ss3sim (version 0.9.0)

bias_ss3: Perform a single bias adjustment run

Description

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

• usesr4ssfunctionSS_outputto read in the output from a single bias adjustment run
• usesr4ssfunctionSS_fitbiasrampto calculate the bias adjustment parameters for that run
• Writes the bias adjustment parameters to the fileAdjustBias.DATwithin thedirfolder, overwriting the file ifiter = 1(the first run) and appending the file otherwise

Usage

bias_ss3(iter, dir)

Arguments

iter

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

dir

Passes dir from the function run_bias_ss3 to bias_ss3. In run_bias_ss3 this is run within an

Value

• 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.

References

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