Open ywteh opened 4 years ago
Use simulator here to evaluate: https://www.medrxiv.org/content/10.1101/2020.06.18.20134858v2.full.pdf
Added code to compute predictive probs and forecasting here: https://github.com/rs-delve/Rmap/commit/45d3a682cd58266404c1706df6d0db742e3dfd49
Note that main file for this change is now run_cori_eval.r and cori-gp-immi-eval.stan Sorry for the terrible version management. It involves also some refactoring so didn't want to override cori-gp-immi.stan.
Sorry for trouble.
Added code, following options and stan functions approach of @MJHutchinson to allow options for GP kernels, cross-coupled metapopulation models, and likelihood models.
@shehzaidi is it easy enough to set up ziz runs now?
Switching simulation methods to generate data from our assumed model, rather than from an SEIR model. Update in progress.
Switching simulation methods to generate data from our assumed model, rather than from an SEIR model. Update in progress.
Are we no longer using the metapopulation simulation with changing Rt?
We are using metapopulation effects, just not an SEIR model. Instead, we're generating data from the model we're proposing to check it can recover its own parameters.
ok cool, I was under the impression that we would be doing both.
Evaluate method.
[ ] 1. evaluate short-term forecasting, based on historical data. Compare against:
https://epiforecasts.io approach (Cori et al, with additional data preprocessing)
https://arxiv.org/abs/2006.16487
Look into covid forecasting methods from US (see van der Schaar paper ref)
Evaluate based on predictive probability of future counts.