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,
use_datlist = TRUE,
datlist = file.path(dirname(file), "data_echo.ss_new"),
nseas = NULL,
N_areas = NULL,
Nages = NULL,
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
A logical value specifying if output should be printed to the screen.
- 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.- 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_datlistis 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.