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epiverse-trace / serofoi

Estimates the Force-of-Infection of a given pathogen from population based sero-prevalence studies
https://epiverse-trace.github.io/serofoi/
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Model initialisation #63

Open ben18785 opened 1 year ago

ben18785 commented 1 year ago

Currently, the MCMC is initialised using arbitrary FOI values etc. which vary according to the specific model being fitted. To make this more robust, I'd suggest the following approach:

  1. We run stan::optimisation a number of times (default is say 10), each time starting from random initial values
  2. We select the single parameter set which is the best fitting amongst the above runs
  3. We perform MCMC using the parameter set found in 2 as initial points
ben18785 commented 1 year ago

We probably will also want to give the users the opportunity to perform an optimisation as opposed to sampling. But this is best handled in a separate issue.

rccreswell commented 10 months ago

@ntorresd I'm happy to look at this.