SS_readctl_3.24: read control file from SS version 3.24

In r4ss: R Code for Stock Synthesis

read control file from SS version 3.24

Description

Read Stock Synthesis (version 3.24) control file into list object in R. This function comes with its wrapper function SS_readctl that calls SS_readctl_3.24 (this function) or SS_readctl_3.30 (to be available in future).

Usage

SS_readctl_3.24(
  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 = NA,
  Nfleet = NULL,
  Nsurveys = NULL,
  Do_AgeKey = NULL,
  N_tag_groups = NULL,
  N_CPUE_obs = NULL,
  ptype = FALSE
)

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 : produced from SS_writedat or character : file name of dat 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.
Nfleet	number of fisheries in the model. This information is also not explicitly available in control file
Nsurveys	number of survey fleets in the model. This information is also not explicitly available in control file
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)
N_CPUE_obs	numeric vector of length=Nfleet+Nsurveys containing number of data points of each CPUE time series
ptype	include a column in the output indicating parameter type? (Can be useful, but causes problems for SS_writectl.) Defaults to FALSE.

Author(s)

Yukio Takeuchi, Neil Klaer, Iago Mosqueira, and Kathryn Doering

See Also

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

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