Does Stan take log in the background

Note that we already went through one iteration of trying to come up with solutions to this in an earlier thread. It would be good to include the link to the previous thread for clarity. Anyway, one problem I think the model might have is that Y[i, j]s can contain zeros (as you mention here), although I don’t know if this will completely solve the issues. Here’s my earlier post about this: Survival analysis: initial values rejected