My goals for this project are as follows:
Goal 1: Make a map in R
Goal 2: Collect and format species occurrence data, import into R, plot on map
Goal 3: Construct a species distribution model in R
My main goal for this R class is to develop skills to perform species distribution modeling (SDM) in R. It is possible to do SDM outside of R (and this is how it was first conceived/implemented), but it requires a lot of work in ArcGIS, which is user-friendly, but can be slow and clunky when manipulating a lot of map layers (e.g., many bioclim layers). Recently, a lot of people have been migrating towards using R for their SDM needs. I want to use SDM in red mangroves to complement phylogeographical analyses that I have performed for this species. This SDM work will likely become a chapter of my dissertation. There are several packages available in R that I want to learn how to use.
First, I would like to learn how to make and manipulate maps in R. I think this will be a valuable skill for saving time that would be spent using ArcGIS. Second, I would like to collect species occurrence data, import it into R, and plot it on the map I created. I would also like to be able to manipulate how the data are visualized on the map (e.g., showing only subsamples). Next, I would like to construct a species distribution model using R. I am not entirely sure how long each of these tasks will take, but I imagine making the map will be pretty straightforward.
If this project goes quickly, I would also like to create SDM for black and white mangroves. I am somewhat skeptical that I can find fine enough resolution data to find key differences between the species, since they occupy overlapping zones on the coast. However, I would like to investigate any potential differences in SDMs. I hypothesize that there may be differences based on the different dispersal capabilities of each species.
Another goal I have is to learn how to execute some population genetic analyses in R. This is a secondary goal to learning about creating SDMs, but if there is enough time in the semester, I would like to investigate the possibilities for population genetics in R.