R/FormatCCFRPData.R

In DanOvando/DLSA: Library Data Limited Stock Assessment Modules

#' Format CCFRP Data
#'
#' @param Data
#'
#' @return Formatted data
#' @export
FormatCCFRPData<- function(Data)
{
  # Format Length Data ------------------------------------------------------

  #   Data<- iGFD
  LengthDataNames<- c('Fish','Year','Month','Site','Length','LengthType','Sex','Special','MPA','FisheryDependent','MeanLongitude','MeanLatitude')

  LengthData<- as.data.frame(matrix(NA,nrow=dim(Data)[1],ncol=length(LengthDataNames)))

  colnames(LengthData)<- LengthDataNames

  LengthData$Fish<- Data$CommName

  LengthData$Year<- Data$Year

  LengthData$Month<- Data$Month

  LengthData$SiteType<- Data$SiteId

  LengthData$Length<- Data$length_cm

  LengthData$Length[LengthData$Length==0]<- NA

  LengthData$LengthType<- 'cm'

  LengthData$Sex<- 'Unknown'

  LengthData$Special<- paste('Gear is ',Data$Sample_Type,sep='')

  LengthData$MPA<- Data$MPA_or_REF

  LengthData$MPA[LengthData$MPA=='REF']<- 0

  LengthData$MPA[LengthData$MPA=='MPA']<- 1

  LengthData$MPA<- as.numeric(LengthData$MPA)

  LengthData$FisheryDependent<- 1

  LengthData$MeanLongitude<- Data$MeanLon

  LengthData$MeanLatitude<- Data$MeanLat

  # Format Density Data -----------------------------------------------------
  Data$Weight<- Fish$WeightA* Data$length_cm ^ Fish$WeightB


  DensityData<- Data %>%
    group_by(Year,Month,sample_Idcellday) %>%
    summarize(Count=sum(length_cm>0 | is.na(length_cm),na.rm=T),Biomass=sum(Weight,na.rm=T)
              ,SampleArea= mean(Sample_Area,na.rm=T),AreaUnits=unique(Area_units),DistanceFromBorder=mean(Meters.to.MPA.border,na.rm=T)
              ,SampleType=unique(Sample_Type),MPA=unique(MPA_or_REF),
              DistanceProtected=mean(Meters.to.MPA.border,na.rm=T),MeanLongitude=mean(MeanLon,na.rm=T),
              MeanLatitude=mean(MeanLat,na.rm=T),SiteType=unique(SiteId),Fish=unique(CommName))

  DensityData$MPA[DensityData$MPA=='REF']<- 0

  DensityData$MPA[DensityData$MPA=='MPA']<- 1

  DensityData$MPA<- as.numeric(DensityData$MPA)

  DensityData$DistanceProtected[DensityData$MPA==0]<- (DensityData$DistanceProtected*-1)[DensityData$MPA==0]


  # Format CPUE Data -----------------------------------------------------

  CPUEData<- Data %>%
    group_by(Year,Month,sample_Idcellday) %>%
    summarize(Site='All',Count=sum(length_cm>0 | is.na(length_cm),na.rm=T),Biomass=sum(Weight,na.rm=T)
                   ,AnglerHours= sum(Angler_hours,na.rm=T),DistanceFromBorder=mean(Meters.to.MPA.border,na.rm=T)
                   ,SampleType=unique(Sample_Type),MPA=unique(MPA_or_REF),
                   DistanceProtected=mean(Meters.to.MPA.border,na.rm=T),MeanLongitude=mean(MeanLon,na.rm=T),
                   MeanLatitude=mean(MeanLat,na.rm=T),SiteType=unique(SiteId),Fish=unique(CommName))

  CPUEData<- Data %>%
    group_by(Year,Month,sample_Idcellday) %>%
    summarize(Site='All',Count=sum(length_cm>0 | is.na(length_cm),na.rm=T),Biomass=sum(Weight,na.rm=T)
              ,AnglerHours= sum(Angler_hours,na.rm=T),DistanceFromBorder=mean(Meters.to.MPA.border,na.rm=T)
              ,SampleType=unique(Sample_Type),MPA=unique(MPA_or_REF),
              DistanceProtected=mean(Meters.to.MPA.border,na.rm=T),MeanLongitude=mean(MeanLon,na.rm=T),
              MeanLatitude=mean(MeanLat,na.rm=T),SiteType=unique(SiteId),Fish=unique(CommName))

  CPUEData$MPA[CPUEData$MPA=='REF']<- 0

  CPUEData$MPA[CPUEData$MPA=='MPA']<- 1

  CPUEData$MPA<- as.numeric(CPUEData$MPA)

  CPUEData$DistanceProtected[CPUEData$MPA==0]<- CPUEData$DistanceProtected[CPUEData$MPA==0]*-1

  return(list(LengthData=LengthData,DensityData=DensityData,CPUEData=CPUEData))

}