run_retro: Simulate bam models for running retrospective analysis

In nikolaifish/bamExtras: Functions and Data in Support of Stock Assessments with the Beaufort Assessment Model (BAM)

Simulate bam models for running retrospective analysis

Description

Simulate bam models for running retrospective analysis

Usage

run_retro(
  CommonName = NULL,
  fileName = "bam",
  dir_bam_sim = "sim",
  dir_bam_base = "base",
  bam = NULL,
  dat_file = NULL,
  tpl_file = NULL,
  cxx_file = NULL,
  dat_obj = NULL,
  tpl_obj = NULL,
  cxx_obj = NULL,
  standardize = FALSE,
  nyr_remove = 1:5,
  endyr_reduce_always = c("endyr", "endyr_dev_rec", "endyr_rec_dev", "endyr_rec_phase2",
    "endyr_rec_spr"),
  ncores = NULL,
  ndigits = 4,
  unlink_dir_bam_base = FALSE,
  run_bam_base = TRUE,
  overwrite_bam_base = TRUE,
  admb_options_base = "-nox",
  run_sim = TRUE,
  admb_options_sim = "-est -nox",
  prompt_me = FALSE,
  subset_rdat = list(eq.series = 101, pr.series = 101, t.series = styr:endyr),
  random_seed = 12345,
  admb2r_obj = admb2r.cpp,
  cleanup = list(del = c("*.r0*", "*.p0*", "*.b0*", "*.log", "*.rpt", "*.obj", "*.htp",
    "*.eva", "*.bar", "*.tds", "*.o", "tmp_admb", "variance", "*.dep", "*.hes", "*.tmp"))
)

Arguments

CommonName	Common name of species associated with dat, tpl, and cxx files
fileName	Name given to BAM files, not including file extensions.
dir_bam_sim	Name of directory to write retrospective analysis files to, relative to the working directory.
dir_bam_base	Name of directory to write bam base model files to, relative to the working directory.
bam	Output of bam2r.
dat_file	dat file path
tpl_file	tpl file path
cxx_file	cxx file path
dat_obj	dat file read in as a character vector with readLines(con=dat_file)
tpl_obj	tpl file read in as a character vector with readLines(con=tpl_file)
cxx_obj	cxx file read in as a character vector with readLines(con=cxx_file)
standardize	Should standardize_bam be run by the function before running the BAM
nyr_remove	number of years to remove in the retrospective analysis
endyr_reduce_always	Names of endyr variables that should always be reduced as years are removed from each retrospective run. These names will be searched in among all init variable names starting with endyr and must match exactly. Other endyr variables will only be reduced if they are greater than the terminal year of a particular retrospective run.
ncores	number of cores to use for parallel processing
ndigits	number of digits to round simulated values to
unlink_dir_bam_base	Should dir_bam_base be deleted after this function is run?
run_bam_base	If FALSE, the function will look for an executable named fileName.exe in dir_bam_base and use it as the base model.
overwrite_bam_base	If FALSE, the files in dir_bam_base will not be overwritten if run_bam_base=TRUE
admb_options_base	Character string pasted to fileName to build run_command for the base model when running BAM with shell(run_command) (i.e. run_command <- paste(fileName, admb_options))
run_sim	If FALSE, the simulated data will be generated but won't be used in new BAM runs
admb_options_sim	ADMB code snippet used in shell script when running bam
prompt_me	Turn on/off prompts that ask for user input before deleting files.
subset_rdat	list of rdat objects to subset in different ways. For eq.series and pr.series specify number of evenly spaced values to retain. For t.series specify a series of years to retain. When subsetting eq.series or pr.series, this option can substantially decrease rdat file size, without affecting precision of reference point calculations.
random_seed	random seed value. If NULL, random seed is not set within the function.
admb2r_obj	Character string containing admb2r C++ code, which is written with base::writeLines to dir_bam
cleanup	List object written to cleanup.bat file in dir_bam.

Value

Invisibly returns a data frame, sim_out, containing basic results of sim runs, including total likelihood and maximum gradient values. This data frame is also written to a csv file in dir_bam_sim.

Examples

## Not run: 
Run retrospective analysis, writing files to dir_bam_sim
run_retro("AtlanticMenhaden", dir_bam_base="AtMe_base", dir_bam_sim="AtMe_sim")
run_retro("BlackSeaBass", dir_bam_base="BlSB_base", dir_bam_sim="BlSB_sim",nyr_remove=1:4) # removing 5 years results in an error likely due to closed season commercial pot discards running out of data
run_retro("BluelineTilefish", dir_bam_base="BlTi_base", dir_bam_sim="BlTi_sim")
run_retro("Cobia", dir_bam_base="Cobi_base", dir_bam_sim="Cobi_sim")
run_retro("GagGrouper", dir_bam_base="GaGr_base", dir_bam_sim="GaGr_sim")
run_retro("GrayTriggerfish", dir_bam_base="GrTr_base", dir_bam_sim="GrTr_sim")
run_retro("GreaterAmberjack", dir_bam_base="GrAm_base", dir_bam_sim="GrAm_sim",nyr_remove=1:4) # removing 5 years results in an error because you run out of rGN discard length comps which start in 2013
run_retro("RedGrouper", dir_bam_base="ReGr_base", dir_bam_sim="ReGr_sim")
run_retro("RedPorgy", dir_bam_base="RePo_base", dir_bam_sim="RePo_sim")
run_retro("RedSnapper", dir_bam_base="ReSn_base", dir_bam_sim="ReSn_sim")
run_retro("ScampGrouper", dir_bam_base="ScGr_base", dir_bam_sim="ScGr_sim")
run_retro("SnowyGrouper", dir_bam_base="SnGr_base", dir_bam_sim="SnGr_sim")
run_retro("Tilefish", dir_bam_base="Tile_base", dir_bam_sim="Tile_sim")
run_retro("VermilionSnapper", dir_bam_base="VeSn_base", dir_bam_sim="VeSn_sim")


## End(Not run)

nikolaifish/bamExtras documentation built on April 17, 2025, 9:44 p.m.