SS_RunJitter: Iteratively apply the jitter option in SS

Description Usage Arguments Value Author(s)

View source: R/SS_RunJitter.R

Description

Iteratively runs SS model with different jittered starting parameter values (jitter value must be mannually set in starter.ss). Output files are renamed in the format Report1.sso, Report2.sso, etc.

Usage

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SS_RunJitter(mydir, model = "ss3",
  extras = "-nohess -cbs 500000000 -gbs 500000000", Njitter, Intern = TRUE,
  systemcmd = FALSE, printlikes = TRUE)

Arguments

mydir

Directory where model files are located

model

Executable name

extras

Additional command line arguments passed to executable

Njitter

Number of jitters, or a vector of jitter iterations. If length(Njitter) > 1 only the iterations specified will be ran, else 1:Njitter will be executed.

Intern

Show command line info in R console or keep hidden (Internal=TRUE)

systemcmd

Option to switch between 'shell' and 'system'

printlikes

Print likelihood values to console

Value

A vector of likelihoods for each jitter iteration.

Author(s)

James T. Thorson, Kelli F. Johnson


r4ss documentation built on May 29, 2017, 2:24 p.m.