README_mottiprebas.md

https://github.com/ForModLabUHel/forClimate/blob/main/README_mottiprebas.md# Framework to run PREBAS and Motti under changing climate

Note

Development status: The framework, put together in the mottiprebas.py Python script, can be used with single site Motti initialization files now.

Installation

The following software must be present:

• Python: Tested with Python 3.10 but any "close enough" Python 3.x should do.
• R/RStudio: Tested with Rstudio Version 2023.09.0+463 (2023.09.0+463) but any "close enough" R distribution should do.
• Rtools (Windows): Compilers to build Fortran and C source files in PREBAS.
• Rprebasso: Download from GitHub. Use the instructions in the GitHub README file to install the latest development version in R.
  • forClimate requires that Rprebasso package (i.e. PREBAS) is installed in R.
  • To install Rprebasso from the local download directory:
    • install.packages('path/to/Rprebasso',repos=NULL,type='source')
• forClimate: This project. Download from GitHub.
• Motti workbench mottiwb.exe.

Python, R/RStudio and RTools for Windows are available from Luke Software Center.

Note

Although RTools can be installed from Luke Software Center the content software, most notably Fortran and C compilers, cannot be run from the installation location (for security reasons). Until this problem has been solved the workaround is to download R and RTools from their original CRAN distribution site and install the two software packages under C:\dev directory to be used with mottiprebas. RStudio is the GUI on top of R and not necessary to install Rprebasso in R.

Python virtual environment

Create Python virtual environment (e.g. with the name mottiprebas):

python -m venv mottiprebas 

Activate the virtual environment in Windows operating system

mottiprebas/Scripts/activate

Update pip (Python package installation tool):

python -m pip install --upgrade pip

Install Python package tools setuptools and wheel. Install numpy, pyarrow, pandas, openpyxl and rpy2 packages:

pip install setuptools wheel
pip install numpy pyarrow pandas openpyxl rpy2 

Important

Under Windows install numpy, pyarrow, pandas, openpyxl and rpy2 packages one by one, in the order of appearance. You will encounter errors if trying to install all of them at the same time.

Keep Rprebasso installation up to date. The project is regularly updated.

mottiprebas.py

First, find mottiprebas.py in forClimate and locate the four lines in the beginning of the file for RHOME (Windows), MOTTI_INST_PATH, MOTTIWB and DECIMALMARKER:

#R_HOME for R under Windows (comment out for Mac and Linux)
RHOME='/Program Files/R/R-4.3.3/'
os.environ['R_HOME'] = RHOME
# MottiWB RUNTIME LOCATION including all necessary shared libraries
# Change as needed using '/' for directory path also  under Windows
MOTTI_INST_PATH=pathlib.Path("/dev/MyPrograms/MottiWorkBench/Debug/")
#Motti workbench
MOTTIWB='mottiwb.exe'
#Decimal point used in mottiwb depends on locale. 
DECIMALMARKER='.'

Edit the path strings for RHOME and MOTTI_INST_PATH according to R and Motti workbench installation locations respectively. MOTTIWB is the name of the Motti workbench binary. The Motti workbench binary (default mottiwb.exe) uses decimal marker according to locale in use. Change the default decimal separator in DECIMALMARKER if needed.

To check mottiprebas.py and its runtime environment start the Python virtual environment, go to forClimate directory and type python mottiprebas.py -h for command line help:

python mottiprebas.py -h

usage: mottiprebas.py [-h] -y int [-i int] -m str -d str -s str -t str -c str -r {1,2,3,4,5,6,7} -w {1,2,3,4}
                      [-e int] [-f int]

Run Motti under climate change with Prebas

options:
  -h, --help            show this help message and exit
  -y int, --years int   Total simulation years (default: None)
  -i int, --interval int
                        Prebas simulation years / Motti time step (default: 5)
  -m str, --result_directory str
                        Simulation results main directory (default: None)
  -d str, --initdata str
                        Motti initial data file(s), regular expression (Motti input, full path) (default: None)
  -s str, --stand str   Motti stand file (Motti output, Prebas input, full path) (default: None)
  -t str, --model_trees str
                        Motti model tree file (Motti output, Prebas input, full path) (default: None)
  -c str, --coeff str   Prebas coefficients file (Prebas output, Motti input, full path) (default: None)
  -r {1,2,3,4,5,6,7}, --climate_region {1,2,3,4,5,6,7}
                        Climatic region in Finland (default: None)
  -w {1,2,3,4}, --climate_scenario {1,2,3,4}
                        Climate scenario (see climatedata.py for scenario names) (default: None)
  -e int, --climate_scenario_data_start int
                        Climate scenario data start year (default: 2025)
  -f int, --climate_scenario_start int
                        Climate scenario start year in simulations (default: 2025)

Available climate scenarios: 1: data/tranCanESM2.rcp45.rda 2: data/tranCanESM2.rcp85.rda
3: data/tranCNRM.rcp45.rda 4: data/tranCNRM.rcp85.rda

Simulations with mottiprebas.py

mottiprebas.py runs Motti workbench and PREABAS interchangeably and lets PREABAS to produce a set of coefficients for Motti to take the warming climate into account in simulations. PREBAS simulates forest stand growth with current climate and with a given climate scenario in short 5 year time intervals. The ratio or difference of the two runs gives coefficients that Motti will use to adjust the stand growth under climate change.

To run Motti-Prebas simulations type for example (or copy-paste from the code block icon):

	python mottiprebas.py -y 20 -i 5 -m MottiPrebasSimulations -d initmotti/prebasTest*.txt -s mottistand/Stand.txt -t mottimodeltree/ModelTrees.txt -c prebascoeff/PrebasCoefficient -r 2 -w 1 -e 2025 -f 2025

Scroll to the right to see the full command line.

Important

The mottiprebas.py script must be executed in the forClimate directory. It will use weather and climate scenario databases installed in forClimate project.

The command line option -y 20 gives the simulation time. The last growth step is from 15 to 20, i.e the growth step is 5 years (default value for the -i option). The main directory for results is given with -m MottiPrebasSimulations. Simulation results will appear in subdirectories, one for each Motti initialization file. Motti initialization files are provided with -d initmotti/prebasTest*.txt. Note the possibility to use regular expression to match multiple initialization files for a single simulation session.

Note

Currently each Motti initialization file can have one site only.

Simulation result files are based on user defined template file names (including directory paths) given for Motti stand data (the option -s), Motti model trees (the option -t) and PREBAS coefficients (the option -c). They will appear in their respective directories and named after simulation steps. For example prebascoeff/PrebasCoeff_5-10.txt contains coefficients for Motti for the simulation step 5 to 10. Directory hierarchy for the simulation results starting from the main directory will be created programatically.

The option -r 2 defines climatic region in Finland (7 in total) and the option -w 1 selects the climate scenario (4 in total). The -e 2025 option is the start year in the climate scenario data base and the -f 2025 option is the start year when climate scenario is used.

Current weather for each 5 year simulation period will be randomly selected for a simulation step out of 20 years available in the database for the current climate. Climate scenario is deterministic beginning from a given start year. There are 120 years of scenario data available in each 4 climate scenarios. In other words the current weather tries to model natural variability in the annual weather with randomness but the climate scenarios have calendar time.

Caution

It is up to the user to make sure not to override previous results by accident. No checks for existing files and directories are made.