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README.md

Examples

1. OUPrior

1.1. OUPrior Tests

ouprior_test1.xml-ouprior_test5.xml: Tests to check that the OU-prior implemented in BEAST2 is correct. Check that MCMC samples correct trajectories and that it is possible to estimate parameters given a trajectory. (Results)

1.2. OUPrior examples

With OUPrior

  1. hcv_bdsky_ouprior.xml: Egyptian HCV dataset (contemporaneous sampling only), with relative times (between 0 and 1). OUPrior on reproductive number with dimension 40.
  2. Serial sampling and real times (Ebola)

Comparison xml files (without OUPrior)

  1. hcv_bdsky.xml: Egyptian HCV dataset (contemporaneous sampling only), reproductive number with dimension 40.

2. TreeSlicer

2.1. TreeSlicer Tests

Tests to compare the result of using TreeSlicer to obtaining the same or similar results in a more complicated way without it. Note that some XMLs log more statistics than necessary and contain some unnecessary RPN calculators to check correctness of the results.

With TreeSlicer

  1. dengue4_bdsky_equidistant5_treeslicer.xml: 5 intervals for R_e, equally spaced between tmrca and present, sampling proportion 0 before oldest sample.
  2. dengue4_bdsky_fixeddates_treeslicer.xml: 5 intervals for R_e at specific fixed dates, sampling proportion 0 before oldest sample.
  3. dengue4_bdsky_csc_treeslicer.xml: 2 intervals for R_e, with the shift-date estimated.
  4. dengue4_bdsky_csc_treeslicer_hierarchical.xml: 2 trees, each with 2 intervals for R_e, with a shared shift-date, which is estimated.
  5. dengue4_bdsky_equidistant5_treeslicer_hierarchical.xml: 2 trees, each with the same 3 shared intervals for R_e.

Comparison xml files (without TreeSlicer)

  1. dengue4_bdsky_equidistant5.xml: 5 intervals for R_e, equally spaced between origin and present, sampling proportion 0 before oldest sample.
  2. dengue4_bdsky_equidistant5_rootcondition.xml: 5 intervals for R_e, equally spaced between tmrca and present, sampling proportion 0 before oldest sample (no origin estimated).
  3. dengue4_bdsky_fixeddates.xml: 5 intervals for R_e at specific fixed dates, sampling proportion 0 before oldest sample.
  4. dengue4_bdsky_csc.xml: 2 intervals for R_e, with the shift-time estimated.

2.2 TreeSlicer Examples

Coming soon

Louis du Plessis, 2018