r4ss (version 1.36.1)

SS_RunJitter: Iteratively apply the jitter option in SS

Description

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

Usage

SS_RunJitter(mydir, model = "ss", extras = "-nohess", 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.

Examples

# NOT RUN {
  
# }
# NOT RUN {
    #### Change starter file appropriately (can also edit file directly)
    starter <- SS_readstarter(file.path(mydir, 'starter.ss'))
    # Change to use .par file
    starter$init_values_src = 1
    # Change jitter (0.1 is an arbitrary, but common choice for jitter amount)
    starter$jitter_fraction = 0.1
    # write modified starter file
    SS_writestarter(starter, dir=mydir, overwrite=TRUE)

    #### Run jitter using this function
    jit.likes <- SS_RunJitter(mydir=mydir, Njitter=25)

    #### Read in results using other r4ss functions
    # (note that un-jittered model can be read using keyvec=0:Njitter)
    profilemodels <- SSgetoutput(dirvec=mydir, keyvec=1:Njitter, getcovar=FALSE)
    # summarize output
    profilesummary <- SSsummarize(profilemodels)
    # Likelihoods
    profilesummary$likelihoods[1,]
    # Parameters
    profilesummary$pars
  
# }