A simple function which takes as input the full path and filename of a control file for input to Stock Synthesis. Ideally, a Control.SS_New file will be used, so that it represents what SS thinks the inputs are, and not what the user thinks the inputs are.
Usage
SS_parlines(
ctlfile = "control.ss_new",
dir = NULL,
version = "3.30",
verbose = TRUE,
active = FALSE
)Arguments
- ctlfile
File name of control file including path.
- dir
A file path to the directory of interest. When omitted, functions typically default to the current working directory or the model directory stored in
replist.- 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 = NULLis no longer the default or an allowed entry. The default isversion = "3.30".- verbose
A logical value specifying if output should be printed to the screen.
- active
Should only active parameters (those with positive phase) be output? Default=FALSE.
Details
It returns a table which should contain one line for each parameter in the model. Currently, only the first 7 values are returned, because all parameters have those values. In the future, extended parameter lines could be returned.
Parameter lines are identified as those which have 7 or 14 numeric elements followed by a non-numeric element. It's possible that this system could break down under certain circumstances
Examples
if (FALSE) { # \dontrun{
ctlfile <- file.path(system.file("extdata", "simple_small", package = "r4ss"), "control.ss_new")
parlines <- SS_parlines(ctlfile = ctlfile)
head(parlines)
# LO HI INIT PRIOR PR_type SD PHASE Label Line_num
# 42 0.05 0.15 0.10000 0.10 0 0.8 -3 NatM_p_1_Fem_GP_1 42
# 43 0.05 0.15 0.10000 0.10 0 0.8 -3 NatM_p_2_Fem_GP_1 43
# 44 1.00 45.00 32.28100 36.00 0 10.0 2 L_at_Amin_Fem_GP_1 44
# 45 40.00 90.00 71.34260 70.00 0 10.0 4 L_at_Amax_Fem_GP_1 45
# 46 0.05 0.25 0.15199 0.15 0 0.8 4 VonBert_K_Fem_GP_1 46
# 47 0.05 0.25 0.10000 0.10 0 0.8 -3 CV_young_Fem_GP_1 47
} # }