Return to the Code

Today started with the usual admin and maths tutorials. I managed to make contact with the cork people and give them the high definition outline of SA. Hopefully they will be able to use it and I will have a completed product within a week or so. Having a physical board on which to pin the temperature sites will be great.

After the admin I wanted to add figures etc. to my presentation. Though to do so I realized that I would need to go back into the body of code for the tempssa_3.0 project. And to do that I would need to organize the pipeline. And to do that I would need to download the “assertr” package for R to correctly implement the new quality controls we have envisioned. Unfortunately “assertr” doesn’t work on the current build of R (3.1.2) so that was put on hold. Besides that snag the rest of the pipeline should go together quite well as I left the scripts in pretty good shape last year before I went on holiday. It shouldn’t take more than a day or two to get everything in good working order. “assertr” will need to be added in whenever it is ready. This will introduce a certain level of complexity but I am very excited to see the outcome. This process of re-evaluating the scripts took up most of my coding time for the day and so I didn’t create any ne figures for my presentation… I did however find pdf’s similar to what I was looking for. They aren’t useful enough for what I want to show, but the data are there, which will make the creation process easier

After all of that running in circles I read an article from Griffiths et al. (2010) in which the authors discussed the known knowledge on Marine Biodiversity in South Africa. This paper houses a wealth of technical information and will be a fantastic piece of reference material in the years to come. Numbers of species in taxa, the size of the EEZ and amounts of samples taken at specific depths throughout the entire history of SA are just three solid facts in this concise document. It covers much much more and is a must read for anyone studying the oceans of SA. One odd thing is that the authors repeatedly state (with a cited reference) that the coastline of SA is 3650km whereas I have only ever read ( in many many publications) that the coastline is ~2,700km. I am curious to find out what the source of this discrepancy is. The authors specifically state that that this number does not include the coastline of the Prince Edward Islands, so where do these extra kilometres come from? perhaps a more detailed inclusion of estuaries etc.

2 thoughts on “Return to the Code

    1. If I recall correctly the length of coastline is 2673 km – you can check this in R… I’ll make the biodiversity scripts available to you later today via GitHub.

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