wanted to have a look at another problem of humankind: climate change, wealth distribution or perhaps gender equity. There's so much interesting data beyond the SARS-CoV-2 pandemic! But: the new variant of our most popular pathogen dominated the news of the last four weeks, fueled people's fears and hopes at the same time and spoiled my plans. Yes, your right, that's the Omicron, coined a 'mild' or 'cold-like' coronavirus and expected to change the way we experience and manage the pandemic. Does it hold true? I had to crunch some data to convince myself... Omicron: no more than highly transmissible cold bug? I allow myself to skip an extended introduction on Omicron: it's omnipresent in media and European populations - the chances that you have already experienced an infection or experience one in the forthcoming four weeks are quite good. To sum up:  we're facing an extremely infectious pathogen, w...

Before I begin, I probably need to declare that although I'm a great enthusiast of vaccinations and got a more or less complete list of shots in my life, none of the pharma companies nor Bill Gates have ever offered me shares, honoraria or even a free vaccination. In other words I'm entering this topic highly influenced by subjective opinions and conspiracy theories without any financial conflict of interest and do my best to present you 100% scientific data.   COVID-19 vaccination was promised to be the next topic - it was already a while ago, cause I'm involved in two huge COVID-19 human studies and didn't find enough time for my blog. But I hope, I can report on our, still highly confidential, results in the nearest future.   Initially I thought: let's discuss the principle of vaccination and particular drugs, have a look what was published about efficacy and safety and, finally calculate, if getting an anti-SARS-Cov2 shot is worthwhile. But, I didn't expect ...

In the first post in the, hopefully, better 2021 we'll again make a short trip to the northern Italian province South Tyrol. Well, there are multiple reasons, you may love northern Italy: magnificent alpine landscape, fine wine and cuisine, better coffee than on the other side of the Alps... For a data scientist, there is one more: excellent public data availability, both concerning the COVID-19 pandemic and stats for cities and villages. It's enough, you go to the province or the federal statistical authority portal or the local COVID-19 dashboard and you may freely download even the most insane data for each South Tyrolean and Italian commune - simply great! It gives us a unique opportunity to analyze the course of the SARS-Cov2 outbreak in South Tyrol, in particular the spring and fall/winter waves, and identify some factors fostering the spread and, with a bit of imagination, speculate on a local protective (herd) immunity against the pathogen.   As usual, the scripts of...