R/LoadSimPars.r

In DanOvando/Old-LBSPR: What the package does (short line)

#' This function reads in a csv file that contains the parameters for simulating the LB-SPR model.  See SimData ReadMe for details of
#' contents of SimParFile.  
#' @name LoadSimPars  
#' @title Load LBSPR Simulation Parameters
#' @param PathtoSimFile an object of class \code{character} containing the full path to the Simulation Parameter file
#' @param SimParFileName an object of class \code{character} containing the name of Simulation Parameter file
#' @param SimParExt an object of class \code{character} containing the file extension of Simulation Parameter file (default is ".csv")
#' @param ind an optional \code{numeric} value indicating which column contains the parameters (default is 1)
#' @return Returns a list of simulation parameters
#' @author Adrian Hordyk 
#' @export

LoadSimPars <- function(PathtoSimFile="~/PathToSimFile", SimParFileName="SimData", SimParExt=".csv", ind=1) {
 
  if(SimParExt == ".csv") {
    Dat <- read.csv(file.path(PathtoSimFile, paste0(SimParFileName, SimParExt)), as.is=TRUE)
	row.names(Dat) <- Dat[,1]
		
	# Load new parameters 
	MK     <- as.numeric(Dat["MK",ind+1])
	Mpar   <- as.numeric(Dat["Mpar",ind+1])
	Linf   <- as.numeric(Dat["Linf",ind+1])
	CVLinf <- as.numeric(Dat["CVLinf",ind+1])
	L50    <- as.numeric(Dat["L50",ind+1])
	L95    <- as.numeric(Dat["L95",ind+1])
	Walpha <- as.numeric(Dat["Walpha",ind+1])
	Wbeta  <- as.numeric(Dat["Wbeta",ind+1])
	FecB   <- as.numeric(Dat["FecB",ind+1])
	Mpow   <- as.numeric(Dat["Mpow",ind+1])
	NGTG   <- as.numeric(Dat["NGTG",ind+1])
	
	MaxSD  <- as.numeric(Dat["MaxSD",ind+1])
    GTGLinfBy <- as.numeric(Dat["GTGLinfBy",ind+1]) # for age structured model 
	Linc   <- as.numeric(Dat["Linc",ind+1])

	# Adjustment to different time scale
	TStep  <- as.numeric(Dat["Tstep",ind+1]) # 12 is monthly - only one that is currently supported
	
	# Recruitment
	R0     		<- as.numeric(Dat["R0",ind+1])
	steepness 	<- as.numeric(Dat["steepness",ind+1])
	sigmaR 	<- as.numeric(Dat["sigmaR",ind+1])
	MeanMonth <- as.numeric(Dat["MeanMonth",ind+1])
	MonthSD <- as.numeric(Dat["MonthSD",ind+1])
	
	# Selectivity 
	FM     <- as.numeric(Dat["FM",ind+1])
	startSPR <- as.numeric(Dat["startSPR",ind+1])
	SL50   <- as.numeric(Dat["SL50",ind+1])
	SL95   <- as.numeric(Dat["SL95",ind+1])
	MLL	   <- as.numeric(Dat["MLL",ind+1])
	DisMortFrac <- as.numeric(Dat["DisMortFrac",ind+1])

    # Sampling
    SampleMonthMean	<- as.numeric(Dat["SampleMonthMean",ind+1])
	SampleMonthSD	<- as.numeric(Dat["SampleMonthSD",ind+1])
	SampleSize 		<- as.numeric(Dat["SampleSize",ind+1])
	
	# Projection
	NyearsMulti <- as.numeric(Dat["NyearsMulti",ind+1])
	NYears <- NULL
	if (length(Mpar) > 0) NYears <- ceiling(-log(0.001)/Mpar * NyearsMulti)
	NyearsHCR 	<- as.numeric(Dat["NyearsHCR",ind+1])
	NumIts 		<- as.numeric(Dat["NumIts",ind+1])

	SimPars <- list(MK=MK, Mpar=Mpar, Linf=Linf, CVLinf=CVLinf, L50=L50, L95=L95, 
					Walpha=Walpha, Wbeta=Wbeta, FecB=FecB, Mpow=Mpow, 
					NGTG=NGTG, GTGLinfBy=GTGLinfBy, MaxSD=MaxSD, Linc=Linc, TStep=TStep,
					R0=R0, steepness=steepness, sigmaR=sigmaR, MeanMonth=MeanMonth, MonthSD=MonthSD,
					SL50=SL50, SL95=SL95, FM=FM, startSPR=startSPR, MLL=MLL, DisMortFrac=DisMortFrac,
					SampleMonthMean=SampleMonthMean, SampleMonthSD=SampleMonthSD, SampleSize=SampleSize, NyearsHCR=NyearsHCR, NumIts=NumIts, NyearsMulti=NyearsMulti, NYears=NYears)
  }
  
  if(SimParExt != ".csv") stop("Unrecognized file extension")
  print("Simulation parameters successfully loaded") 
  # print((SimPars))
  return(SimPars)
}