Create "lowest" tax rank for phyloseq

lowest.R

lowest <- function(tax){
  returnPhyseq <- FALSE
  if(class(tax) == "phyloseq"){
    physeq <- tax
    tax <- tax_table(physeq)
    returnPhyseq <- TRUE
  }
  tax <- tax[, colnames(tax) != "lowest"]
  tax <- tax %>% as("matrix")
  low <- tax[,ncol(tax)] %>% as.vector
  for(i in (ncol(tax)-1):1){
    low[low == "unclassified"] <- tax[low == "unclassified",i] %>% as.vector
  }
  tax <- tax %>% cbind(lowest = as.vector(low)) %>% tax_table
  if(returnPhyseq){
    tax_table(physeq) <- tax
    return(physeq)
  }
  else
  	tax
}