inferred biomass biogeochemical model of Mystic Lake
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analysis
bin
calibration
interactive
sensitivity_analysis
.gitignore
README.md
lake.cfg
set_matlab_path.sh

README.md

Mystic

An inferred biomass biogeochemical model of Mystic Lake.

Dependencies

  • Matlab (developed with version 8)
  • Python (developed with version 2.7)

Installation

$ git clone http://github.com/swo/mystic.git

File structure

  • 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.

Usage

Interactive

To run the model interactively,

  • Update lake.cfg with the desired parameters.
  • Under interactive, use write_default_values_script.py to create run_interactive_defaults.m, which supplies the values in lake.cfg to interactive.m.
  • 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.py script to do this.
  • The output of the simulation is stored in concs_history and rates_history variables. You can write them to files using bin/write_data_to_files.m.

Analysis

To make a plot of the Jensen-Shannon divergences between the composition of rates at each depth, run the analysis/divergenes/pipeline.sh.

To compare the simulated Shannon diversity of composition of rates with some observed diversity of rates, run analysis/diversity/get_diversity_depth.m.

To make timecourses and end-time plots for all the rates and chemical concentrations, run analysis/profiles/pipeline.sh.