Removed new refinement methods

[lucadealfaro]

I removed the following code:

                # check if in at least one of multiple habitat ranges
                def in_hab(*ranges: tuple[int, int]) -> bool:
                    return any((r[0] <= map_code < r[1]) for r in ranges)

                if h is not None:
                    if refine_method == "forest" or refine_method == "forest_add308":
                        h["resistance"] = 0 if in_hab(self.FORESTS) else h["resistance"]
                    elif refine_method == "forest_africa":
                        # will have the forest and shrublands set to 0 regardless of the habitat data
                        h["resistance"] = 0 if in_hab(self.FORESTS, self.SHRUBLANDS) else h["resistance"]

                    writer.writerow(h.values())
                else:
                    if refine_method == "forest" or refine_method == "forest_add308":
                        writer.writerow([""] * 5 + [map_code] + [0 if in_hab(self.FORESTS) else 1])
                    elif refine_method == "forest_africa":
                        resistance = 1
                        if in_hab(self.FORESTS, self.SHRUBLANDS):
                            resistance = 0
                        elif in_hab(self.INTRODUCED_VEGETATION):
                            resistance = 0.1
                        elif in_hab(
                            self.SAVANNAS,
                            self.GRASSLANDS,
                            self.WETLANDS,
                            self.ROCKY,
                            self.CAVES,
                            self.OTHER,
                            self.UNKNOWN,
                        ):
                            resistance = 0.9
                        elif in_hab(
                            self.DESERTS,
                            self.MARINE_NERITIC,
                            self.MARINE_OCEANIC,
                            self.MARINE_DEEP,
                            self.MARINE_INTERTIDAL,
                            self.MARINE_COSTAL,
                            self.ARTIFICIAL,
                        ):
                            resistance = 1

I have the following issues with it.

• First, there seem to be some errors. For example, there are branches that are taken if the terrain code is 308, but then 308 is not considered among self.FOREST.
• Second, I think these refinements should happen elsewhere. This layers package should be tasked with deriving terrain and habitat rasters, and some standard simple resistance values. We can then do any post-processing we need in some other place.

As an example of the second point, it's not reasonable to add a forest_africa method -- the africa work should post-process the csv any way they want for resistance.

Rather, this package should be mainly concerned with getting the habitat raster right.

[IanHollow]

@lucadealfaro

• In regards to your second point it sounds like you want to make a new tool. This new tool could either generate resistance.csv's or it could generate a permeability layer. I could create this tool once we define what we would like it to do.
  • When this tool is made we can remove the resitance.csv creation from this tool. This should remove the need for refinement methods as this can happen in the new tool.
  • However, these resistance values are still potential needed for defining what the current habitat of the species.
  • There would need to be a standard way to define habitat. This would be needed as this tool could be used for more than just forest birds.
  • This could be done by saying where ever the habitat is major-importance which is 0 resistance. This would not follow the original paper though as in that paper it ignores IUCN habitat data and just says any forest is habitat.
  • Paper reproducibility could be fixed also by having a parameter that would allow overwriting the standard of using just major-importance with a list of map codes that should be the current habitat.
• Regarding your first point, these definitions of ranges follow the IUCN documentation. It can be found here: https://www.iucnredlist.org/resources/habitat-classification-scheme . In this classification documentation it say that 3.8 which is 308 is a shrubland. It might be confusing if we drift from this documentation.

Let me know what your thoughts are and I will take appropriate action.