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Refactor emergent parameters code #81

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Refactor emergent parameters code #81

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Commits on Oct 30, 2024

  1. create function to dynamically expand the parameter dictionary with p… 

    …lankton
    @nanophyto
    nanophyto committed Oct 30, 2024
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Commits on Oct 31, 2024

  1. added dummy function to create N2P2ZD example palat matrix

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    nanophyto committed Oct 31, 2024
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  2. dummy emergent growth function

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  3. dummy emergent nitrogen saturation function

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    nanophyto committed Oct 31, 2024
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  4. rename dummy palat function

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    nanophyto committed Oct 31, 2024
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  5. dummy emergent nitrogen half saturation function

    @nanophyto
    nanophyto committed Oct 31, 2024
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  6. fix formatting

    @nanophyto
    nanophyto committed Oct 31, 2024
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  7. start merging into one file

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  8. add NamedArrays dependency

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  9. fix formatting...

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Commits on Nov 1, 2024

  1. move emergent functions to one file

    @nanophyto
    nanophyto committed Nov 1, 2024
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  2. move helper functions

    @nanophyto
    nanophyto committed Nov 1, 2024
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  3. create main file that loads functions and creates dict

    @nanophyto
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  4. first try at multiple dispatch (broken)

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  5. formatting...

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Commits on Nov 4, 2024

  1. tidy/fix helper functions

    @nanophyto
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  2. working example

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  3. tidying

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  4. formatting

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  5. move dispatch code to emergent_functions.jl

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    nanophyto committed Nov 4, 2024
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  6. create working example

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  7. formatting

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  8. update parameters to match N2P2D example

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  9. check NamedArrays output

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Commits on Nov 7, 2024

  1. working example of splitting step

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  2. renaming for clarity

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  3. move splitting functions to helper_functions.jl and merge examples

    @nanophyto
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  4. wrap last step into function and merge intermediate_parameter value w… 

    …hich do not have func
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  5. add biogeochem parameters

    @nanophyto
    nanophyto committed Nov 7, 2024
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  6. update N2P2ZD example with constant alpha

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  7. update example with missing parameters

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Commits on Nov 12, 2024

  1. merge main

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    radka-j committed Nov 12, 2024
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Commits on Nov 13, 2024

  1. add tests and argument types

    @nanophyto
    nanophyto committed Nov 13, 2024
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  2. formatting :)

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Commits on Nov 15, 2024

  1. rm outdated function

    @radka-j
    radka-j committed Nov 15, 2024
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  2. fix file path

    @radka-j
    radka-j committed Nov 15, 2024
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  3. start mv functions to parameters

    @radka-j
    radka-j committed Nov 15, 2024
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  4. disable tests for emergent parameters

    @radka-j
    radka-j committed Nov 15, 2024
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  5. Revert "fix file path" 

    This reverts commit dde2eee.
    @radka-j
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  6. revert commit and fix file path

    @radka-j
    radka-j committed Nov 15, 2024
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  7. undo changes

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  8. add separate palatability and assimilation efficiency functions

    @radka-j
    radka-j committed Nov 15, 2024
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  9. Merge branch 'N_plankton' into emergent_params

    @radka-j
    radka-j authored Nov 15, 2024
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  10. disable emergent params tests

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  11. recreate emergent_2D_array

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  12. update emergent functions

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    radka-j committed Nov 15, 2024
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  13. fix assimilation example

    @radka-j
    radka-j committed Nov 15, 2024
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  14. minor clean up

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Commits on Nov 18, 2024

  1. DifferentialEquations -> OrdinaryDiffEq

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  2. get argnames from function, not from list

    @radka-j
    radka-j committed Nov 18, 2024
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  3. refactor emergent functions

    @radka-j
    radka-j committed Nov 18, 2024
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  4. update docstrings

    @radka-j
    radka-j committed Nov 18, 2024
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  5. clean up file

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Commits on Nov 19, 2024

  1. add compute_darwin_parameters function

    @radka-j
    radka-j committed Nov 19, 2024
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  2. fix bugs

    @radka-j
    radka-j committed Nov 19, 2024
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  3. fix bug with param names

    @radka-j
    radka-j committed Nov 19, 2024
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  4. add note about assimilation_efficiency param

    @radka-j
    radka-j committed Nov 19, 2024
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  5. update example

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  6. delete helper functions file

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    radka-j committed Nov 19, 2024
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  7. fix order of args passed to splitting functions

    @radka-j
    radka-j committed Nov 19, 2024
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  8. update docstrings

    @radka-j
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  9. update dummy_emergent_assimilation_efficiency function

    @radka-j
    radka-j committed Nov 19, 2024
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  10. update example parameters to match N2P2ZD example

    @radka-j
    radka-j committed Nov 19, 2024
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  11. update tests

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  12. fix alpha value in example

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  13. compare all parameters in emergent example with N2P2ZD

    @radka-j
    radka-j committed Nov 19, 2024
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  14. formatting

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  15. add note

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    radka-j committed Nov 19, 2024
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  16. update example

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Commits on Nov 20, 2024

  1. add _matrix to palatability and assimilation_efficiency parameters

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Commits on Nov 22, 2024

  1. start parameters refactor, 1D params completed (2D to do)

    @radka-j
    radka-j committed Nov 22, 2024
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  2. update dependencies

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  3. refactor palatability and assimilation

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Commits on Nov 25, 2024

  1. update example

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  2. rename module Dynamic -> Biogeochemistry

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    radka-j committed Nov 25, 2024
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  3. update docstrings

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    radka-j committed Nov 25, 2024
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Commits on Nov 26, 2024

  1. update docstrings

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    radka-j committed Nov 26, 2024
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  2. update docstring

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    radka-j committed Nov 26, 2024
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Commits on Nov 28, 2024

  1. rename light object

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    radka-j committed Nov 28, 2024
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Commits on Dec 2, 2024

  1. merge branch

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    radka-j committed Dec 2, 2024
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  2. update docstring

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    radka-j committed Dec 2, 2024
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  3. re-add dependencies dropped during branch merge

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Commits on Dec 3, 2024

  1. Merge branch 'main' into emergent_params

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  2. Merge branch 'main' into emergent_params

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  3. merge main

    @radka-j
    radka-j committed Dec 3, 2024
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  4. clean up NPZD example 

    avoid duplication of parameters
    @radka-j
    radka-j committed Dec 3, 2024
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  5. add missing example dependency

    @radka-j
    radka-j committed Dec 3, 2024
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  6. add phyto and zoo growth functions using named arrays

    @radka-j
    radka-j committed Dec 3, 2024
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