R/FindFishbase.R

In DanOvando/DLSA: Library Data Limited Stock Assessment Modules

#' FindFishbase
#'
#' @param Data
#'
#' @return Fishbase life history
#' @export
FindFishbase<- function(Data)
{

#    Data<- GFD
  data(mpack)
  # load('Data/mpack.Rdata')

 Fishbase<- mpack$lh

 Fishbase[is.na(Fishbase)]= NA
 rm(mpack)

 spnames<- unique((Data$SciName[is.na(Data$SciName)==F]))

for (i in 1:length(spnames)){

  show(paste(100*(round(i/length(spnames),2)),'% Done With Fishbase Matching',sep=''))

  lh_match=grepl(spnames[i],Fishbase$sname) #find if species name name matches FB data, locate row

  if (sum(lh_match)>0)
  {

    WhereSpecies<- spnames[i]==Data$SciName
#   WhereVb<- spnames[i]==Data$SciName & is.na(Data$VonBertK)
  WhereVb<- WhereSpecies & is.na(Data$vbk)

  WhereAgeMat<-  WhereSpecies & is.na(Data$AgeMat50)
  WhereLinf<- WhereSpecies & is.na(Data$Linf)
#   WhereTemp<- WhereSpecies & is.na(Data$Temp)

    lh_data=Fishbase[lh_match,] #pull out matching data
#     spcat=lh_data$spcat #identify the species category

    #Add in life history
    Data$Linf[WhereLinf]<- lh_data$maxl[1]
    Data$LinfSource[WhereLinf]<-"FishBase"

     Data$vbk[WhereVb]<-lh_data$vbk[1]
    Data$vbkSource[WhereVb]<-"FishBase"
    Data$AgeMat50[WhereAgeMat]<-lh_data$agem[1]
    Data$AgeMatSource[WhereAgeMat]<-"FishBase"
 } #close if loop

} #close species loop

return(Data)

}