Fix translatable strings

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 2.0.0.9006
+Version: 2.0.0.9007
-Date: 2023-04-14
+Date: 2023-04-15
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
   data analysis and to work with microbial and antimicrobial properties by

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 2.0.0.9006
+# AMR 2.0.0.9007
 
 ## Changed
 * formatting fix for `sir_interpretation_history()`

R/mo.R

@@ -947,25 +947,25 @@ convert_colloquial_input <- function(x) {
   out <- rep(NA_character_, length(x))
 
   # Streptococci, like GBS = Group B Streptococci (B_STRPT_GRPB)
-  out[x %like_case% "^g[abcdfghkl]s$"] <- gsub("g([abcdfghkl])s",
+out[x %like_case% "^g[abcdefghijkl]s$"] <- gsub("g([abcdefghijkl])s",
     "B_STRPT_GRP\\U\\1",
-    x[x %like_case% "^g[abcdfghkl]s$"],
+    x[x %like_case% "^g[abcdefghijkl]s$"],
     perl = TRUE
   )
   # Streptococci in different languages, like "estreptococos grupo B"
-  out[x %like_case% "strepto[ck]o[ck].* [abcdfghkl]$"] <- gsub(".*e?strepto[ck]o[ck].* ([abcdfghkl])$",
+  out[x %like_case% "strepto[ck]o[ck].* [abcdefghijkl]$"] <- gsub(".*e?strepto[ck]o[ck].* ([abcdefghijkl])$",
     "B_STRPT_GRP\\U\\1",
-    x[x %like_case% "strepto[ck]o[ck].* [abcdfghkl]$"],
+    x[x %like_case% "strepto[ck]o[ck].* [abcdefghijkl]$"],
     perl = TRUE
   )
-  out[x %like_case% "strep[a-z]* group [abcdfghkl]$"] <- gsub(".* ([abcdfghkl])$",
+  out[x %like_case% "strep[a-z]* group [abcdefghijkl]$"] <- gsub(".* ([abcdefghijkl])$",
     "B_STRPT_GRP\\U\\1",
-    x[x %like_case% "strep[a-z]* group [abcdfghkl]$"],
+    x[x %like_case% "strep[a-z]* group [abcdefghijkl]$"],
     perl = TRUE
   )
-  out[x %like_case% "group [abcdfghkl] strepto[ck]o[ck]"] <- gsub(".*group ([abcdfghkl]) strepto[ck]o[ck].*",
+  out[x %like_case% "group [abcdefghijkl] strepto[ck]o[ck]"] <- gsub(".*group ([abcdefghijkl]) strepto[ck]o[ck].*",
     "B_STRPT_GRP\\U\\1",
-    x[x %like_case% "group [abcdfghkl] strepto[ck]o[ck]"],
+    x[x %like_case% "group [abcdefghijkl] strepto[ck]o[ck]"],
     perl = TRUE
   )
   out[x %like_case% "ha?emoly.*strep"] <- "B_STRPT_HAEM"
@@ -975,14 +975,14 @@ 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.* [abcd]$"] <- gsub(".*salmonella.* ([abcd])$",
+  out[x %like_case% "salmonella.* [abcdefgh]$"] <- gsub(".*salmonella.* ([abcdefgh])$",
     "B_SLMNL_GRP\\U\\1",
-    x[x %like_case% "salmonella.* [abcd]$"],
+    x[x %like_case% "salmonella.* [abcdefgh]$"],
     perl = TRUE
   )
-  out[x %like_case% "group [abcd] salmonella"] <- gsub(".*group ([abcd]) salmonella*",
+  out[x %like_case% "group [abcdefgh] salmonella"] <- gsub(".*group ([abcdefgh]) salmonella*",
     "B_SLMNL_GRP\\U\\1",
-    x[x %like_case% "group [abcd] salmonella"],
+    x[x %like_case% "group [abcdefgh] salmonella"],
     perl = TRUE
   )
 

data-raw/microorganisms.md5

@@ -1 +1 @@
-3d92820386230a7ac3c9367ce6d96db9
+aec0e9d495ebee3079f9aab766d7a38f

data-raw/reproduction_of_microorganisms.R

@@ -1380,6 +1380,9 @@ for (nm in to_restore) {
 
 # Save to package ---------------------------------------------------------
 
+# set class <mo> if still needed (if you run only this part coming from other scripts)
+class(microorganisms$mo) <- c("mo", "character")
+microorganisms <- microorganisms %>% arrange(fullname)
 usethis::use_data(microorganisms, overwrite = TRUE, version = 2, compress = "xz")
 rm(microorganisms)
 

inst/tinytest/test-mo.R

@@ -280,7 +280,7 @@ expect_equal(length(summary(example_isolates$mo)), 6)
 
 # WHONET codes and NA/NaN
 expect_equal(
-  as.character(as.mo(c("xxx", "na", "nan"), debug = TRUE)),
+  as.character(as.mo(c("xxx", "na", "nan"))),
   rep(NA_character_, 3)
 )
 expect_equal(as.character(as.mo("con")), "UNKNOWN")