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r4ss (version 1.44.0)

SS_readctl_3.24: 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.

See Also

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