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Change parameters, bounds, or phases in the control file.

Source: R/SS_changepars.R
SS_changepars.Rd

Loops over a subset of control file to change parameter lines. Current initial value, lower and upper bounds, and phase can be modified, but function could be expanded to control other columns. Depends on SS_parlines(). Used by profile() and the ss3sim package.

Usage

SS_changepars(
  dir = NULL,
  ctlfile = "control.ss_new",
  newctlfile = "control_modified.ss",
  linenums = NULL,
  strings = NULL,
  newvals = NULL,
  repeat.vals = FALSE,
  newlos = NULL,
  newhis = NULL,
  newprior = NULL,
  newprsd = NULL,
  newprtype = NULL,
  estimate = NULL,
  verbose = TRUE,
  newphs = NULL
)

Arguments

dir

A file path to the directory of interest. The default value is dir = NULL, which leads to using the current working directory.

ctlfile

Control file name. Default="control.ss_new".

newctlfile

Name of new control file to be written. Default="control_modified.ss".

linenums

Line numbers of control file to be modified. Either this or the strings argument are needed. Default=NULL.

strings

Strings (with optional partial matching) indicating which parameters to be modified. This is an alternative to linenums. strings correspond to the commented parameter names included in control.ss_new, or whatever is written as comment at the end of the 14 number parameter lines. Default=NULL.

newvals

Vector of new parameter values. Default=NULL. The vector can contain NA values, which will assign the original value to the given parameter but change the remainder parameters, where the vector of values needs to be in the same order as either linenums or strings.

repeat.vals

If multiple parameter lines match criteria, repeat the newvals input for each line.

newlos

Vector of new lower bounds. Default=NULL. The vector can contain NA values, which will assign the original value to the given parameter but change the remainder parameters, where the vector of values needs to be in the same order as either linenums or strings.

newhis

Vector of new high bounds. Must be the same length as newhis Default=NULL. The vector can contain NA values, which will assign the original value to the given parameter but change the remainder parameters, where the vector of values needs to be in the same order as either linenums or strings.

newprior

Vector of new prior values. Default=NULL. The vector can contain NA values, which will assign the original value to the given parameter but change the remainder parameters, where the vector of values needs to be in the same order as either linenums or strings.

newprsd

Vector of new prior sd values. Default=NULL. The vector can contain NA values, which will assign the original value to the given parameter but change the remainder parameters, where the vector of values needs to be in the same order as either linenums or strings.

newprtype

Vector of new prior type. Default=NULL. The vector can contain NA values, which will assign the original value to the given parameter but change the remainder parameters, where the vector of values needs to be in the same order as either linenums or strings.

estimate

Optional vector or single value of TRUE/FALSE for which parameters are to be estimated. Changes sign of phase to be positive or negative. Default NULL causes no change to phase.

verbose

A logical value specifying if output should be printed to the screen.

newphs

Vector of new phases. Can be a single value, which will be repeated for each parameter, the same length as newvals, where each value corresponds to a single parameter, or NULL, where the phases will not be changed. If one wants to strictly turn parameters on or off and not change the phase in which they are estimated use estimate = TRUE or estimate = FALSE, respectively. The vector can contain NA values, which will assign the original value to the given parameter but change the remaining parameters, where the vector of values needs to be in the same order as either linenums or strings.

See also

SS_parlines(), profile()

Author

Ian Taylor, Christine Stawitz, Chantel Wetzel, Kiva L. Oken

Examples

if (FALSE) { # \dontrun{
SS_changepars(
  dir = "C:/ss/SSv3.30.03.05_May11/Simple - Copy",
  strings = c("steep", "sigmaR"), newvals = c(.4, .6)
)
## parameter names in control file matching input vector 'strings' (n=2):
## [1] "SR_BH_steep" "SR_sigmaR"
## These are the ctl file lines as they currently exist:
##     LO HI     INIT PRIOR PR_type SD PHASE env_var&link dev_link dev_minyr dev_maxyr
## 95 0.2  1 0.613717   0.7    0.05  1     4       0       0         0         0
## 96 0.0  2 0.600000   0.8    0.80  0    -4       0       0         0         0
##        dev_PH Block Block_Fxn       Label Linenum
## 95          0     0         0 SR_BH_steep      95
## 96          0     0         0   SR_sigmaR      96
## line numbers in control file (n=2):
## [1] 95 96
##
## wrote new file to control_modified.ss with the following changes:
##    oldvals newvals oldphase newphase oldlos newlos oldhis newhis       comment
## 1 0.613717     0.4        4       -4    0.2    0.2      1      1 # SR_BH_steep
## 2 0.600000     0.6       -4       -4    0.0    0.0      2      2   # SR_sigmaR
} # }