Theory and Background
- The lecture presentation for Annemarie's PCM session (Continuous_2.pdf) is in the QMSS folder "continuous_character_evolution". There are no accompanying notes but references to literature at the end. I especially recommend Charlie Nunn's (2011) "The comparative approach in evolutionary anthropology and biology" and Symonds et al. (2014).
- You should have followed the Phylogenetic Inference / Tree-building materials from Simon Greenhill and Fiona Jordan's PCM for Discrete Character Data before going through these materials.
Practical session
- Files for Annemarie's practical session are in /continuous_character_evolution. They are three tutorials on testing for various PCM analyses in R: phylogenetic signal (phylo_signal.R), estimating ancestral states (ancestral_states.R), and a phylogenetic generalised least squares analysis of a correlation between two continuous features(correlation.R). They all make use of data on number of consonants & vowels from PHOIBLE and thus a very linguistic-y dataset. The other files (tree and data files) are all called in these three R scripts.
- The R scripts include comments and should be easy to follow, remember you can also ask R for help by putting a ? in front of a function, i.e. ?comparative.data.
Please work through at your own pace, and if you are stuck with software or file issues please contact Annemarie on email (verkerk@shh.mpg.de). As I won't be in Jena for the masterclass also feel free to contact me before or afterwards if you have questions about applications to your own data (I am available until the 29th of August and from 11-09 onwards I'll be available again).