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John Lees' blog

Pathogens, informatics and modelling at EMBL-EBI

You know, I'm something of a modeller myself

I recently read a blog post written by Joel Hellewell, who worked on the COVID-19 response team at LSHTM. The post is here https://jhellewell14.github.io/2021/11/16/forecasting-projecting.html. I found it particularly interesting to hear the perspective of someone who had worked on (mathematical) modelling infectious diseases for a longer time, and how the response to the pandemic compared to these activities. I wanted to write a reply which turned out to be a bit too long for a tweet, so here it is.

When to use log scales

log scales seem to have caused a lot of debate recently. When should we use them? I think there are two reasons: Your data is exponentially distributed. You want to transform your data to make certain regions easier to see. Exponentially distributed data The first is a bit of a tautology. For independent variables (usually the x-axis) it’s easy. Perhaps you have collected data at points 1, 2, 4, 8, 16 etc.

Easy debugging of C/C++/CUDA python extensions

Writing an extension called by python (in C, C++ or CUDA)? Not working? Typical. When doing the same from R it’s pretty easy to debug, just run with R -d <debugger name> e.g. R -d valgrind or R -d gdb you get into the debugger, continue, then run interactively as usual. (For a more complex example using both at once see this blog post). Doing this from python seems trickier to me.

p-value < 2.2e-16

A claim: 2.2e-16 is the most popular p-value in research papers, even more popular than 0.05 (or if you’re being cynical 0.049). Why? 2.2e-16 happens to be the epsilon of a double-precision float (i.e. a decimal number stored using 64 bits). Roughly, this means that if you try to calculate 1 - epsilon, with anything smaller than epsilon, the answer will be 1. In R, you can calculate this by running the following code (+2 due to convention):

Honey Roast Parsnips (frozen), Iceland

A review of ‘Honey Roast Parsnips’ - available from Iceland £1.75, 750g This weekend I wanted to buy some parsnips to roast, but they were absent from the produce section (except in a pack coming with four unwanted carrots, and one considerably more unwanted turnip). However, as I was shopping at Iceland, there was a handy pre-prepared frozen alternative: These cost roughly double the amount of buying raw parsnips. I’d estimate there are around four large portions in this bag, you can probably get double that if you’re using a small amount.

Screamadelica, Primal Scream

Why is it only in 2021 that I am listening to Primal Scream’s Screamadelica for the first time? A lot of critically acclaimed music from the 1980s maintains a pop appeal that means it still gets radio play, is featured in club nights, and is heavily promoted in my Youtube home. However, perhaps the post-rock, trip-hop and grunge of the early 1990s doesn’t have the same enduring commercial appeal. Whatever the reason, I’ve been missing out.