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project-aero / measles-ews

A research compedium (data, code, manuscript) for project on detecting critical slowing down in measles dynamics.
MIT License
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Re-do emergence and elimination simulations #19

Closed atredennick closed 5 years ago

atredennick commented 5 years ago

There was an error (now fixed, dae9b94) in the make-pomp-simulator-function.R code: I didn't reset initial values for exposed and infected classes. This doesn't make much of difference for the elimination simulations because they burn in from initial conditions, but it does impact the emergence simulations. For emergence simulations, initial exposed and infected should be set to zero. The function now allows this. Also, simulations now start from the middle of the first year so that dynamics start in the trough of seasonal transmission dynamics. Again, not much of an impact for the elimination simulations, but this better represents the scenario for re-emergence after a big outbreak.

For consistency, need to re-run:

atredennick commented 5 years ago

All done as of commits 624f9b1ef63ffdea934ceeb9acb626cd8743c898, 8027a013a5e50c65cfec34ac7633debe7c715520, 66beeecef32bc4df267d87522f8c1fa9cdbeccf3, and ca11f3b179657647d3f0362a353984a35e037845.