vezy / plantbiophysics.jl Goto Github PK

Apply ExplicitImports.jl on the package to be sure that we explicitly import the functions of our dependencies.

It would be easier to see the parameters g0 and g1 for the stomatal conductance to water vapor and not to CO2.
Either put the stomatal conductance model for water and then transform for CO2 in a specific function or step, or correct the parameters.

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In Walz, we need to use PARTop-ParBot for aPPFD, because PARTop is the incident PAR, not the absorbed PAR, and in the models then we use aPPFD, not PPFD (because we simulate aPPFD with a light interception model).

Related to VirtualPlantLab/PlantSimEngine.jl#30

add an error into the fit of FvCB when the user directly provide PPFD instead of aPPDF.

See VirtualPlantLab/PlantSimEngine.jl#21
And https://vezy.github.io/PlantSimEngine.jl/dev/model_execution/#Parallel-traits

alpha is taken from Duursma (PlantEcophys), which is abs.(1-f)/2 (cf Van Caemmerer 2009). But in PlantBiophysics, the absorbed PPFD is used and not the incident PPFD. So alpha should be (1-f)/2, value of 0.42 instead of 0.24
Planbiophysis used theta=0.7 from Caemmerer whereas used theta=0.85. Should use both value on Von Caemmerer for alpha and theta.
Also should detail in PlantBiophysics the use of aPPFD and not incident PPFD. Calibration of photosynthesis parameters should use aPPFD and not incident PPFD (aPPFD=0.85*iPPFD)

Von Caemmerer 2009:
DOI: 10.1007/978-1-4020-9237-4_9

See their paper here: https://doi.org/10.1111/pce.14070
See also < https://doi.org/10.1111/pce.12098> for more background

Update this doc: https://vezy.github.io/PlantBiophysics.jl/stable/simulation/mtg_simulation/ for new feature of time-step selection while plotting (using the index argument in viz) instead of extracting the time step into the mtg manually.

From the documentation:

9.9 Water Vapor Conductance (GH2O)

According to Caemmerer and Farquhar (1981) the total water vapor conductance GH2O is calculated as follows:

GH2O = E / VPD
where:
GH2O = total water vapor conductance [mmol m-2 s-1],
E = transpiration rate [mmol m-2 s-1],
VPD = (Air-to-Leaf-) Vapor-Pressure-Deficit [Pa/kPa].

VPD can also be expressed in kPa. To obtain this unit, multiply the VPD value by the ambient pressure and divide by 1000.

We use kPa everywhere else in the package, we should use that instead.

We use recipes for Plots in PlantBiophysics, but we use Makie in PlantGeom.
So in the docs we have both. It would be nice to use only one: Makie.