made it so only the functions we intentionally want the user to see are exported (all the rest are hidden)
removed problematic rcpp functions (ones that declare a return type but return void, ones that do implicit coercion of NULL pointers)
made sure all exported functions are documented
cleaned up the DESCRIPTION and NAMESPACE files
I then tested that everything still builds, the unit tests compete, and a bare minimum test of the stochastic dynamics work (i.e. run a model with high immigration and sure enough species richness increases)
I think this can be merged without substantive review...
HOWEVER as we're using the package post merging this PR, we should make sure to document any weird behavior, especially with dynamics as there's a small but none-0 chance I might have messed up how deep copying works
I've done a few things here:
I then tested that everything still builds, the unit tests compete, and a bare minimum test of the stochastic dynamics work (i.e. run a model with high immigration and sure enough species richness increases)
I think this can be merged without substantive review...
HOWEVER as we're using the package post merging this PR, we should make sure to document any weird behavior, especially with dynamics as there's a small but none-0 chance I might have messed up how deep copying works