fix for Salmonella group A, unit tests

R/aa_globals.R

@@ -94,7 +94,9 @@ TAXONOMY_VERSION <- list(
 )
 
 globalVariables(c(
+  ".mo",
   ".rowid",
+  ".syndromic_group",
   "ab",
   "ab_txt",
   "affect_ab_name",
@@ -105,8 +107,10 @@ globalVariables(c(
   "atc_group1",
   "atc_group2",
   "base_ab",
-  "ci_min",
+  "bind_rows",
   "ci_max",
+  "ci_min",
+  "clinical_breakpoints",
   "code",
   "cols",
   "count",
@@ -130,14 +134,15 @@ globalVariables(c(
   "language",
   "lookup",
   "method",
-  "mic",
   "mic ",
+  "mic",
   "microorganism",
   "microorganisms",
   "microorganisms.codes",
   "mo",
   "name",
   "new",
+  "numerator",
   "observations",
   "old",
   "old_name",
@@ -149,13 +154,14 @@ globalVariables(c(
   "reference.rule_group",
   "reference.version",
   "rowid",
-  "sir",
-  "clinical_breakpoints",
   "rule_group",
   "rule_name",
   "se_max",
   "se_min",
+  "SI",
+  "sir",
   "species",
+  "syndromic_group",
   "total",
   "txt",
   "type",

R/bug_drug_combinations.R

@@ -165,7 +165,7 @@ bug_drug_combinations <- function(x,
     out <- run_it(x)
   }
   rownames(out) <- NULL
-  out <- out %>% pm_arrange(mo, ab)
+  out <- out %pm>% pm_arrange(mo, ab)
   out <- as_original_data_class(out, class(x.bak)) # will remove tibble groups
   structure(out, class = c("bug_drug_combinations", ifelse(data_has_groups, "grouped", character(0)), class(out)))
 }

R/mo.R

@@ -966,14 +966,14 @@ convert_colloquial_input <- function(x) {
   out[x %like_case% "(viridans.* (strepto|^s).*|^vgs[^a-z]*$)"] <- "B_STRPT_VIRI"
 
   # Salmonella in different languages, like "Salmonella grupo B"
-  out[x %like_case% "salmonella.* [bcd]$"] <- gsub(".*salmonella.* ([bcd])$",
+  out[x %like_case% "salmonella.* [abcd]$"] <- gsub(".*salmonella.* ([abcd])$",
     "B_SLMNL_GRP\\U\\1",
-    x[x %like_case% "salmonella.* [bcd]$"],
+    x[x %like_case% "salmonella.* [abcd]$"],
     perl = TRUE
   )
-  out[x %like_case% "group [bcd] salmonella"] <- gsub(".*group ([bcd]) salmonella*",
+  out[x %like_case% "group [abcd] salmonella"] <- gsub(".*group ([abcd]) salmonella*",
     "B_SLMNL_GRP\\U\\1",
-    x[x %like_case% "group [bcd] salmonella"],
+    x[x %like_case% "group [abcd] salmonella"],
     perl = TRUE
   )
 

R/mo_property.R

@@ -69,9 +69,8 @@
 #' @return
 #' - An [integer] in case of [mo_year()]
 #' - An [ordered factor][factor] in case of [mo_pathogenicity()]
-#' - A [list] in case of [mo_taxonomy()], [mo_synonyms()] and [mo_info()]
+#' - A [list] in case of [mo_taxonomy()], [mo_synonyms()], [mo_snomed()] and [mo_info()]
 #' - A named [character] in case of [mo_url()]
-#' - A [numeric] in case of [mo_snomed()]
 #' - A [character] in all other cases
 #' @export
 #' @seealso Data set [microorganisms]