A Little R in R

As usually happens when learning something new, it gets pointed out that while i might have achieved my goal, there is a far cooler way of doing the same thing! In this case that would be R.

RinR

Now it seems a shame to have got this far into a career without ever having played around in R. The above is pretty close to the simplest plot posssible, but hey, it was fun!

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R Numbers

A few days ago there was a post on /r/de showing a nice graph of now famous R number for Germany:

hscehxf6c4y41

Exciting for a couple of reasons: that the data-set was available (i’d been looking for it for a while); the reported number was over 1 … which isn’t good.

The post linked to a .pynb script that had been used to produce the image. The code was obviously Python and somehow related to Jupyter Notebook – time to learn something new!

Since the original script was published the Excel spreadsheet download added a cover sheet, which obviously broke things. Having patched things up a little (and translated the labels to English), here is the updated plot:

plot_2020-05-15

One of the labels has gone missing… oops.

Update: the missing label was important! The above graph is for a new RKI dataset that tracks R on a 7 day average, the original series was too sensitive (see below). For “reasons” that series doesn’t include error estimates for the last data points, which broke calculation done on the final point. Below is a new plot on the 4 day averaged series – now really an update of the original image:

plot_2020-05-15

As you can see the R value for the original chart has been revised down, and the current value remains below 1. The brief bump up was attributed to the infection of slaughter house slave labour, housed in cramped shared dormitories. Come of Germany – be better than that!

Update: weekends are obviously good for tracking down datasets and visualizations! There is a GitLab project running model simulations on the regional data, below is the plot for Hamburg:

hamburg

Having no background in epidemiology (or statistical analysis…) all i can do is accept it as presented, and note that it correlates well with the recent decline in reported new infections. The RKI made an interesting observation on the sensitivity of R the other day, noting that as the number of active cases (infections) fell any new hotspots (such as the slaughterhouse outbreaks) would have a larger impact on the reported number.