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Source files for paper on dynamic CO2 assimilaton under fluctuating irradiance
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Intermediate
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.gitignore
DynamicPhotosynthesis.Rproj
INSTALL.R
README.md

README.md

DynamicPhotosynthesis

Source files required to reproduce analysis from the paper "Dynamic modelling of limitations on improving leaf CO2 assimilation under fluctuating irradiance" including the source code of the model and the R scripts required to reproduce all figures in the paper.

Before making use of the scripts, please run the INSTALL.R script to install all dependencies. This will require an Internet connection. Also, if you are using Windows, make sure to have Rtools installed. If you are encounter any issues running this code, please use the Issues tab of this github website to report them.

Scripts for simulations

The scripts required to reproduce the simulations are located in the folder Code organized according to the different types of calculations required. The results of the calculations are cached as binary R files in the folder Intermediate, whereas the final figures will be located in the folder Output.

Source code of the model

Source code of the model

The model was implemented using the ODEDSL library in Julia, and converted into an R package using the SimulationModels R package. This R package is included in the Packages folder under the name ThylakoidMetabolism. Performing simulations with the model only requires this R package (plus all dependences installed by the INSTALL.R file). The actual implementation of the model can be found in the file Packages/MiniModel/src/MiniModel.cpp. This file was automatically generated from a high-level description of the model (see below) so no documentation or comments are provided.

The model was implemented using an ad-hoc domain specific language written in the Julia programming language via the ODEDSL.jl library. Thus, although the model may be extended by modifying the source code inside the ThylakoidMetabolism package provided here, it is more convenient to use ODEDSL and generate a new R package with the new version. For that purpose, the MiniModel.ode file is provided. The virtual mutants used in Figure 7 of the pap, as well as the modified model used

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