R/checkTree.R

In alexology/biomonitoR: biomonitoring indices and metrics

checkTree <- function(x) {
  x.names <- names(x)

  # reverse x.names order while removing Taxa
  x.check <- rev(x.names)[-1]

  # check if there are duplicates in Taxa column of the tree provided by the user

  # initialize the error message

  mes <- c()

  if (nrow(x) != length(unique(x[, "Taxa"]))) {
    x.taxa <- x[, "Taxa"]
    taxa.dup <- x.taxa[duplicated(x.taxa)]
    taxa.dup <- paste(taxa.dup, collapse = ",")
    mes <- paste("Duplicate names are present in the column Taxa:", taxa.dup)
  }


  row.count <- c()

  for (i in 1:length(x.check)) {
    t.t <- x.check[i]
    if (is.null(row.count) == T | length(row.count) == 0) {
      temp.df <- x
    } else {
      temp.df <- x[-row.count, ]
    }

    t.names <- temp.df[, t.t]
    t.nrow <- which(temp.df[, t.t] != "")
    t.names <- t.names[t.nrow]

    # check if duplicate names are present in the columns of the tree provided by the user

    if ((length(unique(t.names)) - length(t.names)) > 0) {
      mes <- paste("Duplicate names are present in ", t.t, " column")
    }

    # check if there is a mismatch between the taxa in the taxonomic level i and the corresponding rows in the Taxa column
    t.check <- sum(x[t.nrow, "Taxa"] == length(t.names))
    if (t.check != 0) {
      t.diff <- setdiff(t.names, x[t.nrow, "Taxa"])
      mes <- paste("Columns Taxa and", t.t, "differ by: ", t.diff)
    }

    row.count <- c(row.count, t.nrow)
  }
  mes
}