Slides, exercise materials, and example source code for the practical activity session at the Workshop on population and speciation genomics to be held in Český Krumlov in January 2025.
Contents of this git repository:
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slides and single-page handouts -- these contain a crash course introduction on using the slendr toolkit for simulations in population genomics that you can use for reference while working on the exercises (I will be going through these slides at the beginning of our activity session)
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exercise materials -- this is the main focus of our activity session (solutions are built-in but hidden by default)
The slides, handouts and exercises are also available for download as self-contained HTML files, just in case Quarto Pub server is down: slides.html, handouts.html, exercises.html.
Refer to the exercises materials for all necessary information on installation and setup.
The goal of every exercise in the activity is to write a self-contained script in R using the slendr R package (one script for each exercise).
It's quite likely you haven't worked with slendr before and that's quite alright, there's no reason to panic. :) Although some of the exercises can get quite complex, even students who have only begun learning population genetics (and aren't even comfortable with R) will be able to follow the activities easily because the exact solutions are built in the exercise materials. In ideal circumstances, students might only need a bit of help with R coding, and you (and I, obviously) will be able to do that by taking a peek at each respective solution R script, as needed. You don't really have to know slendr to be able to help the students! Just use the provided solutions to guide them.
Note that there's quite a lot of content in the exercises, and a lot of it is marked as "bonus". This bonus content is designed for expert R programmers and people who would be otherwise bored. If someone does run into an issue with that and has a question, I will be able to deal with that easily. Don't worry about those at all. In fact, unless things go extremely smoothly, we might not even make it to the very final part of the last exercise. It all depends on how comfortable the participants will be with R programming.
All the information that the students might need to do the exercises is available in the slides and handouts (which are rendered from the slides for easier reference). The activity session will begin by me walking through the slides first to get everyone on the same page before proceeding with the exercises. You don't have to walk through these slides yourself, unless you really want to.