bias_ss3: Perform a single bias adjustment run

Description Usage Arguments Value Author(s) References See Also


This function is run within run_bias_ss3 and for a single run it:

  • uses r4ss function SS_output to read in the output from a single bias adjustment run

  • uses r4ss function SS_fitbiasramp to calculate the bias adjustment parameters for that run

  • Writes the bias adjustment parameters to the file AdjustBias.DAT within the dir folder, overwriting the file if iter = 1 (the first run) and appending the file otherwise


bias_ss3(iter, dir)



Replicate number. Used to identify this iteration if there are multiple adjustment runs.


Passes dir from the function run_bias_ss3 to bias_ss3. In run_bias_ss3 this is run within an sapply function for each of the bias adjustment runs.


A plain text file containing the bias adjustment variables is created at dir/AdjustBias.DAT. A PDF figure is created in dir/biasramp-N.pdf, where N represents the iteration number.


Carey McGilliard


Methot, R. D. and Taylor, I. G. (2011). Adjusting for bias due to variability of estimated recruitments in fishery assessment models. Can. J. Fish. Aquat. Sci., 68(10):1744-1760.

See Also

run_bias_ss3, run_ss3sim, ss3sim_base

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