Remove unnecessary tests

R/match.R

@@ -76,55 +76,3 @@ phenotype_susceptibility <- function (lineage,
   susceptibility_values <- unname(susceptibility_values)
   susceptibility_values
 }
-
-# The 'official' taxonomic ranks supported by this package
-taxonomic_ranks <- c(
-  "Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species")
-
-# Return the first value that is not NA. If all values are NA, return NA. The
-# resultant vector will not have names.
-first_non_na_value <- function (x) {
-  unname(x[whatbacteria::first_true_idx(!is.na(x))])
-}
-
-# For each lineage, return the index of the taxon that is found within the
-# lineage. If no taxa are found, return NA for that element. If multiple taxa
-# are found, we issue a warning and return the index of the first taxon in the
-# vector of taxa.
-match_taxa <- function (lineages, taxa) {
-  n_lineages <- length(lineages)
-  if (length(taxa) == 0) {
-    return(rep_len(NA_character_, length(lineages)))
-  }
-
-  taxa_patterns <- paste0("(?<=__|\\b)(?:", taxa, ")\\b")
-  lineage_matches <- vapply(
-    X = taxa_patterns,
-    FUN = grepl,
-    FUN.VALUE = rep_len(TRUE, n_lineages),
-    x = lineages,
-    perl = TRUE,
-    USE.NAMES = TRUE)
-
-  # If the user passes only one lineage, lineage_matches will be a vector
-  # rather than an array. After some trial and error, I found that it's better
-  # to deal with this at each stage of the computation, rather than trying to
-  # coerce the vector to an array up front.
-  if (n_lineages == 1) {
-    multi_matches <- sum(lineage_matches) > 1
-  } else {
-    multi_matches <- rowSums(lineage_matches) > 1
-  }
-  if (any(multi_matches)) {
-    warning(
-      "The following lineages match more than one taxon:\n",
-      paste(lineages[multi_matches], collapse = "\n"), "\n")
-  }
-
-  if (n_lineages == 1) {
-    taxon_idx <- whatbacteria::first_true_idx(lineage_matches)
-  } else {
-    taxon_idx <- apply(lineage_matches, 1, whatbacteria::first_true_idx)
-  }
-  taxon_idx
-}