microorganisms update, added Salmonella groups

R/data.R

@@ -120,6 +120,7 @@
 #' ### Manual additions
 #' For convenience, some entries were added manually:
 #'
+#' - `r format_included_data_number(which(microorganisms$genus == "Salmonella" & microorganisms$species == "enterica" & microorganisms$source == "manually added"))` entries for the city-like serovars of *Salmonellae*
 #' - 11 entries of *Streptococcus* (beta-haemolytic: groups A, B, C, D, F, G, H, K and unspecified; other: viridans, milleri)
 #' - 2 entries of *Staphylococcus* (coagulase-negative (CoNS) and coagulase-positive (CoPS))
 #' - 1 entry of *Blastocystis* (*B.  hominis*), although it officially does not exist (Noel *et al.* 2005, PMID 15634993)
@@ -140,6 +141,8 @@
 #' * `r TAXONOMY_VERSION$GBIF$citation` Accessed from <`r TAXONOMY_VERSION$GBIF$url`> on `r documentation_date(TAXONOMY_VERSION$GBIF$accessed_date)`.
 #'
 #' * `r TAXONOMY_VERSION$SNOMED$citation` URL: <`r TAXONOMY_VERSION$SNOMED$url`>
+#' 
+#' * Grimont *et al.*. Antigenic Formulae of the Salmonella Serovars, 2007, 9th Edition. WHO Collaborating Centre for Reference and Research on *Salmonella* (WHOCC-SALM).
 #' @seealso [as.mo()], [mo_property()], [microorganisms.codes], [intrinsic_resistant]
 #' @examples
 #' microorganisms

R/mo.R

@@ -429,10 +429,12 @@ as.mo <- function(x,
 
   # Apply Lancefield ----
   if (isTRUE(Lancefield) || Lancefield == "all") {
+    # (using `%like_case%` to also match subspecies)
+    
     # group A - S. pyogenes
-    out[out == "B_STRPT_PYGN"] <- "B_STRPT_GRPA"
+    out[out %like_case% "^B_STRPT_PYGN(_|$)"] <- "B_STRPT_GRPA"
     # group B - S. agalactiae
-    out[out == "B_STRPT_AGLC"] <- "B_STRPT_GRPB"
+    out[out %like_case% "^B_STRPT_AGLC(_|$)"] <- "B_STRPT_GRPB"
     # group C - all subspecies within S. dysgalactiae and S. equi (such as S. equi zooepidemicus)
     out[out %like_case% "^B_STRPT_(DYSG|EQUI)(_|$)"] <- "B_STRPT_GRPC"
     if (Lancefield == "all") {
@@ -441,12 +443,13 @@ as.mo <- function(x,
     }
     # group F - S. anginosus, incl. S. anginosus anginosus and S. anginosus whileyi
     out[out %like_case% "^B_STRPT_ANGN(_|$)"] <- "B_STRPT_GRPF"
-    # group G - only S. dysgalactiae which is also group C, so ignore it here
+    # group G - S. dysgalactiae and S. canis (though dysgalactiae is also group C and will be matched there)
+    out[out %like_case% "^B_STRPT_(DYSG|CANS)(_|$)"] <- "B_STRPT_GRPG"
     # group H - S. sanguinis
-    out[out == "B_STRPT_SNGN"] <- "B_STRPT_GRPH"
+    out[out %like_case% "^B_STRPT_SNGN(_|$)"] <- "B_STRPT_GRPH"
     # group K - S. salivarius, incl. S. salivarius salivariuss and S. salivarius thermophilus
     out[out %like_case% "^B_STRPT_SLVR(_|$)"] <- "B_STRPT_GRPK"
-    # group L - only S. dysgalactiae which is also group C, so ignore it here
+    # group L - only S. dysgalactiae which is also group C & G, so ignore it here
   }
 
   # All unknowns ----