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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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Incidence assumed to start counting from day 0 #9

Open ciarajudge opened 8 months ago

ciarajudge commented 8 months ago

infections from day '0' to the date/index of first incidence are assumed to contribute to the first incidence data point.

Not a problem for now, but something to fix eventually (add in the date/time from which incidence is being noted)

ciarajudge commented 4 months ago

this issue remains open for now, but FYI for any users that this can be overcome by introducing step changes to the 'phi' parameter in priors in the XML, where you have a changetime (fixed parameter) at the date from which you want incidence to start counting, and set the prior for the rate beforehand to a fixed parameter of 0