SS_recdevs: Insert a vector of recruitment deviations into the control...

In r4ss: R code for Stock Synthesis

Description

A function to insert a vector of recruitment deviations into the control file for simulation studies. This can also be achieved by using the .par file, but Ian Taylor prefers this approach for no good reason.

Usage

SS_recdevs(fyr, lyr, ctl = NULL, recdevs = NULL,
rescale = TRUE, scaleyrs = NULL, dir = "working_directory",
ctlfile = "control.ss_new", newctlfile = "control_modified.ss",
verbose = TRUE, writectl = TRUE, returnctl = FALSE, newmaxbias = NULL)

Arguments

fyr	First year of the recdev vector.
lyr	Last year of the recdev vector.
ctl	Either NULL to read anew or an already read control file. Default=NULL.
recdevs	Either NULL to generate anew or an already generated vector of recdevs. Default=NULL.
rescale	Should the recdevs be rescaled to have mean = 0 and std. deviation = sigmaR? Default=TRUE.
scaleyrs	Vector of years over which rescaling (if chosen) should occur.
dir	Directory where files are located. Default is to use the working directory in use by R. Default="working_directory".
ctlfile	Name of control file to modify. Default="control.ss_new".
newctlfile	Name of new file to output modified control file. Default="control_modified.ss".
verbose	Verbose output to R command line? Default=TRUE.
writectl	Write new file? Default=TRUE.
returnctl	Return contents ctl file as an object in the R workspace. Default=FALSE.
newmaxbias	Replace the maximum bias adjustment fraction with any non-NULL value. Default=NULL.

Author(s)

Ian Taylor

r4ss documentation built on May 2, 2019, 4:56 p.m.