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.
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.