readGMACSpar

Read the gmacs.par file. This is an output of GMACS that contains estimates of all parameters

readGMACSpar(
  Dir = NULL,
  FileName = "gmacs.par",
  verbose = NULL,
  DatFile = NULL,
  CtlFile = NULL,
  GMACSdat = NULL
)

Arguments

Dir

(character string)- path to the folder where the parameter file is stored.

FileName

(character string)- name of the parameter file - By default, "gmacs.par"

verbose

(logical)- flag to print processing information

DatFile

(list)- Object containing the .dat file - This is the output of the readGMACSdat() function.

CtlFile

(list)- Object containing the .ctl file - This is the output of the readGMACSctl() function.

GMACSdat

(list)- Object containing the gmacs.dat file - This is the output of the readGMACS.dat() function.

Value

the gmacs.par file as a named list. Where data frame are used, the columns are parameter_ID/value.

• Nparams - The number of parameters.

• ObjFvalue - The objective function value.

• MaxGradComp - The maximum gradient component.

• theta - The key parameter controls (core parameters - theta parameters).

• Grwth - The growth parameters.

• Vul - The vulnerability (selectivity and retention) parameters.

• Envpar_Slx

• Slx_Devs - The selectivity deviations.

• Fbar - The mean fishing mortality parameters.

• Fdev - The fishing fleet-specific weights for male.

• Foff - The female fishing mortality offset to male F.

• Fdov - The fishing fleet-specific weights for female.

• rec_ini - The initial recruitment by size-class.

• rec_dev_est - The year-specific recruitment deviations.

• logit_rec_prop_est - The year-specific sex-ratio recruitment.

• Mdev - The natural mortality deviation.

• M_mat - The sex-specific natural mortality multiplier for each maturity state.

• EffSamp_size - The effective sample size.

• survey_Q - The survey-specific catchability.

• add_cv - The survey-specific additional CV.

See also

readGMACS.dat,readGMACSdat,readGMACSctl, readGMACSprj.

Examples

if (FALSE) {
# Stock ----
stock <- "SNOW_crab"
# GMACS input files ----
datfileName <- "snow_21_M09.dat"
ctlfileName <- "snow_21_M09.ctl"
# read gmacs.dat ----
fileName <- "gmacs.dat"
fileName <- file.path(dir_Base, stock, fileName, fsep = fsep)
GMACSdat <- readGMACS.dat(path = fileName, verbose = TRUE)
# Read the data file ----
datFile <- file.path(dir_Base, stock, datfileName, fsep = fsep)
datFile <- readGMACSdat(FileName = datFile, verbose = T)
# Read the control file ----
ctlFile <- file.path(dir_Base, stock, ctlfileName, fsep = fsep)
ctlFile <- readGMACSctl(
  FileName = ctlFile,
  verbose = T,
  DatFile = datFile,
  nyrRetro = GMACSdat$N_Year_Retro
)
# Read the gmacs.par file ----
GMACSparfile <- readGMACSpar(Dir =file.path(Dir_Dvpt_Vers, "build", stock, fsep = fsep),
FileName = "gmacs.par",
verbose = TRUE,
DatFile = datFile,
CtlFile = ctlFile,
GMACSdat = GMACSdat
)
}