Dynamic Benthic Pelagic Model (DBPM) calibration - ISIMIP3A protocol

This repository contains all code necessary to process inputs used by DBPM. Following protocol ISIMIP3A, this simulation uses inputs from GFDL-MOM6-COBALT2 (horizontal resolution: $0.25^{\circ}$).

Two additional DBPM experiments forced by ACCESS-OM2-025 (horizontal resolution: $0.25^{\circ}$) and ACCESS-OM2-01 (horizontal resolution: $0.10^{\circ}$).

Step 1. Get input (environmental and fishing) data

• Script 01_getinputs_ISIMIP3a.R gets environmental and fishing data for the region of interest
• You can choose any FAO Major Fishing Areas or Large Marine Ecosystems (LMEs)
• Input data will be formatted ready to be used with modelling functions

Step 2. LME-scale calibration

• Script 02_runLMEcalibration.R estimates fishing mortality parameters (catchability and selectivities for each functional group)
• Checks and adjusts search volume parameter
• Creates and saves calibration plots as in PDF format
• Plots can be used to visually inspect fit of predicted catch to observed catch data

Step 3. Running DBPM model (with and without fishing)

• Script 03_rungridbyLME.R takes parameters estimated in step 2 to create initial values by re-running the LME scale inputs
• Gets inputs for gridded_sizemodel() and runs for LME
• Produces diagnostic plots for each LME

Running this repository

Although you could run all scripts included here in your local machine, you will need access to the environmental data to run them. The environmental data comes from three sources:

1. GFDL-MOM6-COBALT2 (horizontal resolution: $0.25^{\circ}$)
2. ACCESS-OM2-025 (horizontal resolution: $0.25^{\circ}$)
3. ACCESS-OM2-01 (horizontal resolution: $0.1^{\circ}$)

Outputs from GFDL-MOM6-COBALT2 are originally available at the Inter-Sectoral Impact Model Intercomparison Project (ISIMIP) as netCDF files. We extracted data for each LME and transformed files to csv format, which are available at the National Computational Infrastructure (NCI). Outputs from both resolutions of the ACCESS-OM2 model are available at NCI.

The scripts in this repository were developed in NCI's Gadi, so the easiest way to run these script is to clone this repository to Gadi. However, to do this you will need an NCI account, which are only available for researchers with an email address from an Australian institution. You can still run these scripts locally, but you will need to download the environmental data from the ISIMIP Data Portal and the NCI Data Catalogue.

In the next section, we include information about how to create an NCI account if you do not have one already. Remember, you must have an email address for an Australian institution to create an NCI account.

Getting an NCI account

1. Create an NCI user account
   • You should use your Australian institution’s email account when signing up
   • When it asks for a project to join:
   • If possible, contact the NCI scheme manager at your institution to find out what NCI project you should use to sign up for your NCI account. This account will provide you with computing power.
2. Join relevant NCI projects
   • Request to join the following NCI projects:
   • vf71 - for access to the environmental data used in this repository
   • hh5 – for the Python conda environment
   • cj50 – ACCESS-OM2 (the Australian ocean model) output
   • ik11 – ACCESS-OM2 (the Australian ocean model) output
   • ol01 – ACCESS-OM2 (the Australian ocean model) output
   • xp65 - for access to the ACCESS-NRI Intake catalog
   • Note that it can take one business day or longer to get approved for projects
3. Verify that you can log into NCI’s Gadi
   • Note that it usually takes more than 30 minutes for your account to be created
   • You are also welcome to follow along with the instructions to set up ssh keys, but this is optional.