Estimate bias adjustment for recruitment deviates

Description

Uses standard error of estimated recruitment deviates to estimate the 5 controls for the bias adjustment in Stock Synthesis

Usage

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SS_fitbiasramp(replist, verbose=FALSE, startvalues=NULL, method="BFGS",
  twoplots=TRUE, transform=FALSE, plot=TRUE, print=FALSE,
  plotdir="default", oldctl=NULL,
  newctl=NULL, nlminb=TRUE, pwidth=7, pheight=7, punits="in",
  ptsize=12, res=300, cex.main=1)

Arguments

replist

Object created using SS_output

verbose

Controls the amount of output to the screen. Default=FALSE.

startvalues

A vector of 5 values for the starting points in the minimization. Default=NULL.

method

A method to apply to the 'optim' function. See ?optim for options. Default="BFGS".

twoplots

Make a two-panel plot showing devs as well as transformed uncertainty, or just the second panel in the set? Default=TRUE.

transform

An experimental option to treat the transform the 5 quantities to improve minimization. Doesn't work well. Default=FALSE.

plot

Plot to active plot device?

print

Print to PNG files?

plotdir

Directory where PNG files will be written. By default it will be the directory where the model was run.

oldctl

Optional name of existing control file to modify. Default=NULL.

newctl

Optional name of new control file to create from old file with estimated bias adjustment values. Default=NULL.

nlminb

Use the 'nlminb' function instead of 'optim'? Default=TRUE

pwidth

Default width of plots printed to files in units of punits. Default=7.

pheight

Default height width of plots printed to files in units of punits. Default=7.

punits

Units for pwidth and pheight. Can be "px" (pixels), "in" (inches), "cm" or "mm". Default="in".

ptsize

Point size for plotted text in plots printed to files (see help("png") in R for details). Default=12.

res

Resolution of plots printed to files. Default=300.

cex.main

Character expansion for plot titles.

Author(s)

Ian Taylor

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., 68:1744-1760.

See Also

SS_output

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