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: $0.10^{\circ}$).
01_getinputs_ISIMIP3a.R
gets environmental and fishing data for the region of interest 02_runLMEcalibration.R
estimates fishing mortality parameters (catchability and selectivities for each functional group) 03_rungridbyLME.R
takes parameters estimated in step 2 to create initial values by re-running the LME scale inputs gridded_sizemodel()
and runs for LME 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:
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.