unit tests

R/mo.R

@@ -385,7 +385,7 @@ as.mo <- function(x,
   lpsn_matches <- AMR::microorganisms$lpsn_renamed_to[match(out, AMR::microorganisms$mo)]
   lpsn_matches[!lpsn_matches %in% AMR::microorganisms$lpsn] <- NA
   # GBIF only for non-bacteria, since we use LPSN as primary source for bacteria
-  # (example is Strep anginosus, renamed according to GBIF, not according to LPSN)
+  # (an example is Strep anginosus, renamed according to GBIF, not according to LPSN)
   gbif_matches <- AMR::microorganisms$gbif_renamed_to[AMR::microorganisms$kingdom != "Bacteria"][match(out, AMR::microorganisms$mo[AMR::microorganisms$kingdom != "Bacteria"])]
   gbif_matches[!gbif_matches %in% AMR::microorganisms$gbif] <- NA
   AMR_env$mo_renamed <- list(

R/mo_property.R

@@ -220,7 +220,7 @@ mo_shortname <- function(x, language = get_AMR_locale(), keep_synonyms = getOpti
   shortnames[shortnames == "S. coagulase-negative"] <- "CoNS"
   shortnames[shortnames == "S. coagulase-positive"] <- "CoPS"
   # exceptions for streptococci: Group A Streptococcus -> GAS
-  shortnames[shortnames %like% "S. group [ABCDFGHK]"] <- paste0("G", gsub("S. group ([ABCDFGHK])", "\\1", shortnames[shortnames %like% "S. group [ABCDFGHK]"], perl = TRUE), "S")
+  shortnames[shortnames %like_case% "S. Group [ABCDFGHK]"] <- paste0("G", gsub("S. Group ([ABCDFGHK])", "\\1", shortnames[shortnames %like_case% "S. Group [ABCDFGHK]"], perl = TRUE), "S")
   # unknown species etc.
   shortnames[shortnames %like% "unknown"] <- paste0("(", trimws2(gsub("[^a-zA-Z -]", "", shortnames[shortnames %like% "unknown"], perl = TRUE)), ")")