First parameter fitting

Parameter fitting is also at the heart of the package, because why making a simulation without good parameter values?

The package provides a fit method that helps fitting model parameters to data.

For example we provide a method to fit the parameters from the Farquhar et al. (1980) model (Fvcb). Here is an example usage:

using PlantBiophysics, PlantSimEngine, DataFrames

df = read_walz(joinpath(dirname(dirname(pathof(PlantBiophysics))),"test","inputs","data","P1F20129.csv"))
# Removing the Rh and light curves for the fitting because temperature varies
filter!(x -> x.curve != "Rh Curve" && x.curve != "ligth Curve", df)

# Fit the parameter values:
VcMaxRef, JMaxRef, RdRef, TPURef = fit(Fvcb, df; Tᵣ = 25.0)

(VcMaxRef = 46.2467784134993, JMaxRef = 80.36773471227262, RdRef = 0.49949504402060546, TPURef = 5.596944472747526, Tᵣ = 25.0)

The fitting method uses the leaf temperature (Tₗ, °C), the Photosynthetic Photon Flux Density (aPPFD, μmol m⁻² s⁻¹) and the intercellular CO₂ concentration (Cᵢ, ppm) from the data to fit the four main parameters of the model.

Wrap-up

We learned to make a simple parameter fitting. For more information, you can head over the Parameter fitting section.