SS_readctl {r4ss}

Read control file from SS

Description

Read control file from Stock Synthesis (SS) into R as a list object. This function acts as a wrapper for version-specific SS_readctl_ functions. For example, if the control file was written using SS 3.24, then SS_readctl will call SS_readctl_3.24. Input arguments that do not pertain to the version of your control file can be left at their default values.

Usage

SS_readctl(
  file,
  version = "3.30",
  verbose = FALSE,
  echoall = lifecycle::deprecated(),
  use_datlist = TRUE,
  datlist = "data.ss_new",
  nseas = NULL,
  N_areas = NULL,
  Nages = NULL,
  Ngenders = lifecycle::deprecated(),
  Nsexes = NULL,
  Npopbins = NA,
  Nfleets = NULL,
  Nfleet = NULL,
  Do_AgeKey = NULL,
  Nsurveys = NULL,
  N_tag_groups = NULL,
  N_CPUE_obs = NULL,
  catch_mult_fleets = NULL,
  predM_fleets = NULL,
  Ntag_fleets = NULL,
  N_rows_equil_catch = NULL,
  N_dirichlet_parms = NULL,
  ptype = FALSE
)

Arguments

file

Filename either with full path or relative to working directory.

See the formal arguments for a possible default filename.

version

SS version number. Currently "3.24" or "3.30" are supported, either as character or numeric values (noting that numeric 3.30 = 3.3). version = NULL is no longer the default or an allowed entry. The default is version = "3.30".

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.

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 fishing fleets and surveys, for 3.30 models.

Nfleet

Number of fishing fleets, for 3.24 and lower version models.

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.

Nsurveys

Number of surveys, for 3.24 and lower version models.

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

Number of CPUE observations. Used only in control file 3.24 syntax if use_datlist = FALSE.

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 fleet or 2) use_datlist = TRUE and datlist is specified. Used only in control file 3.30 syntax if use_datlist = FALSE.

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. Used only in control file 3.30 syntax if use_datlist = FALSE.

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 in control file 3.30 reading if tagging data is in the model and use_datlist = FALSE.

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. Used only in control file 3.30 syntax if use_datlist = FALSE.

N_dirichlet_parms

Integer value of the number of Dirichlet-Multinomial parameters. Defaults to 0. Used only in control file 3.30 syntax if use_datlist = FALSE.

ptype

LOGICAL if TRUE, which is the default, a column will be included in the output indicating parameter type. Using TRUE can be useful, but causes problems for SS_writectl, and therefore is not recommended if you intend to write the list back out into a file. Used only in control file 3.24 syntax.

Value

A list structure where each element is a section of the control file.

Author(s)

Ian G. Taylor, Yukio Takeuchi, Neil L. Klaer

See Also

See the following for version-specific SS_readctl functions: SS_readctl_3.24 SS_readctl_3.30. The returned list structure can be written back to the disk using SS_writectl.
See the following for other SS_read functions: SS_readctl SS_readdat SS_readforecast SS_readstarter SS_readwtatage.

Examples

# Read in the 'simple' example SS model stored in r4ss
# Find the directory
dirsimple <- system.file("extdata", "simple_3.30.13", package = "r4ss")
# Read in the dat file to define the structure of the control file so that
# you don't have to specify things in the function call such as 'Nfleet'
datfilename <- dir(dirsimple, pattern = "data\\.ss", full.names = TRUE)
dat <- r4ss::SS_readdat(file = datfilename, verbose = FALSE)
# Read in the control file using a list object for datlist
ctl <- r4ss::SS_readctl(
  file = dir(dirsimple, pattern = "control\\.ss", full.names = TRUE),
  verbose = FALSE,
  datlist = dat, use_datlist = TRUE
)
# Read in the control file using a file name for datlist
ctl <- r4ss::SS_readctl(
  file = dir(dirsimple, pattern = "control\\.ss", full.names = TRUE),
  verbose = FALSE,
  datlist = datfilename, use_datlist = TRUE
)