standardize_bam: Standardize object names in bam files (dat, tpl, and cxx)

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

Standardize object names in bam files (dat, tpl, and cxx)

Description

This script reads in BAM dat, tpl, and cxx files, and converts them to R objects (character vectors of each line of the code). It then runs a set of gsub() functions to replace object names with preferred naming conventions and returns dat, tpl, and cxx character vectors to use to rewrite the corresponding files with writeLines)

Usage

standardize_bam(
  CommonName = NULL,
  bam = NULL,
  dat_file = NULL,
  tpl_file = NULL,
  cxx_file = NULL,
  dat_obj = NULL,
  tpl_obj = NULL,
  cxx_obj = NULL,
  nm_pattern = NULL,
  nm_replace = NULL,
  match_whole_words = TRUE,
  fleet_key = list(sCT = c("CVT"), sTV = c("CVID", "Mcvt", "mcvt"), sVD = c("VID"), sBT =
    c("Mbft"), sBL = c("sM"), sVL = c("vll"), sFT = c("FST"), sAN = c("nad"), sAM =
    c("mad"), sAS = c("sad"), sJA = c("jai"), sME = c("mareco"), cDV = c("cD"), cHL =
    c("cH", "cHl"), cLL = c("cL"), cOT = c("cO"), cPT = c("cp", "cP"), cTW = c("cT",
    "cTw", "cHTR"), cGN = c("comm"), cRN = c("cRn"), cRS = c("cRs"), cBN = c("cBn"), cBS
    = c("cBs"), rHB = c("HB", "hb", "rHb"), rHD = c("hbd", "HBD"), rGN = c("GR", "mrip",
    "rGe", "rA")),
  fleet_replace = TRUE
)

Arguments

CommonName	Common name of species modeled in BAM files. Only used when accessing dat, tpl, and cxx character vectors named as e.g. dat_CommonName
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)
nm_pattern	Character vector of additional object names (i.e. patterns) to be replaced
nm_replace	Character vector of of replacements for nm1
match_whole_words	Should patterns replace whole words only (pattern is regex enclosed by \b)
fleet_key	key to fleet names as a names list of character vectors. names of list items are the replacements while the character vectors are sets of old fleet names to replace

Examples

## Not run: 
# Read in and standardize of the current BAM models
bam_AtMe <- standardize_bam("AtlanticMenhaden")
bam_BlSB <- standardize_bam("BlackSeaBass")
bam_BlTi <- standardize_bam("BluelineTilefish")
bam_Cobi <- standardize_bam("Cobia")
bam_GagG <- standardize_bam("GagGrouper")
bam_GrTr <- standardize_bam("GrayTriggerfish")
bam_GrAm <- standardize_bam("GreaterAmberjack")
bam_ReGr <- standardize_bam("RedGrouper")
bam_RePo <- standardize_bam("RedPorgy")
bam_ReSn <- standardize_bam("RedSnapper")
bam_ScGr <- standardize_bam("ScampGrouper")
bam_SnGr <- standardize_bam("SnowyGrouper")
bam_Tile <- standardize_bam("Tilefish")
bam_VeSn <- standardize_bam("VermilionSnapper")

# Run a bam model and assign rdat output to object
rdat_RePo <- run_bam(bam=bam_RePo,fileName="RePo")

## End(Not run)

nikolaifish/bamExtras documentation built on July 21, 2023, 8:26 a.m.