Switch from proto to R6 for all classes

[Martin-Jung]

There is some indication that this will have benefits in terms of memory efficiency. Thus we should at some point switch to objects defined by the R6 package instead.

[Martin-Jung]

To do at a later point. Apparently R7 is the newest hot stuff but has not yet matured to a post-beta version.
Transition as soon as R7 is on CRAN and remove the proto dependency.

[Martin-Jung]

Closed and implemented now in dev
FYI @mhesselbarth changed all class structure to R6 from proto. Still some notes to resolve (missing self object) but otherwise this will hopefully be cleaner.
We also have now basic definitions for class-functions, e.g. see https://iiasa.github.io/ibis.iSDM/reference/DistributionModel-class.html

[mhesselbarth]

Perfect! I still have some unmerged changes on a local branch fixing a few of the notes. Will look into this next week how to merge.

[mhesselbarth]

So R6 objects get changed outside the scope of a function? So for example

ibis.iSDM::add_biodiversity_poipa(x = base_model, poipa = ebird_pa, weight = 1,
           field_occurrence = "individualCount")

would change the object base_model even without assigning it?

This seems to be an issue for some functions (e.g., write_model).

Also, the behavior is not consistent across functions I think. For example train does acutally not change it original object

[mhesselbarth]

Also, it seems that the class information about the trained engine is missing now for DistributionModel. Needs to be added again

[Martin-Jung]

So R6 objects get changed outside the scope of a function? So for example

ibis.iSDM::add_biodiversity_poipa(x = base_model, poipa = ebird_pa, weight = 1,
           field_occurrence = "individualCount")

would change the object base_model even without assigning it?

This seems to be an issue for some functions (e.g., write_model).

Also, the behavior is not consistent across functions I think. For example train does acutally not change it original object

I found a similar behaviour for rm_predictors. This is related to object inheritance and unfortunately R6 is a bit more itchy with this, essentially requiering a deep clone of each object when modifying the contents.

[Martin-Jung]

Also, it seems that the class information about the trained engine is missing now for DistributionModel. Needs to be added again

Yes, but I think I changes this throughout so that the class information is saved as public (or private) attribute instead. If there are still come functions in the package that do a class check, this needs to be changed.

[Martin-Jung]

Ok, fixed both issues including the class import check in load_model and added unit tests in 9eff17b
"Class" (or rather algorithm) names can be queried via mod$get_name().
train() or project() should not change the original object I think.

Reopen the issue if you think there is something else that did not work following the R6 transition.