SS_fitbiasramp: Estimate bias adjustment for recruitment deviates
In r4ss: R Code for Stock Synthesis

Description Usage Arguments Author(s) References See Also

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

SS_fitbiasramp(replist, verbose = FALSE, startvalues = NULL,
  method = "BFGS", twoplots = TRUE, transform = FALSE, plot = TRUE,
  print = FALSE, plotdir = "default", shownew = TRUE,
  oldctl = NULL, newctl = NULL, altmethod = "nlminb",
  exclude_forecast = FALSE, pwidth = 6.5, pheight = 5,
  punits = "in", ptsize = 10, res = 300, cex.main = 1)

`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". By default, optim is not used, and the optimization is based on the input `altmethod`.
`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.
`shownew`	Include new estimated bias adjustment values on top of values used in the model? (TRUE/FALSE)
`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.
`altmethod`	Optimization tool to use in place of optim, either "nlminb" or "psoptim". If not equal to either of these, then optim is used.
`exclude_forecast`	Exclude forecast values in the estimation of alternative bias adjustment inputs?
`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.

Ian Taylor

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.

SS_output

r4ss documentation built on Oct. 30, 2019, 11:25 a.m.