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, v0.2.0 Uses a different model for migration probabilities (which is easier to justify, and appears better on nonsister migration at time zero). Version 0.3.0 is available in BEAST2 (install using Beauti).
2017-05-09. DENIM description and results. A description of the model used by DENIM, and some preliminary results.
2017-06-18. Scripts for simulations. R scripts used to run and analyse simulations. Source code for edited version of MCcoal (search for "grj"/"GRJ" in bpp.c).
2017-06-18. Notes on simulations. Describes the way the simulations were set up from MCcoal control files, and documents the R scripts above.
2017-10-14. Simulated data. Simulated data for testing DENIM, made using BPP control files from Adam Leaché, for 4-species scenarios.
2017-10-14. Simulated data. Simulated data for testing DENIM, made using BPP control files from Adam Leaché, for 10-species scenarios.
2017-10-14. Notes on above. Notes on the Leaché simulated data sets.