Paper: Barillot et al. 2021
Developed on Windows 10
RStudio
R version 3.6 or newer
RxODE package
rtools40
add the rtools40 folder to the PATH environmental variable
Model simulation is done as follows:
- make sure that all files are in de same folder
- in the 01_ModelSimulation.R file:
- modify the working directory to that folder
- adapt the PLANTNo parameter under Settings if desired
- Run the entire 01_ModelSimulation.R script
You will have created an RDS file starting with "Simulation_Exp2_" which can be read in R by the readRDS()
function
RDS files
- Input files Transpiration:
- Time - h (0-1 is stabilisation, 1-6 is actual data)
- Transp - g m-2 h-1
- Input file Soil water potential (constant in this case)
- Time - h
- PsiSoil - MPa
- Calib files Leaf elongation:
- Time - h (0-1 is stabilisation, 1-6 is actual data)
- LER - m h-1
- LERnorm (normalised versus the mean of the datafile)
txt file
GrassMod_Exp2.txt: txt file of the model used in Exp2
R files
- Thetas_Exp2.R: generation of the 'thetas_Exp2' named vector based on parameter settings
- Inits_Exp2.R: generation of the 'inits_Exp2' named vector based on initial values of state variables
- 01_ModelSimulation.R: script for model simulation with reference parameters including:
- Loading input data
- Loading Calibration data
- Simulation settings
- Parameter values + automatic calculation of derived parameters and initial conditions
- Model compilation (if necessary)
- Simulation runs for 4 different Transpiration inputs (similar treatment) + mean Transpiration