R/checkBmwpFam.R

In alexology/biomonitoR: biomonitoring indices and metrics

#' @importFrom stats aggregate
checkBmwpFam <- function(DF, famNames, stNames) {
  # initialize the Taxon object with which the aggregation will be done
  # this is needed to avoid warning from R CMD
  Taxon <- NULL

  # transform taxa names to characted
  DF[, "Taxon"] <- as.character(DF[, "Taxon"])

  # subset the taxa that need to be changed
  famCheck <- DF[which(DF[, "Taxon"] %in% famNames[, "Taxon"]), "Taxon"]

  # if taxa that need to be changed are present chenge them, otherwise return the orginal DF
  if (length(famCheck) > 0) {
    for (i in 1:length(famCheck)) {
      taxName <- famCheck[i]
      DF$Taxon[DF$Taxon == taxName] <- as.character(subset(famNames, Taxon == taxName)[, "Correct_Taxon"])
    }

    DF <- aggregate(. ~ Taxon, DF, sum)
    names(DF) <- c("Taxon", stNames)
    return(DF)
  }
  else {
    DF <- DF
    return(DF)
  }
}