Clarify ode methods: Document code and vignettes

traitecoevo / plant

Trait-Driven Models of Ecology and Evolution :evergreen_tree:

https://traitecoevo.github.io/plant

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Clarify ode methods: Document code and vignettes #413

Closed dfalster closed 1 month ago

dfalster commented 1 month ago

This PR better documents the ODE stepper used in plant, both in code and via a new article. In addition, we

move relevant files for ode_solver into a subdirectory inst/include/plant/ode_solver
enable system to continue when minimum step size is reached
rename some items for clarity
- advance -> advance_adaptive
- node_schedule_ode_times -> ode_times
clarify how to control time steps (closes #411, needed for TF24 Soil water milestone)

itowers1 commented 1 month ago

Also includes some renaming of plant -> individual

dfalster commented 1 month ago

Thanks @itowers1 ! Hmm, good suggestion about the warning. If we added it here, you'd get maybe 1000s of messages in the terminal (one every step). Perhaps, best to add at the end of the run, as a post run assessment. That might require storing a flag. We can't just look at the step sizes as some will be short due to cohort introduction. I'm going to add this as a new issue, as it will take a little more programming than I want to do on this branch. See link below.