R/read.sim.R

In ben-mhamed/DEPLr: Simulation Depletion Model with R

#' A function that allow reading an input simulation file
#' 
#' @description Read a simulation input file
#' @import stringr
#' @param x : path of the input file

read.sim <- function(file){
  if(!checkExt(file)){
    return("Error: The extintion of the do not match the correct form")
  }else{
    dat=scan(file = file,what = "character",sep = "\n")
    LW <- as.numeric(str_split(string = str_split(string = dat[3],pattern = "#")[[1]][1],pattern = ",")[[1]][1:2])
    GF <- as.numeric(str_split(string = str_split(string = dat[4],pattern = "#")[[1]][1],pattern = ",")[[1]][1:2])
    cstNM <- as.numeric(str_split(string = dat[5],pattern = " ")[[1]][1])
    valNM <- as.numeric(str_split(string = dat[6],pattern = " ")[[1]][1])
    proErr <- as.numeric(str_split(string = dat[7],pattern = " ")[[1]][1])
    obsErr <- as.numeric(str_split(string = dat[8],pattern = " ")[[1]][1])
    nbrSim <- as.numeric(str_split(string = dat[9],pattern = " ")[[1]][1])
    season <- as.numeric(str_split(string = dat[10],pattern = " ")[[1]][1])
    nbrFleet <- as.numeric(str_split(string = dat[11],pattern = " ")[[1]][1])
    nbrZone <- as.numeric(str_split(string = dat[12],pattern = " ")[[1]][1])
    discard <- as.numeric(str_split(string = dat[13],pattern = " ")[[1]][1])
    recTot <- as.numeric(str_split(string = dat[14],pattern = " ")[[1]][1])
    initLenghts <- as.numeric(str_split(string = str_split(string = dat[15],pattern = "#")[[1]][1],pattern = ",")[[1]][1:nbrZone])
    propRec<- as.numeric(str_split(string = str_split(string = dat[16],pattern = "#")[[1]][1],pattern = ",")[[1]][1:nbrZone])
    initAbund <- as.numeric(str_split(string = str_split(string = dat[17],pattern = "#")[[1]][1],pattern = ",")[[1]][1:nbrZone])
    catchability <- as.numeric(str_split(string = str_split(string = dat[18],pattern = "#")[[1]][1],pattern = ",")[[1]][1:nbrFleet])
    codeData <- str_trim(as.character(str_split(string = dat[19],pattern = "#")[[1]][1]))
    fleetName <- as.character(str_trim(str_split(string = str_split(string = dat[20],pattern = "#")[[1]][1],pattern = ",")[[1]][1:nbrFleet]))
    zoneName <- rep("",nbrZone)
    dt.array <- array(data = NA,dim = c(season,nbrFleet+2,nbrZone))
    index=1
    j=0
    while(index<nbrZone+1){
      j=21+(index-1)*(season+1)
      zoneName[index]=str_trim(as.character(str_split(string = dat[j],pattern = " ")[[1]][1]))
      for(i in 1:season){
        dt.array[i,,index] <-  as.numeric(unlist(str_split(string = str_split(string = dat[j+i],pattern = c(" "))[[1]],pattern = "\t")))
      }
      index=index+1
    }
  }
  dataList=list("LW"=LW,"GF"=GF,"cstNM"=cstNM,"valNM"=valNM,"proErr"=proErr,"obsErr"=obsErr,"nbrSim"=nbrSim,"season"=season,"nbrFleet"=nbrFleet,"nbrZone"=nbrZone,"discard"=discard,"recTot"=recTot,"initLenghts"=initLenghts,"propRec"=propRec,"initAbund"=initAbund,"catchability"=catchability,"codeData"=codeData,"fleetName"=fleetName,"zoneName"=zoneName,"dt.array"=dt.array)
  return(dataList)
}