An inferred biomass biogeochemical model of Mystic Lake.
- by: Scott W Olesen (firstname.lastname@example.org)
- development page: http://github.com/swo/mystic
- main page: http://almlab.mit.edu/mystic.html
- Matlab (developed with version 8)
- Python (developed with version 2.7)
$ git clone http://github.com/swo/mystic.git
- analysis: Tools for analyzing divergences between rates at each depth, diversity of rates, and the profiles for rates and concs.
- bin: Main matlab scripts
- calibration: Tools for calibrating the model parameters using the measured rates and/or OTU data.
- interactive: A script for running the model with easily-adjustable parameters and displaying the output.
- sensitivity_analysis: Tools for analyzing the sensitivity of the rate profiles to the values for each of the input parameters.
- lake.cfg: Configuration for different tools, with lists of the names for processes and some default values from which to generate scripts for the various tools.
- set_matlab_path.sh: Convenience tool for setting the matlab path when running scripts from the terminal.
To run the model interactively,
lake.cfgwith the desired parameters.
- Under interactive, use
run_interactive_defaults.m, which supplies the values in
- In Matlab, run
run_interactive.m. This requires the
bin/folder to be on Matlab's path. If running in the terminal, you can use the
set_matlab_path.pyscript to do this.
- The output of the simulation is stored in
rates_historyvariables. You can write them to files using
To make a plot of the Jensen-Shannon divergences between the composition of rates at each depth, run the
To compare the simulated Shannon diversity of composition of rates with some observed diversity of rates, run
To make timecourses and end-time plots for all the rates and chemical concentrations, run