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Changes to support running ADRIA with external model (ReefMod Engine) data #341

Merged
merged 48 commits into from
May 5, 2023
Merged

Changes to support running ADRIA with external model (ReefMod Engine) data #341

merged 48 commits into from
May 5, 2023

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ConnectedSystems
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As in title.

@ConnectedSystems
Allow use of model_spec() with any domain
3ee41e3
@ConnectedSystems
Initial (unused and incomplete) scenario run function for ADRIA-ReefMod
49f96e2 
Should hypothetically be able to run ADRIA simulations with ReefMod data.
@ConnectedSystems
Allow use of site area functions with any Domain type
bb7f3c8
@ConnectedSystems
Interim changes for simulations with ReefMod inputs
09ce8ba
@ConnectedSystems
Compat changes for v1.0.18
c761298
@ConnectedSystems
Actually handle data set when size deviates from embedded metadata
636b998
@ConnectedSystems
Use shorthand for GeoDataFrames
cffe431
@ConnectedSystems
Adjust precompilation
ca69cc1
@ConnectedSystems
Allow use of unique_sites with any Domain
d468e30
@ConnectedSystems
Extend timeframe
8b12ade
@ConnectedSystems
Write out copy of spatial data (with appended values)
3fb5b8b 
This way the appended dataset gets included as opposed to simply a copy of the original data
@ConnectedSystems
Docstring to indicate what the setup function is setting up
58f44df
@ConnectedSystems
Fix intermediate cover calculation
7f75f39
@ConnectedSystems
Performance changes for ODE
a0c1a27 
Make better use of cache arrays
@ConnectedSystems
Deactivate forced site reselection
529cc51
@ConnectedSystems
update!() should be usable from all Domain types
44f375f
@ConnectedSystems
Standardize dimension names
8f1fd20
@ConnectedSystems
Consider mean of mean and std of DHW/Wave projections
124b410 
and only consider the specified DHW/wave projections rather than all available data cubes
@ConnectedSystems
Use stress centrality instead of katz
bdb5566 
Conceptually simpler
@ConnectedSystems
Changes as stress centrality returns an vector of integers
5fa7e45
@ConnectedSystems
Add arguments to docstring
52df9f4
@ConnectedSystems
Move connectivity strength calculation closer to where it is used
4af68e1
@ConnectedSystems
Comment out undefined exports
1a6c213
@ConnectedSystems
Re-enable RCP switching
f297416
@ConnectedSystems
Move n_adapt from Intervention to Coral component
a96450c 
Makes more conceptual sense as `n_adapt` is not an intervention
@ConnectedSystems
Add additional required packages
7a981e4
@ConnectedSystems
Initial (unused and incomplete) scenario run function for ADRIA-ReefMod
ff1dee5 
Should hypothetically be able to run ADRIA simulations with ReefMod data.
@ConnectedSystems
Compat changes for v1.0.18
02ea22c
@ConnectedSystems
Actually handle data set when size deviates from embedded metadata
ee1155b
@ConnectedSystems
Extend timeframe
df4d33c
@ConnectedSystems
Fix intermediate cover calculation
ded48da
@ConnectedSystems
Performance changes for ODE
60bf076 
Make better use of cache arrays
@ConnectedSystems
Standardize dimension names
a505844
@ConnectedSystems
Move connectivity strength calculation closer to where it is used
201f807
@ConnectedSystems
Re-enable RCP switching
a212d28
@ConnectedSystems
Switch to in/out degree centrality based on findings 2023-04-21
aaa2f45
@ConnectedSystems
Use area weighted connectivities in dMCDA
bbb4266
@ConnectedSystems
Use concrete type
a5b846c
@ConnectedSystems
Centrality measures use floats instead of ints so reverting change
0bdbbaa
@ConnectedSystems
Connectivity strengths are now passed in
2ce5ea7 
Expand docstrings and typing
@ConnectedSystems
Remove unused timestep argument
80107eb
@ConnectedSystems
Use more appropriate types / vectors
2bb5b75
@ConnectedSystems
Specify Matrix for clarity
1fb3929
@ConnectedSystems
Fix: subset to considered site_ids
429ace6
@ConnectedSystems
Correct sample adjustment for plan_horizon
3d6e325
@ConnectedSystems
whitespace
416c7e7 
whitespace
@ConnectedSystems
Fixes and changes for tests
9dbcde1
@ConnectedSystems
Correct typo
0396b6d
@ConnectedSystems ConnectedSystems merged commit 7b5b2d5 into main May 5, 2023
@ConnectedSystems ConnectedSystems deleted the ADRIA-ReefMod branch May 5, 2023 05:42
@Zapiano Zapiano mentioned this pull request Jun 26, 2023
Closed
@JuliaRegistrator JuliaRegistrator mentioned this pull request Jun 26, 2023
Merged
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@ConnectedSystems