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Refactor emergent parameters code #81

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Refactor emergent parameters code #81

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@radka-j radka-j commented Nov 15, 2024 •
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Closes #83

PR overview:

  • renames Dynamic module to Biogeochemistry, this means that models are now accessible as Agate.Models.Biogeochemistry.<struct UUID>
  • adds Parameters module which generates n volumes for each plankton group and computes "emergent" parameters from those
    • emergent_parameters = compute_darwin_parameters(defined_parameters)
  • adds Tracers module....
  • adds Constructors module....
  • updates examples
  • adds tests

@nanophyto
create function to dynamically expand the parameter dictionary with p…
327365f 
…lankton
@nanophyto
added dummy function to create N2P2ZD example palat matrix
6ba3ad5
@nanophyto
dummy emergent growth function
52d3147
@nanophyto
dummy emergent nitrogen saturation function
ab5e047
@nanophyto
rename dummy palat function
1076aed
@nanophyto
dummy emergent nitrogen half saturation function
523195f
@nanophyto
fix formatting
8fa6c3a
@nanophyto
start merging into one file
e5bc6ff
@nanophyto
add NamedArrays dependency
84fcfc2
@nanophyto
fix formatting...
8fa7fc0
@nanophyto
move emergent functions to one file
4fd4c5a
@nanophyto
move helper functions
1e13ffb
@nanophyto
create main file that loads functions and creates dict
3293c74
@nanophyto
first try at multiple dispatch (broken)
188e236
@nanophyto
formatting...
1cef1f4
@nanophyto
tidy/fix helper functions
5d5d558
@nanophyto
working example
e95ec69
@nanophyto
tidying
32f6e89
@nanophyto
formatting
d60f038
@nanophyto
move dispatch code to emergent_functions.jl
30ec979
@nanophyto
create working example
c9a0eda
@nanophyto
formatting
fa5b027
@nanophyto
update parameters to match N2P2D example
9aa203d
@nanophyto
check NamedArrays output
bba282f
@nanophyto
working example of splitting step
cb08e5b
@nanophyto
renaming for clarity
0e8dcc9
@nanophyto
move splitting functions to helper_functions.jl and merge examples
10bb69a
@nanophyto
wrap last step into function and merge intermediate_parameter value w…
28d487a 
…hich do not have func
@nanophyto
add biogeochem parameters
8c1ea22
@nanophyto
update N2P2ZD example with constant alpha
f970dad
@radka-j radka-j marked this pull request as ready for review November 19, 2024 16:15
nanophyto
nanophyto reviewed Nov 20, 2024
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nanophyto
nanophyto reviewed Nov 20, 2024
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nanophyto
nanophyto reviewed Nov 20, 2024
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Had a quick look - looks great so far

@radka-j radka-j changed the base branch from N_plankton to main December 2, 2024 10:50
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New high-level API for specifying models
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@radka-j @nanophyto