Changing Habitats

[eschemmel]

We are adding and removing habitats from the Biodiversity HAB subgoal and Coastal Protection goal.
When you do this in the functions, pressure-matrix and resilience matrix and run the calculate scores you get this error message:
These goal-elements are in the weighting data layers, but not included in the pressure_matrix.csv:
CP-coral, CP-mangrove, CP-saltmarsh, CP-seagrass, CP-seaice_shoreline, CS-mangrove, CS-saltmarsh, HAB-coral, HAB-mangrove, HAB-saltmarsh, HAB-seagrass, HAB-seaice_edge
These goal-elements are in the pressure_matrix.csv, but not included in the weighting data layers:
CP-reef, CP-wetland, CP-beach, CS-wetland, HAB-reef, HAB-wetland, HAB-watershed, HAB-beach

The first error is referring the the global habitats that were removed and the second error is referring to the habitats that I added for the regional assessment.

What is the "weighting data layers" coming from and how to I exchange out the global habitats for the regional.

[jules32]

Hi Eva,

This is definitely confusing and part of what we have been working on to improve (we're in the final testing phases and will roll it out in mid-July and update your repo accordingly!). Right now it is described briefly in 7.1.2.5 of the manual (and we'll update this when we've made the changes too). Right now the Toolbox will still calculate everything and just give these warning messages (they aren't error messages so that you are able to continue past them but correct them as you go).

These goal-elements are in the weighting data layers...

These goal-elements are in the weighting data layers, but not included in the pressure_matrix.csv:
CP-coral, CP-mangrove, CP-saltmarsh, CP-seagrass, CP-seaice_shoreline, ...

What this means is that these layers are listed in the layers identified in conf/config.r but not in conf/pressures_matrix.csv. Looking at conf/config.r, the layer that identifies the habitats for CP is element_wts_cp_km2_x_protection in the layers folder.

So there is this mismatch:
element_wts_cp_km2_x_protection shows:

while the (conf/pressures_matrix.csv](https://github.com/OHI-Science/mhi/blob/master/region2017/conf/pressures_matrix.csv) shows:

These goal-elements are in the pressure_matrix.csv....

You'll handle this warning message the same way you did the one above to take care of the mismatches :)