I shall be spending next week (4th-9th March) at the UCLA Department of Linguistics, where I shall give five hours of talks on Statistics for Historical Linguistics: a two-hour review of the field (Thursday morning), a two-hour presentation of my own DPhil work (pdf) (Friday afternoon), and a one-hour tutorial on TraitLab (Friday afternoon?). Abstracts:
Joint work with Geoff Nicholls
3. Tutorial and practical: TraitLab, a package for phylogenies of linguistic and cultural traits
In this tutorial, I shall present how to use the TraitLab package, which was initially developed specifically for the modelling of core vocabulary change through time, and guide interested attendants through an analysis of a simple data set. TraitLab is a software package for simulating, fitting and analysing tree-like binary data under a stochastic Dollo model of evolution. It handles “catastrophic” rate heterogeneity and missing data. The core of the package is a Markov chain Monte Carlo (MCMC) sampling algorithm that enables the user to sample from the Bayesian joint posterior distributions for tree topologies, clade and root ages, and the trait loss and catastrophe rates for a given data set. Data can be simulated according to the fitted Dollo model or according to a number of generalized models that allow for borrowing (horizontal transfer) of traits, heterogeneity in the trait loss rate and biases in the data collection process. Both the raw data and the output of MCMC runs can be inspected using a number of useful graphical and analytical tools provided within the package. TraitLab is freely available and runs within the Matlab computing environment.
Attendants who wish to use TraitLab during the practical should have a computer with Matlab installed.
TraitLab was developed jointly with Geoff Nicholls and David Welch.