R/as.CatDynData.R

In CatDyn: Fishery Stock Assessment by Catch Dynamics Models

as.CatDynData <-
function(x,step,fleet.name,coleff,colcat,colmbw,unitseff,unitscat,unitsmbw,nmult,season.dates)
   {
    if(step != "day" && step != "week" && step != "month")
      {stop("step for the catch dynamics must be 'day', 'week', or 'month' ")}
    if(length(fleet.name) < 1 || length(fleet.name) > 2){stop("The number of fleets must be 1 or 2")}
    if(length(unique(fleet.name)) != length(fleet.name)){stop("Fleets must have unique names")}
    if(any(x[,coleff] < 0) || any(x[,colcat] < 0) || any(x[,colmbw] < 0))
      {stop("Catch, effort, and mean body weight observations must all be non-negative")}
    if(sum(is.na(x[,c(coleff,colcat)])) > 0){stop("NAs are not allowed in the catch, effort series")}
    if(any(coleff > dim(x)[2])){stop("coleff are the columns where the effort data is stored")}
    if(any(colcat > dim(x)[2])){stop("colcat are the columns where the catch data is stored")}
    if(any(colmbw > dim(x)[2])){stop("colmbw are the columns where the mean body weight is stored")}
    if(unitscat != "kg" && unitscat != "ton" && unitscat != "ind") {stop("unitscat must be a character (all fleets same unit) either kilograms ('kg'), tonnes ('ton') or numbers ('ind')")}
    if(unitsmbw != "kg" && unitsmbw != "g" && unitsmbw != "ind") {stop("unitsmbw must be a character (all fleets same unit) either grams ('g'), kilograms ('kg') or numbers ('ind')")}
    if(length(unitscat) > 1 || length(unitsmbw) > 1) {stop("The catches and mean body weight of all fleets must be in the same units, thus this parameter must be of length 1")}
    if(nmult != "bill" && nmult != "mill" && nmult != "thou" && nmult != "hund" && nmult != "ind") {stop("nmult, the catch in numbers multiplier, must be 'bill' (billions), 'mill' (millions), 'thou' (thousands), 'hund' (hundreds), or 'ind' (single individuals)")}
    if(length(nmult) > 1) {stop("Since the catches and mean body weight are in the same unit for both fleets, the nmult parameter must be of length 1")}
    if(paste(substr(season.dates[1],5,5),substr(season.dates[1],8,8),sep="") != "--" || paste(substr(season.dates[2],5,5),substr(season.dates[2],8,8),sep="") != "--")
      {stop("season.dates must be a length-2 character vector (start of season, end of season) with dates in the ISO 8601 international standard, i.e. yyyy-mm-dd")}
    cateff                         <- vector("list",2);
    names(cateff)                  <- c("Properties","Data");
    cateff$Data                    <- vector("list",length(fleet.name));
    names(cateff$Data)             <- fleet.name
    cateff$Properties              <- vector("list",3)
    names(cateff$Properties)       <- c("Units","Fleets","Dates")
    cateff$Properties$Units        <- c(step,unitscat,unitsmbw,nmult)
    names(cateff$Properties$Units) <- c("Time Step","Catch","Bodymass","NumbersMultiplier")
    cateff$Properties$Fleets       <- data.frame(Fleet=fleet.name,Units=unitseff,stringsAsFactors=FALSE)
    cateff$Properties$Dates        <- season.dates
    names(cateff$Properties$Dates) <- c("StartDate","EndDate")
    if(step == "day")
      {
       if(paste(substr(season.dates[1],5,5),substr(season.dates[1],8,8),sep="") != "--" || paste(substr(season.dates[2],5,5),substr(season.dates[2],8,8),sep="") != "--")
        {stop("dates of daily catch dynamics must be a length 2 character vector with dates in the ISO 8601 international standard, i.e. yyyy-mm-dd")}
       if(as.numeric(format(as.Date(season.dates[2],"%Y-%m-%d"), "%Y")) - as.numeric(format(as.Date(season.dates[1],"%Y-%m-%d"), "%Y")) > 1)
         {stop("For a daily time step the modeling is seasonal, involving no more than two calendar years")}
       if(as.numeric(format(as.Date(season.dates[1],"%Y-%m-%d"), "%Y")) > as.numeric(format(as.Date(season.dates[2],"%Y-%m-%d"), "%Y")))
         {stop("Dates must be arranged in ascending order")}
       if(as.numeric(format(as.Date(season.dates[1],"%Y-%m-%d"), "%Y")) == as.numeric(format(as.Date(season.dates[2],"%Y-%m-%d"), "%Y")) &&
          as.numeric(format(as.Date(season.dates[1],"%Y-%m-%d"), "%m")) >  as.numeric(format(as.Date(season.dates[2],"%Y-%m-%d"), "%m")))
         {stop("Dates must be arranged in ascending order")}          
       if(as.numeric(format(as.Date(season.dates[1],"%Y-%m-%d"), "%Y")) == as.numeric(format(as.Date(season.dates[2],"%Y-%m-%d"), "%Y")) &&
          as.numeric(format(as.Date(season.dates[1],"%Y-%m-%d"), "%m")) == as.numeric(format(as.Date(season.dates[2],"%Y-%m-%d"), "%m")) &&
          as.numeric(format(as.Date(season.dates[1],"%Y-%m-%d"), "%d")) >  as.numeric(format(as.Date(season.dates[2],"%Y-%m-%d"), "%d")))
         {stop("Dates must be arranged in ascending order")}          
       start <- as.numeric(julian(as.Date(season.dates[1],"%Y-%m-%d"),origin=as.Date(paste(substr(season.dates[1],1,4),"-01-01",sep="")))) + 1;
       for(i in 1:length(fleet.name))
         {
          (if(as.numeric(format(as.Date(season.dates[1],"%Y-%m-%d"), "%Y")) == as.numeric(format(as.Date(season.dates[2],"%Y-%m-%d"), "%Y"))) 
            {end <-  as.numeric(julian(as.Date(season.dates[2],"%Y-%m-%d"),
                                       origin=as.Date(paste(substr(season.dates[2],1,4),"-01-01",sep=""))) + 1)
             cateff$Data[[i]] <- data.frame(time.step=start:end,x[,coleff[i]],x[,colcat[i]],x[,colmbw[i]])}
           else 
            {end <- (as.numeric(julian(as.Date(paste(substr(season.dates[1],1,4),"-12-31",sep="")),
                                       origin=as.Date(paste(substr(season.dates[1],1,4),"-01-01",sep=""))))-start+2) + 
                     as.numeric(julian(as.Date(season.dates[2],"%Y-%m-%d"),origin=as.Date(paste(substr(season.dates[2],1,4),"-01-01",sep="")))) + 1
             cateff$Data[[i]] <- data.frame(time.step=1:end,x[,coleff[i]],x[,colcat[i]],x[,colmbw[i]]);})
#         if(length(start:(start+end)) != dim(x)[1])
#           {stop("Check season.dates, you have a number of days that is not identical to the number of effort/catch/mean body weight observations \n Consider changing the dates")}
#         cateff$Data[[i]]              <- data.frame(time.step=start:end,x[,coleff[i]],x[,colcat[i]],x[,colmbw[i]]);
         names(cateff$Data[[i]])[2:4]  <-c(paste("obseff.",unitseff[i],sep=""),
                                           paste("obscat.",unitscat,sep=""),
                                           paste("obsmbw.",unitsmbw,sep="")); 
         if(nmult == "bill" && unitscat == "ton" && unitsmbw == "g")
          { 
           cateff$Data[[i]]$obscat.bill    <- ifelse(cateff$Data[[i]][,3]==0,0,1e-9*1e6*cateff$Data[[i]][,3]/cateff$Data[[i]][,4]);
          }
         else if(nmult == "bill" && unitscat == "ton" && unitsmbw == "kg")
          {
           cateff$Data[[i]]$obscat.bill    <- ifelse(cateff$Data[[i]][,3]==0,0,1e-9*1e3*cateff$Data[[i]][,3]/cateff$Data[[i]][,4]);
          }
         else if(nmult == "bill" && unitscat == "kg" && unitsmbw == "g")
          {
           cateff$Data[[i]]$obscat.bill    <- ifelse(cateff$Data[[i]][,3]==0,0,1e-9*1e3*cateff$Data[[i]][,3]/cateff$Data[[i]][,4]);
          }
         else if(nmult == "bill" && unitscat == "kg" && unitsmbw == "kg")
          {
           cateff$Data[[i]]$obscat.bill    <- ifelse(cateff$Data[[i]][,3]==0,0,1e-9*cateff$Data[[i]][,3]/cateff$Data[[i]][,4]);
          }
          else if(nmult == "mill" && unitscat == "ton" && unitsmbw == "g")
          { 
           cateff$Data[[i]]$obscat.mill    <- ifelse(cateff$Data[[i]][,3]==0,0,1e-6*1e6*cateff$Data[[i]][,3]/cateff$Data[[i]][,4]);
          }
         else if(nmult == "mill" && unitscat == "ton" && unitsmbw == "kg")
          {
           cateff$Data[[i]]$obscat.mill    <- ifelse(cateff$Data[[i]][,3]==0,0,1e-6*1e3*cateff$Data[[i]][,3]/cateff$Data[[i]][,4]);
          }
         else if(nmult == "mill" && unitscat == "kg" && unitsmbw == "g")
          {
           cateff$Data[[i]]$obscat.mill    <- ifelse(cateff$Data[[i]][,3]==0,0,1e-6*1e3*cateff$Data[[i]][,3]/cateff$Data[[i]][,4]);
          }
         else if(nmult == "mill" && unitscat == "kg" && unitsmbw == "kg")
          {
           cateff$Data[[i]]$obscat.mill    <- ifelse(cateff$Data[[i]][,3]==0,0,1e-6*cateff$Data[[i]][,3]/cateff$Data[[i]][,4]);
          }
         else if(nmult == "thou" && unitscat == "ton" && unitsmbw == "g")
          {
           cateff$Data[[i]]$obscat.thou    <- ifelse(cateff$Data[[i]][,3]==0,0,1e-3*1e6*cateff$Data[[i]][,3]/cateff$Data[[i]][,4]);
          }
         else if(nmult == "thou" && unitscat == "ton" && unitsmbw == "kg")
          {
           cateff$Data[[i]]$obscat.thou    <- ifelse(cateff$Data[[i]][,3]==0,0,1e-3*1e3*cateff[,3][[i]]/cateff$Data[[i]][,4]);
          }
         else if(nmult == "thou" && unitscat == "kg" && unitsmbw == "g")
          {
           cateff$Data[[i]]$obscat.thou    <- ifelse(cateff$Data[[i]][,3]==0,0,1e-3*1e3*cateff$Data[[i]][,3]/cateff$Data[[i]][,4]);
          }
         else if(nmult == "thou" && unitscat == "kg" && unitsmbw == "kg")
          {
           cateff$Data[[i]]$obscat.thou    <- ifelse(cateff$Data[[i]][,3]==0,0,1e-3*cateff$Data[[i]][,3]/cateff$Data[[i]][,4]);
          }
         else if(nmult == "hund" && unitscat == "ton" && unitsmbw == "g")
          {
           cateff$Data[[i]]$obscat.hund    <- ifelse(cateff$Data[[i]][,3]==0,0,1e-2*1e6*cateff$Data[[i]][,3]/cateff$Data[[i]][,4]);
          }
         else if(nmult == "hund" && unitscat == "ton" && unitsmbw == "kg")
          {
           cateff$Data[[i]]$obscat.hund    <- ifelse(cateff$Data[[i]][,3]==0,0,1e-2*1e3*cateff$Data[[i]][,3]/cateff$Data[[i]][,4]);
          }
         else if(nmult == "hund" && unitscat == "kg" && unitsmbw == "g")
          {
           cateff$Data[[i]]$obscat.hund    <- ifelse(cateff$Data[[i]][,3]==0,0,1e-2*1e3*cateff$Data[[i]][,3]/cateff$Data[[i]][,4]);
          }
         else if(nmult == "hund" && unitscat == "kg" && unitsmbw == "kg")
          {
           cateff$Data[[i]]$obscat.hund    <- ifelse(cateff$Data[[i]][,3]==0,0,1e-2*cateff$Data[[i]][,3]/cateff$Data[[i]][,4]);
          }
         else if(nmult == "bill" && unitscat == "ind" && unitsmbw == "ind")
          {
           cateff$Data[[i]]$obscat.bill    <- ifelse(cateff$Data[[i]][,3]==0,0,1e-9*cateff$Data[[i]][,3]/cateff$Data[[i]][,4]);
          }
         else if(nmult == "mill" && unitscat == "ind" && unitsmbw == "ind")
          {
           cateff$Data[[i]]$obscat.mill    <- ifelse(cateff$Data[[i]][,3]==0,0,1e-6*cateff$Data[[i]][,3]/cateff$Data[[i]][,4]);
          }
         else if(nmult == "thou" && unitscat == "ind" && unitsmbw == "ind")
          {
           cateff$Data[[i]]$obscat.thou    <- ifelse(cateff$Data[[i]][,3]==0,0,1e-3*cateff$Data[[i]][,3]/cateff$Data[[i]][,4]);
          }
         else if(nmult == "hund" && unitscat == "ind" && unitsmbw == "ind")
          {
           cateff$Data[[i]]$obscat.hund    <- ifelse(cateff$Data[[i]][,3]==0,0,1e-2*cateff$Data[[i]][,3]/cateff$Data[[i]][,4]);
          }
         else if(nmult == "ind" && unitscat == "ind" && unitsmbw == "ind")
          {
           cateff$Data[[i]]$obscat.ind2    <- ifelse(cateff$Data[[i]][,3]==0,0,cateff$Data[[i]][,3]/cateff$Data[[i]][,4]);
          }
         cateff$Data[[i]]$spikecat  <- unlist(10*(cateff$Data[[i]][5]/max(cateff$Data[[i]][5])-cateff$Data[[i]][2]/max(cateff$Data[[i]][2])));
        }
      }
    else if(step == "week")
      {
       if(paste(substr(season.dates[1],5,5),substr(season.dates[1],8,8),sep="") != "--" || paste(substr(season.dates[2],5,5),substr(season.dates[2],8,8),sep="") != "--")
        {stop("dates of weekly catch dynamics must be a length 2 character vector with dates in the ISO 8601 international standard, i.e. yyyy-mm-dd")}
       if(as.numeric(format(as.Date(season.dates[2],"%Y-%m-%d"), "%Y")) - as.numeric(format(as.Date(season.dates[1],"%Y-%m-%d"), "%Y")) > 1)
         {stop("For a weekly time step the modeling is seasonal, involving no more than two calendar years")}
       if(as.numeric(format(as.Date(season.dates[1],"%Y-%m-%d"), "%Y")) > as.numeric(format(as.Date(season.dates[2],"%Y-%m-%d"), "%Y")))
         {stop("Dates must be arranged in ascending order")}
       if(as.numeric(format(as.Date(season.dates[1],"%Y-%m-%d"), "%Y")) == as.numeric(format(as.Date(season.dates[2],"%Y-%m-%d"), "%Y")) &&
          as.numeric(format(as.Date(season.dates[1],"%Y-%m-%d"), "%m")) >  as.numeric(format(as.Date(season.dates[2],"%Y-%m-%d"), "%m")))
         {stop("Dates must be arranged in ascending order")}          
       if(as.numeric(format(as.Date(season.dates[1],"%Y-%m-%d"), "%Y")) == as.numeric(format(as.Date(season.dates[2],"%Y-%m-%d"), "%Y")) &&
          as.numeric(format(as.Date(season.dates[1],"%Y-%m-%d"), "%m")) == as.numeric(format(as.Date(season.dates[2],"%Y-%m-%d"), "%m")) &&
          as.numeric(format(as.Date(season.dates[1],"%Y-%m-%d"), "%d")) >  as.numeric(format(as.Date(season.dates[2],"%Y-%m-%d"), "%d")))
         {stop("Dates must be arranged in ascending order")}          
       start         <- as.numeric(format(as.Date(season.dates[1],"%Y-%m-%d"),"%W"));
       (if(as.numeric(format(as.Date(season.dates[1],"%Y-%m-%d"), "%Y")) == as.numeric(format(as.Date(season.dates[2],"%Y-%m-%d"), "%Y"))) 
          {end <- as.numeric(format(as.Date(season.dates[2],"%Y-%m-%d"),"%W"))}
        else 
          {end <- as.numeric(format(as.Date(paste(substr(season.dates[1],1,4),"-12-31",sep="")),"%W")) + 1 +
                     as.numeric(format(as.Date(season.dates[2],"%Y-%m-%d"),"%W"))})
       for(i in 1:length(fleet.name))
         {
#         if(length(start:end) != length(x[,coleff[i]]))
#           {stop("Check season.dates, you have a number of weeks that is not identical to the number of effort/catch/mean body weight observations \n Consider changing the dates")}
         cateff$Data[[i]]              <- data.frame(time.step=start:end,x[,coleff[i]],x[,colcat[i]],x[,colmbw[i]]);
         names(cateff$Data[[i]])[2:4]  <-c(paste("obseff.",unitseff[i],sep=""),
                                           paste("obscat.",unitscat,sep=""),
                                           paste("obsmbw.",unitsmbw,sep="")); 
         if(nmult == "bill" && unitscat == "ton" && unitsmbw == "g")
          { 
           cateff$Data[[i]]$obscat.bill    <- ifelse(cateff$Data[[i]][,3]==0,0,1e-9*1e6*cateff$Data[[i]][,3]/cateff$Data[[i]][,4]);
          }
         else if(nmult == "bill" && unitscat == "ton" && unitsmbw == "kg")
          {
           cateff$Data[[i]]$obscat.bill    <- ifelse(cateff$Data[[i]][,3]==0,0,1e-9*1e3*cateff$Data[[i]][,3]/cateff$Data[[i]][,4]);
          }
         else if(nmult == "bill" && unitscat == "kg" && unitsmbw == "g")
          {
           cateff$Data[[i]]$obscat.bill    <- ifelse(cateff$Data[[i]][,3]==0,0,1e-9*1e3*cateff$Data[[i]][,3]/cateff$Data[[i]][,4]);
          }
         else if(nmult == "bill" && unitscat == "kg" && unitsmbw == "kg")
          {
           cateff$Data[[i]]$obscat.bill    <- ifelse(cateff$Data[[i]][,3]==0,0,1e-9*cateff$Data[[i]][,3]/cateff$Data[[i]][,4]);
          }
         else if(nmult == "mill" && unitscat == "ton" && unitsmbw == "g")
          { 
           cateff$Data[[i]]$obscat.mill    <- ifelse(cateff$Data[[i]][,3]==0,0,1e-6*1e6*cateff$Data[[i]][,3]/cateff$Data[[i]][,4]);
          }
         else if(nmult == "mill" && unitscat == "ton" && unitsmbw == "kg")
          {
           cateff$Data[[i]]$obscat.mill    <- ifelse(cateff$Data[[i]][,3]==0,0,1e-6*1e3*cateff$Data[[i]][,3]/cateff$Data[[i]][,4]);
          }
         else if(nmult == "mill" && unitscat == "kg" && unitsmbw == "g")
          {
           cateff$Data[[i]]$obscat.mill    <- ifelse(cateff$Data[[i]][,3]==0,0,1e-6*1e3*cateff$Data[[i]][,3]/cateff$Data[[i]][,4]);
          }
         else if(nmult == "mill" && unitscat == "kg" && unitsmbw == "kg")
          {
           cateff$Data[[i]]$obscat.mill    <- ifelse(cateff$Data[[i]][,3]==0,0,1e-6*cateff$Data[[i]][,3]/cateff$Data[[i]][,4]);
          }
         else if(nmult == "thou" && unitscat == "ton" && unitsmbw == "g")
          {
           cateff$Data[[i]]$obscat.thou    <- ifelse(cateff$Data[[i]][,3]==0,0,1e-3*1e6*cateff$Data[[i]][,3]/cateff$Data[[i]][,4]);
          }
         else if(nmult == "thou" && unitscat == "ton" && unitsmbw == "kg")
          {
           cateff$Data[[i]]$obscat.thou    <- ifelse(cateff$Data[[i]][,3]==0,0,1e-3*1e3*cateff[,4][[i]]/cateff$Data[[i]][,4]);
          }
         else if(nmult == "thou" && unitscat == "kg" && unitsmbw == "g")
          {
           cateff$Data[[i]]$obscat.thou    <- ifelse(cateff$Data[[i]][,3]==0,0,1e-3*1e3*cateff$Data[[i]][,3]/cateff$Data[[i]][,4]);
          }
         else if(nmult == "thou" && unitscat == "kg" && unitsmbw == "kg")
          {
           cateff$Data[[i]]$obscat.thou    <- ifelse(cateff$Data[[i]][,3]==0,0,1e-3*cateff$Data[[i]][,3]/cateff$Data[[i]][,4]);
          }
         else if(nmult == "hund" && unitscat == "ton" && unitsmbw == "g")
          {
           cateff$Data[[i]]$obscat.hund    <- ifelse(cateff$Data[[i]][,3]==0,0,1e-2*1e6*cateff$Data[[i]][,3]/cateff$Data[[i]][,4]);
          }
         else if(nmult == "hund" && unitscat == "ton" && unitsmbw == "kg")
          {
           cateff$Data[[i]]$obscat.hund    <- ifelse(cateff$Data[[i]][,3]==0,0,1e-2*1e3*cateff$Data[[i]][,3]/cateff$Data[[i]][,4]);
          }
         else if(nmult == "hund" && unitscat == "kg" && unitsmbw == "g")
          {
           cateff$Data[[i]]$obscat.hund    <- ifelse(cateff$Data[[i]][,3]==0,0,1e-2*1e3*cateff$Data[[i]][,3]/cateff$Data[[i]][,4]);
          }
         else if(nmult == "hund" && unitscat == "kg" && unitsmbw == "kg")
          {
           cateff$Data[[i]]$obscat.hund    <- ifelse(cateff$Data[[i]][,3]==0,0,1e-2*cateff$Data[[i]][,3]/cateff$Data[[i]][,4]);
          }
         else if(nmult == "bill" && unitscat == "ind" && unitsmbw == "ind")
          {
           cateff$Data[[i]]$obscat.bill    <- ifelse(cateff$Data[[i]][,3]==0,0,1e-9*cateff$Data[[i]][,3]/cateff$Data[[i]][,4]);
          }
         else if(nmult == "mill" && unitscat == "ind" && unitsmbw == "ind")
          {
           cateff$Data[[i]]$obscat.mill    <- ifelse(cateff$Data[[i]][,3]==0,0,1e-6*cateff$Data[[i]][,3]/cateff$Data[[i]][,4]);
          }
         else if(nmult == "thou" && unitscat == "ind" && unitsmbw == "ind")
          {
           cateff$Data[[i]]$obscat.thou    <- ifelse(cateff$Data[[i]][,3]==0,0,1e-3*cateff$Data[[i]][,3]/cateff$Data[[i]][,4]);
          }
         else if(nmult == "hund" && unitscat == "ind" && unitsmbw == "ind")
          {
           cateff$Data[[i]]$obscat.hund    <- ifelse(cateff$Data[[i]][,3]==0,0,1e-2*cateff$Data[[i]][,3]/cateff$Data[[i]][,4]);
          }
         else if(nmult == "ind" && unitscat == "ind" && unitsmbw == "ind")
          {
           cateff$Data[[i]]$obscat.ind2    <- ifelse(cateff$Data[[i]][,3]==0,0,cateff$Data[[i]][,3]/cateff$Data[[i]][,4]);
          }
         cateff$Data[[i]]$spikecat  <- unlist(10*(cateff$Data[[i]][5]/max(cateff$Data[[i]][5])-cateff$Data[[i]][2]/max(cateff$Data[[i]][2])));
        }
      }
    else
      {
       if(paste(substr(season.dates[1],5,5),substr(season.dates[1],8,8),sep="") != "--" || paste(substr(season.dates[2],5,5),substr(season.dates[2],8,8),sep="") != "--")
         {stop("dates of monthly catch dynamics must be a length 2 character vector with dates in the ISO 8601 international standard, i.e. yyyy-mm-dd")}
       if(as.numeric(format(as.Date(season.dates[1],"%Y-%m-%d"), "%Y")) > as.numeric(format(as.Date(season.dates[2],"%Y-%m-%d"), "%Y")))
         {stop("Dates must be arranged in ascending order")}
       if(as.numeric(format(as.Date(season.dates[1],"%Y-%m-%d"), "%Y")) == as.numeric(format(as.Date(season.dates[2],"%Y-%m-%d"), "%Y")) &&
          as.numeric(format(as.Date(season.dates[1],"%Y-%m-%d"), "%m")) >  as.numeric(format(as.Date(season.dates[2],"%Y-%m-%d"), "%m")))
         {stop("Dates must be arranged in ascending order")}          
       if(as.numeric(format(as.Date(season.dates[1],"%Y-%m-%d"), "%Y")) == as.numeric(format(as.Date(season.dates[2],"%Y-%m-%d"), "%Y")) &&
          as.numeric(format(as.Date(season.dates[1],"%Y-%m-%d"), "%m")) == as.numeric(format(as.Date(season.dates[2],"%Y-%m-%d"), "%m")) &&
          as.numeric(format(as.Date(season.dates[1],"%Y-%m-%d"), "%d")) >  as.numeric(format(as.Date(season.dates[2],"%Y-%m-%d"), "%d")))
         {stop("Dates must be arranged in ascending order")}          
       start         <- as.numeric(format(as.Date(season.dates[1],"%Y-%m-%d"),"%m"));
       end           <- as.numeric(format(as.Date(season.dates[2],"%Y-%m-%d"),"%m"))*
                       (as.numeric(format(as.Date(season.dates[2],"%Y-%m-%d"),"%Y"))-as.numeric(format(as.Date(season.dates[1],"%Y-%m-%d"),"%Y"))+1);
       if(start >= end) {stop("Dates must be arranged in ascending order")}
       if(as.numeric(format(as.Date(season.dates[1],"%Y-%m-%d"),"%m")) > 1)
         {stop("For multi-annual models with monthly time step the catch and effort data must start in January of the first year. \n If the fishing season starts at a later month, add lines with 0s to the catch and effort of earlier months backward to January")}
       if(as.numeric(format(as.Date(season.dates[2],"%Y-%m-%d"),"%m")) < 12)
         {stop("For multi-annual models with monthly time step the catch and effort data must end in December of the last year. \n If the fishing season ends at an earlier month, add lines with 0s to the catch and effort of later months forward to December")}
       for(i in 1:length(fleet.name))
         {
         cateff$Data[[i]]              <- data.frame(time.step=seq(start,end,1),x[,coleff[i]],x[,colcat[i]],x[,colmbw[i]]);
         names(cateff$Data[[i]])[2:4]  <-c(paste("obseff.",unitseff[i],sep=""),
                                           paste("obscat.",unitscat,sep=""),
                                           paste("obsmbw.",unitsmbw,sep="")); 
         if(nmult == "bill" && unitscat == "ton" && unitsmbw == "g")
          { 
           cateff$Data[[i]]$obscat.bill    <- ifelse(cateff$Data[[i]][,3]==0,0,1e-9*1e6*cateff$Data[[i]][,3]/cateff$Data[[i]][,4]);
          }
         else if(nmult == "bill" && unitscat == "ton" && unitsmbw == "kg")
          {
           cateff$Data[[i]]$obscat.bill    <- ifelse(cateff$Data[[i]][,3]==0,0,1e-9*1e3*cateff$Data[[i]][,3]/cateff$Data[[i]][,4]);
          }
         else if(nmult == "bill" && unitscat == "kg" && unitsmbw == "g")
          {
           cateff$Data[[i]]$obscat.bill    <- ifelse(cateff$Data[[i]][,3]==0,0,1e-9*1e3*cateff$Data[[i]][,3]/cateff$Data[[i]][,4]);
          }
         else if(nmult == "bill" && unitscat == "kg" && unitsmbw == "kg")
          {
           cateff$Data[[i]]$obscat.bill    <- ifelse(cateff$Data[[i]][,3]==0,0,1e-9*cateff$Data[[i]][,3]/cateff$Data[[i]][,4]);
          }
         else if(nmult == "mill" && unitscat == "ton" && unitsmbw == "g")
          { 
           cateff$Data[[i]]$obscat.mill    <- ifelse(cateff$Data[[i]][,3]==0,0,1e-6*1e6*cateff$Data[[i]][,3]/cateff$Data[[i]][,4]);
          }
         else if(nmult == "mill" && unitscat == "ton" && unitsmbw == "kg")
          {
           cateff$Data[[i]]$obscat.mill    <- ifelse(cateff$Data[[i]][,3]==0,0,1e-6*1e3*cateff$Data[[i]][,3]/cateff$Data[[i]][,4]);
          }
         else if(nmult == "mill" && unitscat == "kg" && unitsmbw == "g")
          {
           cateff$Data[[i]]$obscat.mill    <- ifelse(cateff$Data[[i]][,3]==0,0,1e-6*1e3*cateff$Data[[i]][,3]/cateff$Data[[i]][,4]);
          }
         else if(nmult == "mill" && unitscat == "kg" && unitsmbw == "kg")
          {
           cateff$Data[[i]]$obscat.mill    <- ifelse(cateff$Data[[i]][,3]==0,0,1e-6*cateff$Data[[i]][,3]/cateff$Data[[i]][,4]);
          }
         else if(nmult == "thou" && unitscat == "ton" && unitsmbw == "g")
          {
           cateff$Data[[i]]$obscat.thou    <- ifelse(cateff$Data[[i]][,3]==0,0,1e-3*1e6*cateff$Data[[i]][,3]/cateff$Data[[i]][,4]);
          }
         else if(nmult == "thou" && unitscat == "ton" && unitsmbw == "kg")
          {
           cateff$Data[[i]]$obscat.thou    <- ifelse(cateff$Data[[i]][,3]==0,0,1e-3*1e3*cateff[,3][[i]]/cateff$Data[[i]][,4]);
          }
         else if(nmult == "thou" && unitscat == "kg" && unitsmbw == "g")
          {
           cateff$Data[[i]]$obscat.thou    <- ifelse(cateff$Data[[i]][,3]==0,0,1e-3*1e3*cateff$Data[[i]][,3]/cateff$Data[[i]][,4]);
          }
         else if(nmult == "thou" && unitscat == "kg" && unitsmbw == "kg")
          {
           cateff$Data[[i]]$obscat.thou    <- ifelse(cateff$Data[[i]][,3]==0,0,1e-3*cateff$Data[[i]][,3]/cateff$Data[[i]][,4]);
          }
         else if(nmult == "hund" && unitscat == "ton" && unitsmbw == "g")
          {
           cateff$Data[[i]]$obscat.hund    <- ifelse(cateff$Data[[i]][,3]==0,0,1e-2*1e6*cateff$Data[[i]][,3]/cateff$Data[[i]][,4]);
          }
         else if(nmult == "hund" && unitscat == "ton" && unitsmbw == "kg")
          {
           cateff$Data[[i]]$obscat.hund    <- ifelse(cateff$Data[[i]][,3]==0,0,1e-2*1e3*cateff$Data[[i]][,3]/cateff$Data[[i]][,4]);
          }
         else if(nmult == "hund" && unitscat == "kg" && unitsmbw == "g")
          {
           cateff$Data[[i]]$obscat.hund    <- ifelse(cateff$Data[[i]][,3]==0,0,1e-2*1e3*cateff$Data[[i]][,3]/cateff$Data[[i]][,4]);
          }
         else if(nmult == "hund" && unitscat == "kg" && unitsmbw == "kg")
          {
           cateff$Data[[i]]$obscat.hund    <- ifelse(cateff$Data[[i]][,3]==0,0,1e-2*cateff$Data[[i]][,3]/cateff$Data[[i]][,4]);
          }
         else if(nmult == "bill" && unitscat == "ind" && unitsmbw == "ind")
          {
           cateff$Data[[i]]$obscat.bill    <- ifelse(cateff$Data[[i]][,3]==0,0,1e-9*cateff$Data[[i]][,3]/cateff$Data[[i]][,4]);
          }
         else if(nmult == "mill" && unitscat == "ind" && unitsmbw == "ind")
          {
           cateff$Data[[i]]$obscat.mill    <- ifelse(cateff$Data[[i]][,3]==0,0,1e-6*cateff$Data[[i]][,3]/cateff$Data[[i]][,4]);
          }
         else if(nmult == "thou" && unitscat == "ind" && unitsmbw == "ind")
          {
           cateff$Data[[i]]$obscat.thou    <- ifelse(cateff$Data[[i]][,3]==0,0,1e-3*cateff$Data[[i]][,3]/cateff$Data[[i]][,4]);
          }
         else if(nmult == "hund" && unitscat == "ind" && unitsmbw == "ind")
          {
           cateff$Data[[i]]$obscat.hund    <- ifelse(cateff$Data[[i]][,3]==0,0,1e-2*cateff$Data[[i]][,3]/cateff$Data[[i]][,4]);
          }
         else if(nmult == "ind" && unitscat == "ind" && unitsmbw == "ind")
          {
           cateff$Data[[i]]$obscat.ind2    <- ifelse(cateff$Data[[i]][,3]==0,0,cateff$Data[[i]][,3]/cateff$Data[[i]][,4]);
          }
         cateff$Data[[i]]$spikecat  <- unlist(10*(cateff$Data[[i]][5]/max(cateff$Data[[i]][5])-cateff$Data[[i]][2]/max(cateff$Data[[i]][2])));
        }
      }
    oldClass(cateff) <- "CatDynData" 
    return(cateff)
   }