Working notes for 2015

2015-01-07. Tests of three MCMC moves in BEAST2 package STACEY. These moves are for the multi-species coalescent model. The tests are based on sampling from prior distributions.

2013-03-22 Preprint of STACEY paper at bioRχiv. Species delimitation and phylogeny estimation under the multispecies coalescent.

2013-03-22. Various files related to the STACEY paper above. There are R scripts used to generate the BEAST2 XML files, analyse the results, and latex source. This is largely undocumented dump.

2015-05-07. Bias in BiSSE. Part of unpublished paper on diversification rates of neopolyploids by Soltis et al (2015). Demonstrates systematic bias in BiSSE. There is also Supplementary material and R scripts.

2015-06-14. BEAST2 and Intellij. How to make a new version of STACEY for a new version of BEAST.

2015-08-31. Using STACEY on larger data sets.

2015-11-01. More tests of using STACEY on larger data sets.