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Add single-step leaf-level P-model function - #302

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fabern merged 23 commits into
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simple_pmodel_v2
Jul 28, 2025
Merged

Add single-step leaf-level P-model function#302
fabern merged 23 commits into
masterfrom
simple_pmodel_v2

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@fabern fabern commented Jul 7, 2025

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Adds function for single-step leaf-level simulations of the P-model (run_pmodel_onestep_f_bysite).

This is based on the former branch simple_pmodel. This branch should be used instead of the former since it has been rebased at the end of the commit history after the luluc merge.

@fabern fabern changed the title Simple pmodel v2 Add single-step leaf-level P-model function Jul 7, 2025
fabern added 6 commits July 8, 2025 07:11
@fabern
Fix typo in biomee interface
75193bd
@fabern
Make pmodel_onestep_f public
e99eaa5
@fabern
Refactor pmodel output following biomee code
5b8ca3c 
Biomee code of run_biomee_f_bysite() had been refactored using a suite of build_x() functions with the LULUC merge. This commit applies the same logic to  the output preparation for pmodel .
@fabern
Reorder arguments of run_pmodel_f_bysite() to prepare refactoring
ff59c8f 
This prepares a refactoring with the aim to have similar matrix arguments as luluc biomee model.
@fabern
Refactor pmodel_onestep output following biomee code
ee3a7c6
@fabern
Add simple test for run_pmodel_onestep_f_bysite()
df4e0ff
@fabern

fabern commented Jul 8, 2025 •
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This currently does NOT give the same result as rpmodel::rpmodel(), see vignette or test-model-runs.R.

  • needs to be fixed

@fabern

fabern commented Jul 18, 2025 •
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The differences between rpmodel::rpmodel() and run_pmodel_onestep_f_bysite() were due to different method_jmaxlim and also different units:

  • iwue (Pa vs -),
  • rd (mol C m-2 vs. g C m-2), and
  • gs or gs_accl (mol C m-2 Pa-1 vs mol C / molPhotons / Pa).

@fabern
fabern force-pushed the simple_pmodel_v2 branch from bb1b8cb to d4c5518 Compare July 21, 2025 11:49
@fabern
fabern marked this pull request as ready for review July 21, 2025 12:14
@fabern fabern mentioned this pull request Jul 25, 2025
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fabern requested a review from stineb July 25, 2025 16:20
@fabern

fabern commented Jul 25, 2025 •
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This is now ready for review and merge.

  • Besides the functionality for the single-step p-model function, I also:
  • double-checkd and corrected many of the code comments specifying units (of ppfd, vcmax, etc...)
  • slightly refactored the Fortran-R interface of p-model similar to the current (LULUC-)BiomeE

@fabern fabern mentioned this pull request Jul 28, 2025
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fabern added 3 commits July 28, 2025 14:00
@fabern
Return explicitly NA if pmodel not run
0139958 
No change, already previously array() gave back NA is not initialized. This is now just more explicit.
@fabern
Follow style of NEWS.md
3ee4cfd 
https://style.tidyverse.org/news.html#news-release
@fabern
Decrease pkg-tarball size <5MB for CRAN
228d624 
Simply by using compressed RDS in vignettes
@fabern fabern mentioned this pull request Jul 28, 2025
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@fabern
fabern merged commit 01691f8 into master Jul 28, 2025
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@fabern
fabern deleted the simple_pmodel_v2 branch July 28, 2025 16:41
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