Usage
SSrunsims(sims = 1, newrun = TRUE, sim = FALSE, fit = FALSE, simfolder =
"sims", fitfolder = "fits", masterfolder = "fits", MLEdata = FALSE,
skipfiles = TRUE, simchoices = 1, fitchoices = 1, samedatafile = FALSE,
homepath = "c:/myfiles/", recdevmatrix = NULL, rescale = TRUE,
fitbiasramp = FALSE, exe = "ss3_opt", simextras = "-nox -nohess",
fitextras = "-nox -gbs 1000000000 -cbs 1000000000",
fyr = NULL, lyr = NULL, printfile=TRUE, intern = FALSE, verbose = TRUE)
Arguments
sims
Vector of simulations to run for each case.
newrun
Define some settings? Pretty much always required. Default=TRUE.
sim
Do simulations? Default = FALSE.
fit
Do estimations? Default = FALSE.
simfolder
Name of folder where simulations are run. Default = "sims".
fitfolder
Name of folder where estimations are run. Default = "fits".
masterfolder
Name of folder to collect estimation results (if run in parallel). Default = "fits".
MLEdata
Use MLE values in estimation rather than bootstrap values. For model
testing. Default = FALSE.
skipfiles
Skip any simulations that have already been run? Default = TRUE.
simchoices
Vector of indices of scenarios (combination of control and/or data file) to be
simulated. Values are numeric, but correspond to letters in file
names (1=ctl_simA.ss, 2=ctl_simB.ss). Default=1.
fitchoices
Vector of indices of scenarios (combination of control and/or data file) to be
estimated. Values are numeric, but correspond to letters in file
names (1=ctl_fitA.ss, 2=ctl_fitB.ss). Default=1.
samedatafile
Use the same data file for all simulations? (Alternative is one data
file for each control file). Default=FALSE.
homepath
Location where the input files are located, and in which the above
inputs for simfolder and fitfolder are located.
recdevmatrix
Matrix of recruit deviations. NULL = read from file or create new file if
one doesn't exists. Default=NULL.
rescale
Argument passed to SS_recdevs: should the recdevs be
rescaled to have mean = 0 and std. deviation = sigmaR? Default=TRUE. fitbiasramp
Use the function SS_fitbiasramp to estimate bias
adjustment inputs in control file during estimation mode? This
requires running each model twice: once with no change to control
file, exe
Command to run executable. Default="ss3_opt".
simextras
Additional inputs to run model when in simulation mode. Default="-nox -nohess".
fitextras
Additional inputs to run model when in estimation mode. Default="-nox -gbs 1000000000 -cbs 1000000000".
fyr
First year of stochastic recruitment deviations to include in
simulation models. NULL will run SS_readctl to get
setting from control file. Default=NULL.
lyr
Last year of stochastic recruitment deviations to include in
simulation models. NULL will run SS_readctl to get
setting from control file. Default=NULL.
printfile
Switch to determine whether description of completed runs is printed
to a file or not. Default=TRUE.
intern
Input passed to system command. If FALSE then output from ADMB is
printed to screen during model run otherwise it is written to a file.
verbose
Print various messages to the command line as the function runs? Default=TRUE.