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ciarajudge / EpiFusion

Repository for EpiFusion, an infectious disease modelling framework built on the principles of phylodynamics and epidemiology
GNU General Public License v3.0
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Phylo Likelihood, discrete days or segmented days #4

Closed ciarajudge closed 10 months ago

ciarajudge commented 11 months ago

There's either a bug in day() that isn't in segmentedDay() in ProcessModel, or segmentedDays = true is absolutely essential (for the statistical validity). Would be good to get to the bottom of it, as segmented days are slower overall. But for now just keeping segmentedDays true means the phylo likelihood is accurate

ciarajudge commented 10 months ago

Figured this out and it wasn't a bug, it's just that if there is a lot of things happening on the tree within a day, segmentedDays = true helps the phylo weighting keep itself together working with the importance sampling