This is quite close now! I made some small changes to mosquito parameters, remove individual mosquitoes and so that it could run on my machine.
It seems like there are a few things left:
[ ] investigate clinical incidence in Treatment
[ ] investigate SMC, bednet and spraying distribution
[ ] why does RTS,S and MDA have no effect?
[ ] re-introduce warmup period
[ ] remove mlgts from the vignette
[ ] remove tidyverse from vignette
Here are some extra thoughts on it. Please add/remove from the list as you like!
investigate clinical incidence in Treatment
It looks like malariasimulation and mlgts have different measures for clinical incidence (since the prevalence matches up very well!) What is mlgts counting?
investigate SMC, bednet and spraying distribution
mlgts seems to be distributing these interventions more regularly, whereas malariasimulation distributes them once off at 5 years. How should malariasimulation schedule these interventions to match mlgts?
why does RTS,S and MDA have no effect?
There doesn't appear to be an MDA parameterisation yet. And the RTS,S paramterisation for mlgts doesn't seem to have any effect at the moment. What should it be?
re-introduce warmup period
After things look vaguely correct, I'm sure adding a warmup period would help things line up even better.
remove mlgts from the vignette
If we want this vignette to run on GitHub, we can't have private packages like mlgts. We can come up with a script to run it locally once and save the outputs.
This is quite close now! I made some small changes to mosquito parameters, remove individual mosquitoes and so that it could run on my machine.
It seems like there are a few things left:
Here are some extra thoughts on it. Please add/remove from the list as you like!
investigate clinical incidence in Treatment
It looks like malariasimulation and mlgts have different measures for clinical incidence (since the prevalence matches up very well!) What is mlgts counting?
investigate SMC, bednet and spraying distribution
mlgts seems to be distributing these interventions more regularly, whereas malariasimulation distributes them once off at 5 years. How should malariasimulation schedule these interventions to match mlgts?
why does RTS,S and MDA have no effect?
There doesn't appear to be an MDA parameterisation yet. And the RTS,S paramterisation for mlgts doesn't seem to have any effect at the moment. What should it be?
re-introduce warmup period
After things look vaguely correct, I'm sure adding a warmup period would help things line up even better.
remove mlgts from the vignette
If we want this vignette to run on GitHub, we can't have private packages like mlgts. We can come up with a script to run it locally once and save the outputs.
remove tidyverse from vignette
:D