SS_readctl_3.30: read control file from SS version 3.30

In r4ss: R Code for Stock Synthesis

read control file from SS version 3.30

Description

Read Stock Synthesis (version 3.30) control file into list object in R. This function should be called from SS_readctl.

Usage

SS_readctl_3.30(
  file,
  verbose = FALSE,
  echoall = lifecycle::deprecated(),
  version = lifecycle::deprecated(),
  use_datlist = TRUE,
  datlist = "data.ss_new",
  nseas = NULL,
  N_areas = NULL,
  Nages = NULL,
  Ngenders = lifecycle::deprecated(),
  Nsexes = NULL,
  Npopbins = NULL,
  Nfleets = NULL,
  Ntag_fleets = NULL,
  Do_AgeKey = NULL,
  N_tag_groups = NULL,
  catch_mult_fleets = NULL,
  predM_fleets = NULL,
  N_rows_equil_catch = NULL,
  N_dirichlet_parms = NULL
)

Arguments

file	Filename either with full path or relative to working directory. See the formal arguments for a possible default filename.
verbose	Should there be verbose output while running the file? Defaults to FALSE.
echoall	Deprecated. Debugging tool (not fully implemented) of echoing blocks of values as it is being read.
version	Deprecated. SS version number. Currently only "3.24" or "3.30" are supported, either as character or numeric values (noting that numeric 3.30 = 3.3).
use_datlist	LOGICAL. If TRUE, use datlist to derive parameters which can not be determined from control file. Defaults to TRUE.
datlist	list or character. If list, should be a list produced from SS_writedat(). If character, should be the file name of an SS data file.
nseas	number of seasons in the model. This information is not explicitly available in control file and used only if use_datlist = FALSE.
N_areas	number of spatial areas in the model. Default = 1. This information is not explicitly available in control file and used only if if use_datlist = FALSE.
Nages	oldest age in the model. This information is also not explicitly available in control file and used only if use_datlist = FALSE.
Ngenders	Deprecated. Number of sexes in the model. This information is also not explicitly available in control file and used only if use_datlist = FALSE.
Nsexes	number of sexes in the model. This information is also not explicitly available in control file and used only if use_datlist = FALSE.
Npopbins	number of population bins in the model. This information is also not explicitly available in control file and this information is only required if length based maturity vector is directly supplied (Maturity option of 6). and used only if use_datlist = FALSE.
Nfleets	number of fishery and survey fleets in the model. This information is also not explicitly available in control file
Ntag_fleets	The number of catch fleets in the model (fleets of ) type 1 or 2; not surveys). Used to set the number of survey parameters. Only used if tagging data is in the model and use_datlist is FALSE.
Do_AgeKey	Flag to indicate if 7 additional ageing error parameters to be read set 1 (but in fact any non zero numeric in R) or TRUE to enable to read them 0 or FALSE to disable them. This information is not explicitly available in control file and used only if use_datlist = FALSE.
N_tag_groups	number of tag release group. Default =NA. This information is not explicitly available control file and used only if use_datlist = FALSE. This information is only required if custom tag parameters is enabled (TG_custom=1)
catch_mult_fleets	integer vector of fleets using the catch multiplier option. Defaults to NULL and should be left as such if 1) the catch multiplier option is not used for any fleets or 2) use_datlist = TRUE and datlist is specified.
predM_fleets	integer vector of fleets with predator mortality included. Predator mortality fleets are only available in v3.30.18 and higher. Defaults to NULL and should be left as such if 1) predation mortality is not used for any fleets; 2) use_datlist = TRUE and datlist is specified; or 3) if comments in the control file should be used instead to determine the the predM_fleets.
N_rows_equil_catch	Integer value of the number of parameter lines to read for equilibrium catch. Defaults to NULL, which means the function will attempt to figure out how many lines of equilibrium catch to read from the control file comments.
N_dirichlet_parms	Integer value of the number of Dirichlet multinomial parameters. Defaults to 0.

Author(s)

Neil Klaer, Yukio Takeuchi, Watal M. Iwasaki, and Kathryn Doering

See Also

SS_readctl(), SS_readdat() SS_readdat_3.24(),SS_readdat_3.30() SS_readctl_3.24(), SS_readstarter(), SS_readforecast(), SS_writestarter(), SS_writeforecast(), SS_writedat()

r4ss documentation built on May 28, 2022, 1:11 a.m.