Wednesday, July 24
8:30 am – 5:00 pm (Lunch is included)
The Cliff Lodge, Ballroom 2
Student & Postdocs: $50
Limited to 60 participants, minimum of 15 needed for workshop to happen.
A team of four or five instructors will lead a hands-on introduction to several of the most common and widely-used phylogenetic comparative methods in R. The workshop will provide a basic introduction to the theory behind these methods, but is not intended to be a comprehensive course on comparative phylogenetic methods. You will learn to use elements of the R packages phytools, ape, geiger, geomorph, fishtree, rfishbase, phyloEM and others to analyze real data. Topics will include tree visualization, phylomorphospace plotting, calculation of phylogenetic signal, ancestral state reconstruction, phylogenetic regression, evolutionary model fitting and other topics. Tree inference is not included. You will receive numerous code snippets that they can take home and use as templates when creating new workflows, and will have an opportunity to apply skills learned in the workshop on their own datasets during open lab time.
This is an intermediate level workshop, targeted at those who already have basic familiarity with scripting in R, but not necessarily experience with phylogenetic comparative methods. The workshop aims to reduce the access barrier to these methods, and to help more members of the JMIH community implement these methods in their own work, emphasizing the benefits of clear, repeatable analysis through R scripting. The methods can be applied to questions in any taxon, and should interest herpetologists and ichthyologists alike.
8:30 a.m. Participants arrive and get settled
9 a.m. Introductions and package installation
9:45 a.m. Importing and visualizing phylogenies
10:30 a.m. Coffee break
11 a.m. Linking trait data to phylogenies
12 p.m. Lunch
1 p.m. Phylogenetic signal and regression
2 p.m. Ancestral state reconstruction and phylomorphospace visualization
3 p.m. Coffee break
3:30 p.m. Evolutionary model fitting
4:30 p.m. Wrap up and participant surveys