Just after the holidays, we held the second short course, as part of the SCATE project, on Phylogenetic Comparative Analysis of Integrated Anatomical Traits at the SSB 2020 meeting in Gainesville, FL. The course is an introduction to ontologies and their application in phylogenetic comparative analyses. We demonstrated how to use anatomical dependencies derived from ontologies to better model character evolution, and how semantic similarity of traits could be integrated in a comparative analysis.
The hands on sessions included demos of RPhenoscape and the PARAMO pipeline. Using these tools, attendees learned how to query for phenotypes in the Phenoscape KB and build character matrices that take anatomical dependencies into account. They also learned to construct stochastic character maps for body regions and whole organismal anatomies on a phylogeny. The large number of attendees (37!) came with a range of abilities, from novice R users to experienced developers, and from a range of career stages, from undergraduate students to postdocs and faculty. Anticipating that running a workshop with a group this large would be challenging because of the possible technical issues that can arise, we built in “tech troubleshooting” time at the beginning of the course to help install the R package. Participants either interactively followed the tutorials using the RMarkdown files in RStudio or followed a rendered version of the course materials on the course website.
For those interested in trying out the course materials without needing to install the required software, we’ve published a Code Ocean capsule containing the code and tutorials. The capsule runs in a web browser, without needing to install R, R packages, or any dependencies.