PlantFATE Eco-evolutionary vegetation model

Plant-FATE, standing for Plant FunctionAl Trait Evolution, is an eco-evolutionary vegetation model that accounts for multi-timescale adaptations of invdividual plants and plant species to the environment.

Prerequisites

Plant-FATE can be built without any third party libraries as shown here (but GSL and Eigen can be optionally used - we will not cover these cases for now).

You do need git to select the appropriate branches for compiling. Instructions to install git can be found here: https://github.com/git-guides/install-git

Installation

You need three repos to run PlantFATE:

1. P-hydro: photosynthesis model
2. libpspm: PSPM solver library
3. PlantFATE: The PlantFATE EVM

Create a folder that will serve as a root folder for cloning these repos. Clone all three repos in same (root) folder, so that your directory structure looks like this:

  root
  |---- phydro
  |     |--- inst/include
  |
  |---- libpspm
  |     |--- include
  |     |--- lib
  |
  |---- Plant-FATE
  |     |--- inst/include

For each repo, we clone it and checkout the appropriate branch. The latest branches that should be used are shown in the commands below.

cd <path/to/root>

git clone https://github.com/jaideep777/phydro
cd phydro
git checkout master
cd ..

git clone https://github.com/jaideep777/libpspm
cd libpspm
git checkout develop
cd ..

git clone https://github.com/jaideep777/Plant-FATE
cd Plant-FATE
git checkout feature_evolution
cd ..

Prepare input data and simulation configuration

1. Paste data files in folder tests/data

2. Simulation config is in tests/params/p.ini. Change these parameters as necessary. Particularly, set the output folder: output files will be generated in the folder specified in a folder hierarchy as follows: Plant_FATE/outDir/exptName

R Installation

Prerequisites

If you are using R in Windows, you also need to install a C++ compiler for R and the Rcpp package. Please follow these guidelines to install both: https://teuder.github.io/rcpp4everyone_en/020_install.html

Compiling the PlantFATE R package

After cloning the three repos and checking out the appropriate branches, create a new R Project, select 'Exisiting Directory' in the wizard, and select the Plant-FATE folder. At the end of this step, you should have the following files in the Plant-FATE folder (among others):

  root
  |---- Plant-FATE
  |     |--- ...
  |     |--- Plant-FATE.Rproj
  |     |--- DESCRIPTION
  |     |--- NAMESPACE
  |     |--- vignettes
  |     |--- ...

Open the project and simply perform a build (type ctrl+shift+B or via the menu, click on Build/Install Package). In Windows, if you get a prompt saying you need additional build tools, go ahead and install them.

Please see the vignettes folder for demos on how to use the PlantFATE and TreeLife models in R.

Native C++ Installation

Perform these steps from the root folder:

Compile and test libpspm

cd libpspm
make clean testclean
make
make check

(all tests should pass)

Test Phydro

cd phydro
make clean testclean
make check

(all tests should pass)

Compile and run PlantFATE

The main program to run Plant-FATE is in tests/pf.cpp:

make clean testclean
make check TEST_FILES=tests/pf.cpp

Analyse results

Analyse results with tests/Rscripts/amazon_calibration.R Dont forget to change path to Working dir

Author Contact

Jaideep Joshi (jaideep777@gmail.com)

Acknowledgements

This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Actions fellowship (grant agreement No 841283).