Working notes for 2020

2020-03-24. Notes on SARS-CoV-2

2020-03-30, updated 2020-05-17. Simulation code. R and Python scripts for simulating outbreak data (sequences, dates, etc), plus example of output. See notes-on-simulation-code.txt in the zip.

2020-04-08. Tailoring BADTRIP or PoMo for SARS-CoV-2. Preliminary notes about the PoMo and BADTRIP models, and a possible speedup suited to SARS-CoV-2.

2020-04-30. Java source code for PoMoCoV2. This is source code for BEAST 2.5.1 plus BADTRIP, and edited by me. I'm calling it PoMoCoV2. It implements a new version of the drift-only part of the likelihood calculation and a tree prior using information about SARS-CoV-2 transmission times.

2020-05-01. Model for tree prior. A description of the model I plan to implement. It provides a prior for the transmission tree, and deals with unobserved hosts.

2020-05-16. PoMoCoV. A BEAST2 program implementing the model described above (2020-05-01-fillingin-transmt-distr.pdf).