r4ss (version 1.36.1)

NegLogInt_Fn: Perform SS implementation of Laplace Approximation

Description

(Attempt to) perform the SS implementation of the Laplace Approximation from Thorson, Hicks and Methot (2014) ICES J. Mar. Sci.

Usage

NegLogInt_Fn(File = NA, Input_SD_Group_Vec, CTL_linenum_List,
  ESTPAR_num_List, PAR_num_Vec, Int_Group_List = list(1),
  StartFromPar = TRUE, Intern = TRUE, ReDoBiasRamp = FALSE,
  BiasRamp_linenum_Vec = NULL, CTL_linenum_Type = NULL,
  systemcmd = FALSE, exe = "ss")

Arguments

File

Directory containing Stock Synthesis files (e.g., "C:/Users/James Thorson/Desktop/")

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 Input_SD_Group_Vec), where each element is a vector giving the line number(s) for the random effect standard deviation parameter or penalty in the CTL file (and where each line will correspond to a 7-parameter or 14-parameter line).

ESTPAR_num_List

List (same length as Input_SD_Group_Vec), where each element is a vector giving the parameter number for the random effect coefficients in that group of random effects. These "parameter numbers" correspond to the number of these parameters in the list of parameters in the ".cor" output file.

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

Logical flag saying whether to display all ss3 runtime output in the R terminal

ReDoBiasRamp

Logical flag saying whether to re-do the bias ramp (using SS_fitbiasramp) each time Stock Synthesis is run.

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 Input_SD_Group_Vec), where each element is either "Short_Param", "Long_Penalty", "Long_Penalty". Default is NULL, and if not explicitly specified the program will attempt to detect these automatically based on the length of relevant lines from the CTL file.

systemcmd

Should R call SS using "system" function instead of "shell". This may be required when running R in Emacs on Windows. Default = FALSE.

exe

SS executable name (excluding extension), either "ss" or "ss3". This string is used for both calling the executable and also finding the output files like ss.par. For 3.30, it should always be "ss" since the output file names are hardwired in the TPL code.

References

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.

See Also

read.admbFit, getADMBHessian

Examples

# NOT RUN {
  
# }
# NOT RUN {
    direc <- "C:/Models/LaplaceApprox/base"  #need the full path because wd is changed in function
    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,
                   File=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)
  
# }