Description Usage Arguments Author(s) References See Also Examples
compile and run NOAA-IRATE models from within R
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setup.file |
Character string defining IRATE setup to be run. Check IRATE.examples for preinstalled IRATE setup examples and make.dat to create new or remake.dat to alter existing setup files. |
safe |
(logical) Compile in safe mode? (default = FALSE) |
re |
(logical) Compile in random effects (ADMB-RE) mode? (default = FALSE) |
verbose |
(logical) Verbose output? (default = TRUE) |
admb_errors |
(character) how to handle compilation/linking errors? |
mcmc |
(logical) run post-hoc MCMC? (default = FALSE) |
mcmc.opts |
options for MCMC run (see mcmc.control) |
profile |
(logical) Run likelihood profiles? (default = FALSE) |
extra.args |
(character) extra (ADMB-) arguments for IRATE run |
Robert K. Bauer
http://nft.nefsc.noaa.gov/IRATE.html
To check model setup files see: read.dat and make.dat.
To read run results see: read.rep and read.par.
For preinstalled example runs see: run.IRATE.example.
To delete run files see: clean.IRATE.
For more information on admb model compiliation and run prodcudres see: compile_admb and run_admb from the R2admb-package
1 2 3 4 5 6 7 8 9 10 | example.setup <- IRATE.examples()
new.setup <- new.setup.path <- example.setup[1] # select old IRATE setup to reparameterize
print(new.setup) # print setup name to be run
old.setup.path <- system.file(paste0("IRATE.examples/",new.setup,".dat"), package = "IRATER")
system(paste("mkdir -p ",new.setup.path)) # create run folder for new setup
system(paste("cp",old.setup.path, new.setup.path)) # copy old setup in new run folder
setwd(new.setup.path)
run.IRATE(new.setup) # compile and run setup
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