Description Usage Arguments Author(s) References See Also
View source: R/SS_fitbiasramp.R
Uses standard error of estimated recruitment deviates to estimate the 5 controls for the bias adjustment in Stock Synthesis
1 2 3 4 5 6 | 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 |
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 |
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
|
pheight |
Default height width of plots printed to files in units of
|
punits |
Units for |
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.
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