(v0.7.0.9008) T. vaginalis, rsi_df

data-raw/reproduction_of_microorganisms.R

@@ -444,7 +444,43 @@ MOs <- MOs %>%
              fullname = "Beta-haemolytic Streptococcus",
              ref = NA_character_,
              species_id = "",
-             source = "manually added")
+             source = "manually added"),
+    # Trichomonas vaginalis is missing, same order as Dientamoeba
+    MOs %>%
+      filter(fullname == "Dientamoeba") %>%
+      mutate(mo = gsub("DNTMB", "THMNS", mo),
+             col_id = NA,
+             fullname = "Trichomonas",
+             family = "Trichomonadidae",
+             genus = "Trichomonas",
+             source = "manually added",
+             ref = "Donne, 1836",
+             species_id = ""),
+    MOs %>%
+      filter(fullname == "Dientamoeba fragilis") %>%
+      mutate(mo = gsub("DNTMB", "THMNS", mo),
+             mo = gsub("FRA", "VAG", mo),
+             col_id = NA,
+             fullname = "Trichomonas vaginalis",
+             family = "Trichomonadidae",
+             genus = "Trichomonas",
+             species = "vaginalis",
+             source = "manually added",
+             ref = "Donne, 1836",
+             species_id = ""),
+    MOs %>% # add family as such too
+      filter(fullname == "Monocercomonadidae") %>%
+      mutate(mo = gsub("MNCRCMND", "TRCHMNDD", mo),
+             col_id = NA,
+             fullname = "Trichomonadidae",
+             family = "Trichomonadidae",
+             rank = "family",
+             genus = "",
+             species = "",
+             source = "manually added",
+             ref = "",
+             species_id = ""),
+
   )
 
 
@@ -485,8 +521,12 @@ MOs <- MOs %>%
     TRUE ~ 3
   ))
 
+# arrange
+MOs <- MOs %>% arrange(fullname)
+MOs.old <- MOs.old %>% arrange(fullname)
+
 # save it
-MOs <- as.data.frame(MOs %>% arrange(fullname), stringsAsFactors = FALSE)
+MOs <- as.data.frame(MOs, stringsAsFactors = FALSE)
 MOs.old <- as.data.frame(MOs.old, stringsAsFactors = FALSE)
 class(MOs$mo) <- "mo"
 

data-raw/translations.tsv

@@ -154,6 +154,8 @@ pt	vegetative	vegetativo	FALSE	FALSE
 pt	([([ ]*?)group	\\1grupo	FALSE	FALSE
 pt	([([ ]*?)Group	\\1Grupo	FALSE	FALSE
 
+de	clavulanic acid	Clavulansäure	FALSE	TRUE
+
 nl	4-aminosalicylic acid	4-aminosalicylzuur
 nl	Adefovir dipivoxil	Adefovir
 nl	Aldesulfone sodium	Aldesulfon
@@ -348,8 +350,10 @@ nl	Thiamphenicol	Thiamfenicol
 nl	Thioacetazone/isoniazid	Thioacetazon/isoniazide
 nl	Ticarcillin	Ticarcilline
 nl	Ticarcillin/beta-lactamase inhibitor	Ticarcilline/enzymremmer
+nl	Ticarcillin/clavulanic acid	Ticarcilline/clavulaanzuur
 nl	Tinidazole	Tinidazol
 nl	Tobramycin	Tobramycine
+nl	Trimethoprim/sulfamethoxazole	Trimethoprim/sulfamethoxazol
 nl	Troleandomycin	Troleandomycine
 nl	Trovafloxacin	Trovafloxacine
 nl	Vancomycin	Vancomycine