readGMACSctl

Source: R/readGMACSctl.R

Read the GMACS control file.

readGMACSctl(FileName = NULL, verbose = TRUE, DatFile = NULL, nyrRetro = NULL)

Arguments

FileName

(character string)- path (and name (e.g. snow.ctl)) of the control file

verbose

(logical)- (TRUE/FALSE); flag to print processing information

DatFile

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

nyrRetro

(integer)- Number of year for the retrospective analysis

Value

A list with the content of the model.ctl file.

  • sourcefile - The file source.

  • Comments - Specifications about the GMACS version used and the stock assessed.

  • ntheta - The number of key parameters control.

  • theta_control - The matrix pf teh key parameters control.

  • lw_type - The type of length-weight (LW) relationship.

  • lw_alfa - The alpha parameter of the LW relationship (if lw_type = 1).

  • lw_beta - The beta parameter of the LW relationship (if lw_type = 1).

  • mean_wt_in - The vector/matrix of mean weight-at-size (if lw_type = 2,3).

  • maturity - The proportion of mature at size by sex.

  • legal_maturity - The legal definition of the proportion of mature at size by sex.

  • Func_maturity_TermMolting - Use functional maturity for terminally molting animals?

  • bUseCustomGrowthMatrix - The selected option for the growth matrix.

  • bUseGrowthIncrementModel - The selected option for the growth increment model.

  • bUseCustomMoltProbability - The selected molt probability function.

  • bUseCustomMatureProbability - The selected option for the maturity probability (only applicable if nmature = 2)

  • nSizeClassRec - The maximum size-class for recruitment

  • nSizeIncVaries - The number of size increment periods

  • iYrsSizeIncChanges - The year(s) for which the size increment change.

  • nMoltVaries - The number of molt periods.

  • iYrsMoltChanges - The year(s) for which molt change.

  • BetaParRelative - Are the beta parameters relative?

  • nMatureVaries - The number of maturity probability periods

  • iYrsMatureChanges - The year(s) for which maturity probability change.

  • nGrwth - The total number of growth parameters (depends upon nSizeIncVaries).

  • nSizeIncPar - The number of size increment parameters.

  • Grwth_control - The matrix of growth controls.

  • MoltProb_control - The matrix of molting probability controls.

  • MatureProb_control - The matrix of mature probability controls.

  • CustomGrowthMatrix - The custom growth-increment matrix or size-transition matrix.

  • CustomMoltProbabilityMatrix - The custom molt probability matrix.

  • slx_nsel_period_in - The number of selectivity time period per fleet.

  • slx_bsex_in - The number of sex specific selectivity.

  • slx_type_in - The sex-specific selectivity type.

  • slx_include_in - Is there any insertion of a fleet selectivity in another?

  • slx_extra_in - Extra parameter for each selectivity pattern.

  • ret_nret_period_in - The number of retention time period per fleet.

  • ret_bsex_in - The number of sex specific retention.

  • ret_type_in - The sex-specific retention type.

  • ret_extra_in - Extra parameter for each retention pattern.

  • slx_nret - Boolean for retention/discard.

  • slx_max_at_1_in - Is the selectivity for the maximum size class forced to be 1?

  • slx_cols - The number of parameter required for each vulnerability pattern.

  • slx_npar - The number of parameter for each pattern of selectivity.

  • nslx_pars - The total number of vulnerability parameters.

  • Selex_control - the matrix of selectivity control.

  • Ret_control - The matrix of retention control.

  • NumAsympRet - The number of asymptotic vulnerability parameters.

  • AsympSel_control - The asymptotic parameter control.

  • nslx_envpars - The number of climate-driven selectivity parameters.

  • NSlx_devs_param - The number of parameters controlling selectivity deviations.

  • devParPhase - The estimation phase for the deviation parameter (when a random walk is considered).

  • q_controls - The catchability control parameters.

  • add_cv_controls - Additional CV control parameters for catchability.

  • add_cv_links - Use of additional variance for each survey (0: ignore; >0 use).

  • f_controls - The fishing mortality control.

  • nAgeCompType - The size composition likelihood type.

  • bTailCompression - The auto tail compression specification.

  • nvn_ival - The initial value(s) for effective sample size.

  • nvn_phz - The phase of estimation for the effective sample size.

  • iCompAggregator - Should the data be aggregated?

  • lf_catch - The type of predictions for the size composition data (survey-like / catch-like)

  • lf_lambda - The lamdba for effective sample size.

  • lf_emphasis - The weight (lambda) for the overall likelihood

  • m_type - The type of natural mortality.

  • MrelFem- How does M for females relate to that for males (0 absolute; 1 relative)

  • Mdev_phz_def - The phase of estimation for natural mortality.

  • m_stdev - The standard deviation used in the natural mortality deviations.

  • m_nNodes_sex - The sex-specific number of nodes in natural mortality.

  • m_nodeyear_sex - The sex-specific years for nodes in natural mortality.

  • nSizeDevs - The number of breakpoints in natural mortality by size class.

  • m_size_nodeyear - The specific years for the deviations (blocks) in natural mortality by size class.

  • Init_Mdev - Use a specific initial value for natural mortality deviations?

  • nMdev - The number of natural mortality deviations.

  • Mdev_controls - Natural mortality deviation control.

  • tag_emphasis - The emphasis (weight) for the tagging likelihood.

  • m_maturity - Is there any maturity-specific natural mortality?

  • m_mat_controls - Immature/mature natural mortality control if any.

  • rdv_syr - The first year of recruitment estimation deviations.

  • rdv_eyr - The last year of recruitment estimation deviations.

  • Term_molt - Consider terminal molting in the model?

  • rdv_phz - The phase for recruitment estimation.

  • rec_prop_phz - The phase for recruitment sex-ratio estimation.

  • init_sex_ratio - The initial value for expected sex-ratio.

  • rec_ini_phz - The phase for initial recruitment estimation.

  • bInitializeUnfished - The specification for the initial conditions (unfished, steady-state, free params, free params revised)

  • spr_lambda - The proportion of mature male biomass for SPR reference points.

  • nSRR_flag - The stock-Recruit-Relationship (none, Beverton-Holt)

  • BRP_rec_sexR - Use years specified to computed average sex ratio in the calculation of average recruitment for reference points.

  • NyrEquil - The year to compute equilibrium.

  • catch_emphasis - The weight on catch for the likelihood component.

  • Penalty_fdevs - Penalties on deviations.

  • Penalty_emphasis - Penalties on priors

  • eof - Logical indicating the end of the file (used for checking the reading).

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
)
}