(v0.7.1.9035) cephalosporins and unit tests

data-raw/reproduction_of_antibiotics.R

@@ -294,6 +294,8 @@ antibiotics[which(antibiotics$ab == "RIF"), "name"] <- "Rifampicin"
 # PME and PVM1 (the J0 one) both mean 'Pivmecillinam', so:
 antibiotics <- filter(antibiotics, ab != "PME")
 antibiotics[which(antibiotics$ab == "PVM1"), "ab"] <- "PME"
+# Remove Sinecatechins
+antibiotics <- filter(antibiotics, ab != "SNC")
 # ESBL E-test codes:
 antibiotics[which(antibiotics$ab == "CCV"), "abbreviations"][[1]] <- list(c("xtzl"))
 antibiotics[which(antibiotics$ab == "CAZ"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CAZ"), "abbreviations"][[1]], "xtz", "cefta"))
@@ -304,6 +306,44 @@ antibiotics[which(antibiotics$ab == "CTX"), "abbreviations"][[1]] <- list(c(anti
 
 antibiotics <- antibiotics %>% arrange(name)
 
+# set cephalosporins groups for the ones that could not be determined automatically:
+antibiotics <- antibiotics %>% 
+  mutate(group = case_when(
+    name == "Cefcapene" ~ "Cephalosporins (3rd gen.)",
+    name == "Cefcapene pivoxil" ~ "Cephalosporins (3rd gen.)",
+    name == "Cefditoren pivoxil" ~ "Cephalosporins (3rd gen.)",
+    name == "Cefepime/clavulanic acid" ~ "Cephalosporins (4th gen.)",
+    name == "Cefepime/tazobactam" ~ "Cephalosporins (4th gen.)",
+    name == "Cefetamet pivoxil" ~ "Cephalosporins (3rd gen.)",
+    name == "Cefetecol (Cefcatacol)" ~ "Cephalosporins (4th gen.)",
+    name == "Cefetrizole" ~ "Cephalosporins (unclassified gen.)",
+    name == "Cefoselis" ~ "Cephalosporins (4th gen.)",
+    name == "Cefotaxime/clavulanic acid" ~ "Cephalosporins (3rd gen.)",
+    name == "Cefotaxime/sulbactam" ~ "Cephalosporins (3rd gen.)",
+    name == "Cefotiam hexetil" ~ "Cephalosporins (3rd gen.)",
+    name == "Cefovecin" ~ "Cephalosporins (3rd gen.)",
+    name == "Cefozopran" ~ "Cephalosporins (4th gen.)",
+    name == "Cefpimizole" ~ "Cephalosporins (3rd gen.)",
+    name == "Cefpodoxime proxetil" ~ "Cephalosporins (3rd gen.)",
+    name == "Cefpodoxime/clavulanic acid" ~ "Cephalosporins (3rd gen.)",
+    name == "Cefquinome" ~ "Cephalosporins (4th gen.)",
+    name == "Cefsumide" ~ "Cephalosporins (unclassified gen.)",
+    name == "Ceftaroline" ~ "Cephalosporins (5th gen.)",
+    name == "Ceftaroline/avibactam" ~ "Cephalosporins (5th gen.)",
+    name == "Ceftazidime/avibactam" ~ "Cephalosporins (3rd gen.)",
+    name == "Cefteram" ~ "Cephalosporins (3rd gen.)",
+    name == "Cefteram pivoxil" ~ "Cephalosporins (3rd gen.)",
+    name == "Ceftiofur" ~ "Cephalosporins (3rd gen.)",
+    name == "Ceftizoxime alapivoxil" ~ "Cephalosporins (3rd gen.)",
+    name == "Ceftobiprole" ~ "Cephalosporins (5th gen.)",
+    name == "Ceftobiprole medocaril" ~ "Cephalosporins (5th gen.)",
+    name == "Ceftolozane/enzyme inhibitor" ~ "Cephalosporins (5th gen.)",
+    name == "Ceftolozane/tazobactam" ~ "Cephalosporins (5th gen.)",
+    name == "Cefuroxime axetil" ~ "Cephalosporins (2nd gen.)",
+    TRUE ~ group))
+
+# set as data.frame again
+antibiotics <- as.data.frame(antibiotics, stringsAsFactors = FALSE)
 class(antibiotics$ab) <- "ab"
 
 dim(antibiotics) # for R/data.R

data-raw/translations.tsv

@@ -368,6 +368,8 @@ nl	Cephalosporins (1st gen.)	Cefalosporines (1e gen.)	TRUE	FALSE
 nl	Cephalosporins (2nd gen.)	Cefalosporines (2e gen.)	TRUE	FALSE
 nl	Cephalosporins (3rd gen.)	Cefalosporines (3e gen.)	TRUE	FALSE
 nl	Cephalosporins (4th gen.)	Cefalosporines (4e gen.)	TRUE	FALSE
+nl	Cephalosporins (5th gen.)	Cefalosporines (5e gen.)	TRUE	FALSE
+nl	Cephalosporins (unclassified gen.)	Cefalosporines (ongeclassificeerd)	TRUE	FALSE
 nl	Cephalosporins	Cefalosporines	TRUE	FALSE
 nl	Glycopeptides	Glycopeptiden	TRUE	FALSE
 nl	Macrolides/lincosamides	Macroliden/lincosamiden	TRUE	FALSE