NegLogInt_Fn | R Documentation |
(Attempt to) perform the SS implementation of the Laplace Approximation from Thorson, Hicks and Methot (2014) ICES J. Mar. Sci.
NegLogInt_Fn(
dir = getwd(),
File = lifecycle::deprecated(),
Input_SD_Group_Vec,
CTL_linenum_List,
ESTPAR_num_List,
PAR_num_Vec,
Int_Group_List = list(1),
StartFromPar = TRUE,
Intern = lifecycle::deprecated(),
ReDoBiasRamp = FALSE,
BiasRamp_linenum_Vec = NULL,
CTL_linenum_Type = NULL,
exe = "ss3",
verbose = FALSE,
...
)
dir |
Directory containing Stock Synthesis files. |
File |
Deprecated. Use |
Input_SD_Group_Vec |
Vector where each element is the standard deviation for a group of random effects (e.g., a model with a single group of random effects will have Input_SD_Group_Vec be a vector of length one) |
CTL_linenum_List |
List (same length as |
ESTPAR_num_List |
List (same length as |
PAR_num_Vec |
Vector giving the number in the ".par" vector for each random effect coefficient. |
Int_Group_List |
List where each element is a vector, providing a way of grouping different random effect groups into a single category. Although this input is still required, it is no has the former input Version has been hardwired to Version = 1. |
StartFromPar |
Logical flag (TRUE or FALSE) saying whether to start each round of optimization from a ".par" file (I recommend TRUE) |
Intern |
Deprecated. Use |
ReDoBiasRamp |
Logical flag saying whether to re-do the bias ramp
(using |
BiasRamp_linenum_Vec |
Vector giving the line numbers from the CTL file that contain the information about the bias ramp. |
CTL_linenum_Type |
Character vector (same length as
|
exe |
Executable name. Can be just the name of the executable
file if it is in the specified directory or in the user's PATH. Can
also include the absolute path or a path relative to the specified
directory. Needs to be a single character string, not a vector.
On Windows, |
verbose |
A logical value specifying if output should be printed to the screen. |
... |
Additional arguments passed to |
James Thorson
Thorson, J.T., Hicks, A.C., and Methot, R.D. 2014. Random effect estimation of time-varying factors in Stock Synthesis. ICES J. Mar. Sci.
read.admbFit()
, getADMBHessian()
## Not run:
# need the full path because wd is changed in function
direc <- "C:/Models/LaplaceApprox/base"
if ("Optimization_record.txt" %in% list.files(direc)) {
file.remove(file.path(direc, "Optimization_record.txt"))
}
Opt <- optimize(
f = NegLogInt_Fn,
interval = c(0.001, 0.12),
maximum = FALSE,
dir = direc,
Input_SD_Group_Vec = 1,
CTL_linenum_List = list(127:131),
ESTPAR_num_List = list(86:205),
Int_Group_List = 1,
PAR_num_Vec = NA,
Intern = TRUE
)
## End(Not run)
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