Before arriving to our next Friday tutorial (Jan 17) you will have:
1) created an RStudio Cloud account,
2) a general understanding of what R and RStudio are,
3) completed the RStudio primer “The Basics”,
4) researched 2-3 of your favourite animals as potential study organisms for your term paper.
For this week, you have nothing to hand in, or code!
Like most scientific fields, biology research generates and requires the analysis of large datasets. In biogeography, we often want to estimate where species occur on continental scales, and how these species are related. Solving these problems is made tractable by employing programming tools, such as R. If this is your first time hearing about R, I recommend reading section 1.1 of “R for Data Science” to understand what R is (and isn’t!) and why it is so widely used within the many sub-disciplines of biology.
Having the ability to analyse, manipulate, and visualize data is a sought-after skill in the modern job market. But it’s also a useful skill for completing your term paper! Check out this brief description of your term project. More details on your term project are coming soon, but we can get the ball rolling now! That brings us to this week’s homework.
RStudio is an interactive environment that houses the R programming language. You don’t need RStudio to use R, but it certainly makes things easier! RStudio can be downloaded onto your laptop, but isn’t easily installed onto tablets. For this class, we’ll be using RStudio Cloud, which allows us to use RStudio online, without downloading anything. Let’s get started!
Go to RStudio Cloud and create an account.
Select the option “Primers” on the left-side panel and complete the tutorial “The Basics”. You will benefit immensely from completing the tutorials “Work with Data”, “Visualize Data”, and “Tidy Your Data”. You won’t be evaluated on this portion of the assignment, but future-you will thank present-you 1000 times over when it comes time to do the assignments. A minute spent understanding the Primers will save you an hour of troubleshooting later in the term.
Now is a great time to start thinking about a study organism for your term paper, but there are some things to consider. I’ve taken this exerpt from last year’s term paper assignment instructions:
“Choose an animal species, genus or family, and describe the natural distribution (i.e., non-human altered), habitat use and phylogeny of its subgroups. You can focus your animal group on one of several taxonomic ranks. If you choose a species, the focus should be on subspecies (phylogroups, genetically distinct populations, or ecotypes). If you choose a genus, the focus can be on species within that genus. If you choose a family, the focus can be on genera within the family. Don’t choose a taxonomic group with a higher rank than the family level, because it will be more challenging to gather specific distribution maps and phylogenetic information for families and orders.”
Let’s say you like foxes. A good way to start is to search “fox taxonomy” (not taxodermy!) to see whether ‘fox’ refers to a single speceis, a group of species, or a family. You’ll find that ‘fox’ is shorthand for referring to the genus Vulpes (hence the pokemon Vulpix?). The genus Vulpes is a group of 12 species. This is a good taxonomic size for your term paper. On the other hand if you look up “mosquito taxonomy”, you’ll find that these flies comprise the Culicidae family, containing >3500 species. Not a feasible group for your term paper! But don’t give up - it’s really a matter of scope. If we ‘zoom in’ to the subgenus level, you’ll find some mosquito subgenera have ~10 species, e.g. Culex subgenus Micraedes has eight species.
Your task for this week is to research the taxonomy of your favourite animals and find 2-3 candidates that are suitable for your term paper. Next Friday (Jan 17) we will formally introduce RStudio Cloud and learn how to interpret some code, and enter our chosen organism into a spreadsheet.
Note: Take a look at this list to see what is considered an “Animal”.
Use this invitation link to join the BIOL413 RStudio Workspace. You’ll see that there are three (empty) assignments in our workspace, and one project named “Organism Sign Up”.
Go to the project named “Organism Sign Up” (it takes a minute to load). You’ll see a lot of stuff. Give this a read to get a sense of what all these windows and buttons are - we’ll review in next Friday’s tutorial.
If you can help it, please don’t modify the code.
Have a great week!