Thursday, 19 August 2021

The quest for covid vaccination side effects


I had been working hard for six weeks solid. I needed some time off but did not want to dip into those valuable annual leave days. How could I do this? Pulling a sickie these days is pretty difficult, doctors charge so much for their notes. 


My wife had been anxious for some time now to get the COVID 19 vaccination. In our remote rural setting, access had not been straight forward, and we had been waiting weeks despite registering via the official channels. Meanwhile, Anja's family had all been vaccinated in Germany and had returned to a normal life. We were all suffering from vaccine envy. 


While we were suffering from vaccine envy, it appeared as though those around us were suffering from vaccine hesitancy. Several of our acquaintances from our neighbourhood had expressed concerns about vaccine side effects. One lady, who has worked for us for a long time, told me that there were two types of vaccines. I was quite impressed with this knowledge. She then went on to elaborate that there was one that helps you and one that kills you. 


I had to point out that my parents had been vaccinated the previous month and were still not dead. As the stories from those who had been vaccinated rolled in it appeared that they were some side effects: sore muscles, fatigue, headaches, flat tyres, and generally anything else for which an excuse was needed. 


Perhaps then, getting the vaccine could get me a few legitimate days off. I craftily scheduled an appointment for the middle of the week, expecting some side effects that would knock off Thursday and Friday. I called the clinic in George to see if we would be able to make an appointment. There had been a lot on the news about the lack of vaccine uptake and empty vaccination centres and I was not surprised when the receptionist I spoke to said we could drop in anytime during the morning. 


The following day, Anja had paracetamol laid out on the table to prevent headaches and asked if I wanted one pre-emptively. I pointed out I was doing this all for the side effects, and that under no circumstances would I be taking a paracetamol. Knowing that a sore arm was a standard symptom, I did penetrate the aura of guilt and abandonment that my home gym constantly emits for a quick work out.  


As my wife drove us down to George, I scanned through the headlines of News 24. One of the articles of the day was about a vocal anti vaxxer are who had decided to get vaccinated after all. When we arrived at the vaccination centre, it was like a scene from the Kabul airport. There was a long queue of people around the clinic, which I could only presume were those anti vaxxers who had suddenly realised they have been abandoned by their leader. Among the elderly queuing up for their second shots, there was now also a ragtag bunch of nervous, shaven headed, tattooed, middle-aged people who likely digested information from alternative herbal based websites sponsored by Harley Davidson. 


Over the next few hours, we navigated our way through the clinic in an elaborate game of musical chairs. Eventually we found ourselves in the room with needle wielding nurses. I must admit to being underwhelmed by the size of the needle and vile which contained the lifesaving serum of Pfizer-Biontech. The nurse explained to me the possible side effects associated with the vaccine: headaches and possibly more severe symptoms that might require a visit to a doctor. I nodded in eager anticipation.  


The injection was over in a blink and we were herded to the waiting area where people are obliged to spend 15 minutes under observation to make sure there are no adverse effects. The open area was full of people drinking coffee, eating buns, checking phones. There was a disappointing lack of people passing out or requiring medical attention. After my coffee, and feeling fine, I attempted to depart the waiting area only to be stopped by a nurse who would not allow me to leave because I had lost my sticky tag of paper which gave the time of my inoculation and confirmed I’d served my limited quarantine time. I had to be rescued by Anja 

“I must be getting absent minded because of the vaccine!” 

“How interesting that this side effect started before you got the vaccine this morning when you left your bag at home”, said Anja dryly. 


Anja went off to do some shopping while I waited in the car to catch up on emails. After a while I noticed that I was hot and sweating. Finally, another one of the symptoms was kicking in. I felt most pleased. Shortly, Anja returned, started the car, turned on the air conditioning, and commented: It is hot in here, isn't it?. Was my side effect just a result of sitting in a car that had been standing in the sun, while forgetting to take off my jacket? While taking it off I was pleased to note that both my arms were sore, not just the one I’d been injected in. Clearly the pre-emptive early morning workout had been a good idea. 


During the drive home I tried to explain to my wife the benefits of hierarchical sampling methods for detection-non detection data and the finer points of spatial distribution modelling. She started yawning. I started yawning. Clearly, we were getting tired! Another side effect! That night she would also complain about a headache, despite the paracetamol. Disappointingly, mine never materialised.  


But that was okay, because on the last section of the drive home, I had the coolest side effect of all. I couldn’t believe my eyes. I stared down the muddy road to the rain clouds over the distance mountains. I rubbed my eyes, but it was still happening: the road had turned into a rainbow.  



For some reason, I never got my day off.  


Wednesday, 11 August 2021

Just another problem with Bayesian statistical programs


As someone who uses the R coding statistical environment lots, I much prefer frequentist methods for analyzing datasets. Generalized linear models or just linear models and more complicated things like GAMs, run really fast in R. Literally as soon as you press enter on the keyboard in most cases. And sometimes even before you push enter on the keyboard because you accidentally brushed the mouse pad or pushed some random key combination that magically made it all work.

 For anyone who's trying to solve the problem of the likelihood of you having an illness because a test came back positive for that illness but with the background knowledge that there are false positives and false negatives for a test will be aware that probability is far from straightforward or intuitive. You have to subtract some things from each other and divide it by the other things and sometimes you swap the order of those things around. It is about as intuitive as trying to just eat the holes in Swiss cheese. Like most normal people I will fail to solve these probability problems unless the correct formula is written down next to me from some cheatsheet and I have a computer to plug the proper values into.

 Bayesian statistical programs in R are even worse. Bayesian statistical programs run on multiple iterations of complicated probability surfaces. Running even simple formula in them takes a rather long time. But the first challenge is to install one.  My recent experience at attempting to install code submitted in reproducible formats for a peer reviewed journal made me realize that installing Bayesian statistical libraries is a bit like throwing a dart at a dartboard, where things only work if you hit the bulls eye. Except it is based on the prior assumption that you are holding a dart. Then when you throw the dart it turns out you were actually holding a Bunny. And this leads to all sorts of philosophical conundrums and dead ends and circular thinking. Am I allowed to throw bunnies at dartboards? Should I now be throwing the board at the bunny? But I don’t want rabbit for dinner, all I wanted to do was play darts! Or was it install JAGs? Then I get stuck in 10000 iterations of tangential meanderings over probability surfaces that look like dartboards created either using LSD or a randomization function applied to RColorBrewer. 

I emerged from it all burnt out after a too long burn in period, and much reduced self-confidence intervals. While I have so far frequently solved my analytical problems, I fear that I can no longer run away from the Bayesian hounds closing in. I really hope that when they catch me, they turn out just to be baying bunnies. 

Full credit to Rasmus Baath for the basis for the visualisation:


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