SS_readctl: Read control file from SS
In r4ss: R Code for Stock Synthesis

SS_readctl

R Documentation

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

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
)

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