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unknown codes, rsi fix

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dr. M.S. (Matthijs) Berends
2019-03-02 22:47:04 +01:00
parent c5efb272fd
commit e835525cf6
31 changed files with 528 additions and 409 deletions
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68
R/mo_property.R
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@ -364,7 +364,7 @@ mo_translate <- function(x, language) {
}
x_tobetranslated <- grepl(x = x,
pattern = "(Coagulase Negative Staphylococcus|Coagulase Positive Staphylococcus|Beta-haemolytic Streptococcus|unknown Gram negatives|unknown Gram positives|CoNS|CoPS|no MO|Gram negative|Gram positive|Bacteria|Fungi|Protozoa|biogroup|biotype|vegetative|group|Group)")
pattern = "(Coagulase Negative Staphylococcus|Coagulase Positive Staphylococcus|Beta-haemolytic Streptococcus|unknown Gram negatives|unknown Gram positives|unknown name|unknown kingdom|unknown phylum|unknown class|unknown order|unknown family|unknown genus|unknown species|unknown subspecies|unknown rank|CoNS|CoPS|Gram negative|Gram positive|Bacteria|Fungi|Protozoa|biogroup|biotype|vegetative|group|Group)")
if (sum(x_tobetranslated, na.rm = TRUE) == 0) {
return(x)
@ -379,9 +379,18 @@ mo_translate <- function(x, language) {
gsub("Beta-haemolytic Streptococcus", "Beta-h\u00e4molytischer Streptococcus", ., fixed = TRUE) %>%
gsub("unknown Gram negatives", "unbekannte Gramnegativen", ., fixed = TRUE) %>%
gsub("unknown Gram positives", "unbekannte Grampositiven", ., fixed = TRUE) %>%
gsub("unknown name", "unbekannte Name", ., fixed = TRUE) %>%
gsub("unknown kingdom", "unbekanntes Reich", ., fixed = TRUE) %>%
gsub("unknown phylum", "unbekannter Stamm", ., fixed = TRUE) %>%
gsub("unknown class", "unbekannte Klasse", ., fixed = TRUE) %>%
gsub("unknown order", "unbekannte Ordnung", ., fixed = TRUE) %>%
gsub("unknown family", "unbekannte Familie", ., fixed = TRUE) %>%
gsub("unknown genus", "unbekannte Gattung", ., fixed = TRUE) %>%
gsub("unknown species", "unbekannte Art", ., fixed = TRUE) %>%
gsub("unknown subspecies", "unbekannte Unterart", ., fixed = TRUE) %>%
gsub("unknown rank", "unbekannter Rang", ., fixed = TRUE) %>%
gsub("(CoNS)", "(KNS)", ., fixed = TRUE) %>%
gsub("(CoPS)", "(KPS)", ., fixed = TRUE) %>%
gsub("(no MO)", "(kein MO)", ., fixed = TRUE) %>%
gsub("Gram negative", "Gramnegativ", ., fixed = TRUE) %>%
gsub("Gram positive", "Grampositiv", ., fixed = TRUE) %>%
gsub("Bacteria", "Bakterien", ., fixed = TRUE) %>%
@ -401,7 +410,16 @@ mo_translate <- function(x, language) {
gsub("Beta-haemolytic Streptococcus", "Beta-hemolytische Streptococcus", ., fixed = TRUE) %>%
gsub("unknown Gram negatives", "onbekende Gram-negatieven", ., fixed = TRUE) %>%
gsub("unknown Gram positives", "onbekende Gram-positieven", ., fixed = TRUE) %>%
gsub("(no MO)", "(geen MO)", ., fixed = TRUE) %>%
gsub("unknown name", "onbekende naam", ., fixed = TRUE) %>%
gsub("unknown kingdom", "onbekend koninkrijk", ., fixed = TRUE) %>%
gsub("unknown phylum", "onbekende fylum", ., fixed = TRUE) %>%
gsub("unknown class", "onbekende klasse", ., fixed = TRUE) %>%
gsub("unknown order", "onbekende orde", ., fixed = TRUE) %>%
gsub("unknown family", "onbekende familie", ., fixed = TRUE) %>%
gsub("unknown genus", "onbekend geslacht", ., fixed = TRUE) %>%
gsub("unknown species", "onbekende soort", ., fixed = TRUE) %>%
gsub("unknown subspecies", "onbekende ondersoort", ., fixed = TRUE) %>%
gsub("unknown rank", "onbekende rang", ., fixed = TRUE) %>%
gsub("(CoNS)", "(CNS)", ., fixed = TRUE) %>%
gsub("(CoPS)", "(CPS)", ., fixed = TRUE) %>%
gsub("Gram negative", "Gram-negatief", ., fixed = TRUE) %>%
@ -423,7 +441,16 @@ mo_translate <- function(x, language) {
gsub("Beta-haemolytic Streptococcus", "Streptococcus Beta-hemol\u00edtico", ., fixed = TRUE) %>%
gsub("unknown Gram negatives", "Gram negativos desconocidos", ., fixed = TRUE) %>%
gsub("unknown Gram positives", "Gram positivos desconocidos", ., fixed = TRUE) %>%
gsub("(no MO)", "(sin MO)", ., fixed = TRUE) %>%
gsub("unknown name", "nombre desconocido", ., fixed = TRUE) %>%
gsub("unknown kingdom", "reino desconocido", ., fixed = TRUE) %>%
gsub("unknown phylum", "filo desconocido", ., fixed = TRUE) %>%
gsub("unknown class", "clase desconocida", ., fixed = TRUE) %>%
gsub("unknown order", "orden desconocido", ., fixed = TRUE) %>%
gsub("unknown family", "familia desconocida", ., fixed = TRUE) %>%
gsub("unknown genus", "g\u00e9nero desconocido", ., fixed = TRUE) %>%
gsub("unknown species", "especie desconocida", ., fixed = TRUE) %>%
gsub("unknown subspecies", "subespecie desconocida", ., fixed = TRUE) %>%
gsub("unknown rank", "rango desconocido", ., fixed = TRUE) %>%
gsub("Gram negative", "Gram negativo", ., fixed = TRUE) %>%
gsub("Gram positive", "Gram positivo", ., fixed = TRUE) %>%
gsub("Bacteria", "Bacterias", ., fixed = TRUE) %>%
@ -443,7 +470,16 @@ mo_translate <- function(x, language) {
gsub("Beta-haemolytic Streptococcus", "Streptococcus Beta-emolitico", ., fixed = TRUE) %>%
gsub("unknown Gram negatives", "Gram negativi sconosciuti", ., fixed = TRUE) %>%
gsub("unknown Gram positives", "Gram positivi sconosciuti", ., fixed = TRUE) %>%
gsub("(no MO)", "(non MO)", ., fixed = TRUE) %>%
gsub("unknown name", "nome sconosciuto", ., fixed = TRUE) %>%
gsub("unknown kingdom", "regno sconosciuto", ., fixed = TRUE) %>%
gsub("unknown phylum", "phylum sconosciuto", ., fixed = TRUE) %>%
gsub("unknown class", "classe sconosciuta", ., fixed = TRUE) %>%
gsub("unknown order", "ordine sconosciuto", ., fixed = TRUE) %>%
gsub("unknown family", "famiglia sconosciuta", ., fixed = TRUE) %>%
gsub("unknown genus", "genere sconosciuto", ., fixed = TRUE) %>%
gsub("unknown species", "specie sconosciute", ., fixed = TRUE) %>%
gsub("unknown subspecies", "sottospecie sconosciute", ., fixed = TRUE) %>%
gsub("unknown rank", "grado sconosciuto", ., fixed = TRUE) %>%
gsub("Gram negative", "Gram negativo", ., fixed = TRUE) %>%
gsub("Gram positive", "Gram positivo", ., fixed = TRUE) %>%
gsub("Bacteria", "Batteri", ., fixed = TRUE) %>%
@ -462,7 +498,16 @@ mo_translate <- function(x, language) {
gsub("Beta-haemolytic Streptococcus", "Streptococcus B\u00eata-h\u00e9molytique", ., fixed = TRUE) %>%
gsub("unknown Gram negatives", "Gram n\u00e9gatifs inconnus", ., fixed = TRUE) %>%
gsub("unknown Gram positives", "Gram positifs inconnus", ., fixed = TRUE) %>%
gsub("(no MO)", "(pas MO)", ., fixed = TRUE) %>%
gsub("unknown name", "nom inconnu", ., fixed = TRUE) %>%
gsub("unknown kingdom", "r\u00e8gme inconnu", ., fixed = TRUE) %>%
gsub("unknown phylum", "embranchement inconnu", ., fixed = TRUE) %>%
gsub("unknown class", "classe inconnue", ., fixed = TRUE) %>%
gsub("unknown order", "ordre inconnu", ., fixed = TRUE) %>%
gsub("unknown family", "famille inconnue", ., fixed = TRUE) %>%
gsub("unknown genus", "genre inconnu", ., fixed = TRUE) %>%
gsub("unknown species", "esp\u00e8ce inconnue", ., fixed = TRUE) %>%
gsub("unknown subspecies", "sous-esp\u00e8ce inconnue", ., fixed = TRUE) %>%
gsub("unknown rank", "rang inconnu", ., fixed = TRUE) %>%
gsub("Gram negative", "Gram n\u00e9gatif", ., fixed = TRUE) %>%
gsub("Gram positive", "Gram positif", ., fixed = TRUE) %>%
gsub("Bacteria", "Bact\u00e9ries", ., fixed = TRUE) %>%
@ -482,7 +527,16 @@ mo_translate <- function(x, language) {
gsub("Beta-haemolytic Streptococcus", "Streptococcus Beta-hemol\u00edtico", ., fixed = TRUE) %>%
gsub("unknown Gram negatives", "Gram negativos desconhecidos", ., fixed = TRUE) %>%
gsub("unknown Gram positives", "Gram positivos desconhecidos", ., fixed = TRUE) %>%
gsub("(no MO)", "(sem MO)", ., fixed = TRUE) %>%
gsub("unknown name", "nome desconhecido", ., fixed = TRUE) %>%
gsub("unknown kingdom", "reino desconhecido", ., fixed = TRUE) %>%
gsub("unknown phylum", "filo desconhecido", ., fixed = TRUE) %>%
gsub("unknown class", "classe desconhecida", ., fixed = TRUE) %>%
gsub("unknown order", "ordem desconhecido", ., fixed = TRUE) %>%
gsub("unknown family", "fam\u00edlia desconhecida", ., fixed = TRUE) %>%
gsub("unknown genus", "g\u00eanero desconhecido", ., fixed = TRUE) %>%
gsub("unknown species", "esp\u00e9cies desconhecida", ., fixed = TRUE) %>%
gsub("unknown subspecies", "subesp\u00e9cies desconhecida", ., fixed = TRUE) %>%
gsub("unknown rank", "classifica\u00e7\u00e3o desconhecido", ., fixed = TRUE) %>%
gsub("Gram negative", "Gram negativo", ., fixed = TRUE) %>%
gsub("Gram positive", "Gram positivo", ., fixed = TRUE) %>%
gsub("Bacteria", "Bact\u00e9rias", ., fixed = TRUE) %>%