Please cite Traitlab as:
L. J. Kelly, G. K. Nicholls, R. J. Ryder and D. Welch, TraitLab: a Matlab package for fitting and simulating binary tree-like data. arXiv:2308.09060, 2023.
The theoretical aspects of the model and inference are discussed, along with applications to Indo-European lexical data, in:
Geoff K. Nicholls and Russell D. Gray. Dated ancestral trees from binary trait data and its application to the diversification of languages. Journal of the Royal Statistical Society, series B, 70(3):545-566, 2008.
Robin J. Ryder and Geoff K. Nicholls. Missing data in a stochastic Dollo model for binary trait data, and its application to the dating of Proto-Indo-European. Journal of the Royal Statistical Society Series C, 2011.
Robin J. Ryder. Phylogenetic Models of Language Diversification. PhD thesis, University of Oxford, 2010.
The extension to lateral trait transfer with application to the Eastern Polynesian language family are described in:
Luke J. Kelly and Geoff K. Nicholls. Lateral transfer in stochastic Dollo models. The Annals of Applied Statistics, 11(2): 1146-1168, 2017.
Luke J. Kelly. A stochastic Dollo model for lateral transfer. PhD thesis, University of Oxford, 2016.
Couplings of Markov chains to diagnose convergence on the space of phylogenies and model parameters is described in:
Luke J. Kelly, Robin J. Ryder and Grégoire Clarté. Lagged couplings diagnose Markov chain Monte Carlo phylogenetic inference. The Annals of Applied Statistics, 17 (2), 1419– 1443.