R/ConvertFishbaseFood.R

In sborstein/dietr: Diet Estimated Trophic Levels

#' Converts FishBase/SealifBase food item diet data obtained from the diet function into a usable format for dietr
#' @param FishBaseFood a data frame produced by the rfishbase fooditem function
#' @param ExcludeStage a character, indicating which life stages to exclude. Must match stage names given by rfishbase (i.e. larvae, rec./juveniles, juv./adults, adults).
#' @return a list of length two, with two data frames. One containing the re-formatted food item data and one containing the Taxonomy with species names.
#' @details This converts the data frame produced by rfishbase fooditem function into a usable format for dietr.
#' @author Samuel Borstein
#' @examplesIf interactive()
#' \donttest{
#' #Get rfishbase food item data for a few species
#' my.food <- try(as.data.frame(rfishbase::fooditems(c("Lutjanus apodus","Epinephelus itajara"))))
#' if (!"try-error" %in% class(my.food)) {
#' #use the ConvertFishbaseFood function to format it for dietr and exclude recruits/juveniles
#' cleaned.food <- ConvertFishbaseFood(FishBaseFood=my.food, ExcludeStage=c("larvae","recruits/juv."))
#' cleaned.food
#' }
#' }
#' @export

ConvertFishbaseFood <- function(FishBaseFood,ExcludeStage=NULL){
  if(!length(colnames(FishBaseFood))==30){#check if right format
    stop('Error: Not Raw rfishbase Food Data')#kill if it is not right format
  }else{
    unique.life <- unique(FishBaseFood$PredatorStage)#get the life stages to exclude
    if(!is.null(ExcludeStage)){
    for(ExcludeStage.index in 1:length(ExcludeStage)){#trim exclude lifestages out
      FishBaseFood <- subset(FishBaseFood,!FishBaseFood$PredatorStage==ExcludeStage[ExcludeStage.index])#subset bad lifestages
    }
      Taxonomy <- as.data.frame(FishBaseFood$Species,stringsAsFactors = F)
      colnames(Taxonomy)<-"Species"
      FoodItems <- cbind.data.frame(FishBaseFood$Species,FishBaseFood$FoodI,FishBaseFood$FoodII,FishBaseFood$FoodIII,FishBaseFood$PreyStage)
      colnames(FoodItems) <- c("Species","FoodI","FoodII","FoodIII","Stage")
      ConvertedStuff <- list(FoodItems,Taxonomy)
      names(ConvertedStuff) <- c("FoodItems","Taxonomy") 
    }else{
    Taxonomy <- as.data.frame(unique(FishBaseFood$Species),stringsAsFactors = F)
    colnames(Taxonomy) <- "Species"
    FoodItems <- cbind(FishBaseFood$Species,FishBaseFood$FoodI,FishBaseFood$FoodII,FishBaseFood$FoodIII,FishBaseFood$PreyStage)
    colnames(FoodItems) <- c("Species","FoodI","FoodII","FoodIII","Stage")
    FoodItems <- as.data.frame(FoodItems, stringsAsFactors = F)
    ConvertedStuff <- list(FoodItems,Taxonomy)
    names(ConvertedStuff) <- c("FoodItems","Taxonomy")
    }
  ConvertedStuff
  }
}