This folder contains backward tracking individal-based runs for Wilkinson Basin (WB) copepod Calanus finmarchicus populations in the Gulf of Maine.
Copepod life history development is modeled based on temperature- and food-dependency
Temperature and flow field are interpolated from FVCOM-GOM3 model forcing.
Food is estimated from MODIS satellite chlorophyll product.
Two tracking schemes are used: depth-keeping and DVM.

The detailed description of modeling concepts, equations and interpretation can be found at:

Ji, R., Z. Feng, B. T. Jones, C. Thompson, C. Chen, N. R. Record, and J. A. Runge. 2017. Coastal amplification of supply and transport (CAST): a new hypothesis about the persistence of Calanus finmarchicus in the Gulf of Maine. ICES Journal of Marine Science, https://doi.org/10.1093/icesjms/fsw253.


There are 6 subfolders:

fiscm: Individual-based model source code (in Fortran 95)
gom_hourly:  Hourly FVCOM model output as forcing data for the individual-based model runs
data_files:  Auxiliary data for model runs, including grid information, coastal and bathymetry, and WB polygon location. 
depth_keeping: Depth-keeping model runs, including model setup and output (fiscm_group_001.nc) in netcdf format
Matlab_data: Model data generated after processing the raw model output netcdf file from depth_keeping folder. 
Matlab_scripts: Matlab codes for preparing model run files and postprocessing modeloutput