Bias adjustment is performed to ensure that the only the most informative
data available are used when estimating recruitment deviations.
This process involves running the estimation method with the hessian
both before this function and then running the estimation method again with
the new values. Estimation files in the original folder will be deleted to
ensure that convergence afterwards is not based on the input run.
These files are permanently archived in the bias_[0-9]{2} folder
within the directory. Only the three middle steps listed below are performed
using calculate_bias, and the rest of the steps must be performed
externally.
calculate_bias(dir, ctl_file_in)A character string specifying the path to the folder with the results from a stock assessment model run. Paths are passed without a terminal slash.
A string providing the path to the input Stock Synthesis .ctl file.
A list of bias adjustment parameters.
Estimate recruitment and the standard error about those estimates.
Correct the estimates given their estimated uncertainty using a ramp.
Save a new control file.
Move original estimation files.
Estimate model parameters.