csiem-marvl : plotting and visualisation tools for CSIEM

Overview

csiem-marvl refers to the Cockburn Sound Integrated Ecosystem Model - Model Assessment, Reporting and Visualisation Library, which is a collection of scripts and tools for assisting users visualise model outputs and observational datasets, and for evaluating the model's performance. csiem-marvl uses the more generic aed-marvl package for core functions for plotting and evaluating model output, in addition to a suite of custom scripts developed for specific applications.

Repository Organisation

• aed-marvl: core plotting and model performance evaluation scripts for AED simulations;
• configs: pre-saved configuration setups for csiem plotting tasks;
• custom_m: a library of matlab scripts associated with custom model assessment and reporting;
• custom_py: a library of pyhton scripts associated with custom model assessment and reporting;
• data: place-holder for storing observed/modelled datasets (users will add data into here);
• gis: shape files for defining polygons, transect, and sites for plotting;
• outputs: place-holder folder users must create where locally generated outputs can reside;

Getting started

To access the repository, use a client like GitHub Desktop, or download from the command line via:

git clone [email protected]:SEAF-CS/csiem-marvl

or if you want the embedded sub-module(s):

git clone --recurse-submodules [email protected]:SEAF-CS/csiem-marvl

Once you have the main repository, create an output directory to store items that are created.

Running aed-marvl for polygon time-series plots

• For the main aed-marvl polygon-timeseries plotting, open Matlab (version 2020 or later), go to the local csiem-marvl folder and add the paths to tools/libraries by entering:

addpath(genpath('./'))

• Go to config folder, edit the MARVL.m to configure the plots (use the 'MARVL.m' under example folder as templates);
• Under the config path, start the plotting by entering

 run_AEDmarvl('./MARVL.m','matlab')

or if you wish to use YAML style configuration

  run_AEDmarvl('./MARVL.m','yaml')

• For these scripts to work effectively, the data products from the csiem-data repository must be sourced and added to the data folder. For more information on the observed data available for these scripts, please visit the csiem-data wiki
• A range of other marvl plots are configurable and can be applied to the Cockburn Sound model - see the wiki here specific to the aed-marvl repo for further examples.

Running custom matlab scripts

• For the custom matlab scripts (organised in custom_m), you can run locally or in a virtual machine.

Running custom python scripts

• For the custom python scripts (organised in custom_py), you can run locally or they have also been design to run in the cloud-based Databricks environment.

Further Information

For the key features and modules of aed-marvl the readers are refered to https://github.com/AquaticEcoDynamics/aed-marvl. MARVL user documentation is available the repository (under docs/MARVL user instruction), and refer to the example templates for configuration.

For an overaching summary of the data ecosystem, please see the The Cockburn Sound Integrated Ecosystem Model Manual

Contributing

The csiem-marvl team welcomes collaborators, and encourages pull-requests for improvements and additions to the scripts.