Working notes for 2017

2017-03-03. DENIM package, v0.01. A BEAST package for estimating a species tree despite small amounts of migration, based on ideas in 2016-10-31-approx-idea.pdf. It must be installed manually. (DENIM=Divergence Estimation Notwithstanding ILS and Migration.)

2017-03-03. Notes on how to test DENIM. This is for prior only, and using MCcoal to generate data. There are some preliminary results for prior only, and an XML for one scenario on simulated data.

2017-03-07. Scripts for testing DENIM. MCcoal control files, R scripts for converting MCcoal output to NEX or XML, and analysing results.

2017-05-09. DENIM package, v0.02. Uses a different model for migration probabilities (which is easier to justify, and appears better on nonsister migration at time zero).

2017-05-09. DENIM description and results. A description of the model used by DENIM, and some preliminary results.

2017-06-18. DENIM description and results. A description of the model used by DENIM, and some preliminary results. Significant update of 05-09 version, with migration rate parameters integrated out.