Assessment for BSAI flatfish (mainly yellowfin sole and N rock sole).

Maintained by Jim Ianelli and Carey McGilliard

This repo was formerly called “flatfish” and was owned by Jim Ianelli with Carey McGilliard, Ingrid Spies, and Meaghan Bryan as collaborators. The code is used for the BSAI northern rock sole assessment. Input files for accepted operational model runs for BSAI northern rock sole, as well as up-to-date R plotting code for model output is located here: https://github.com/noaa-afsc/BSAI_NRS. The BSAI yellowfin sole assessment code came from this repo and has been modified separately over the last few years.

Source code

The source main source code is called fm.tpl: https://github.com/noaa-afsc/flatfish_assessment_code/blob/main/src/fm.tpl. The code is written in ADMB: https://github.com/admb-project. Many old examples using the code can be found in the examples folder.

Instructions for compiling the fm.tpl code

Option 1: Simple

1. Install admb: https://github.com/admb-project (ADMB 13.0 recommended)
2. From the ADMB command line:
   cd flatfish_assessment_code  admb fm.tpl

Option 2: uses make.bat file to create debug and release options

If admb needs compiling (first time always does) go to “src” directory and type “make” e.g.,: 1. Install admb: https://github.com/admb-project (ADMB 13.0 recommended)
2. From the ADMB command line:
cd flatfish_assessment_code make

Instructions for running fm.exe once compiled

Estimation model runs

The code can be run as an estimation model, and includes a projection component, consistent with Tier 1 fisheries management for the NPFMC. To use the code for an estimation model, from the command line:

cd estimation_run_directory
fm

To run projections only

Projections only runs are conducted without estimation using an existing run (necessary for Harvest Projection SAFE documents where an accepted operational model from a previous year is being used as the basis for projections)

• set phase_proj in mod.ctl equal to 1 (typically 7 is used to specify doing projections in phase 7 of estimation)
• copy the fm.par file from the desired estimation run folder to the projections-only run folder and rename it to fm.pin
• update the last partial year of catches in the .dat input file to include the full year’s realized catches
• run from the command line:
  cd projection_only_folder
  fm -phase 0

Inputs

The input files necessary for running the code are called:

mod.ctl: (select model configuration options)
fm.dat (which can point to other .dat files such as c1.dat from the nrs example c1mod4): input data which includes

• catches
• empirical weight-at-age by year and sex
• survey biomass index and standard deviation
• survey age composition data by year and sex
• fishery age composition data by year and sex

future_catch.dat: estimated future catches for use in the projection model
future_temp.dat (not used but still required)

Outputs

The main model output files are
fm.rep
ABC_OFL.rep
future_ABC.rep

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