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(v1.5.0.9007) updated unit tests

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dr. M.S. (Matthijs) Berends committed 2021-01-18 18:45:43 +01:00
1 parent 4eab095306
commit 27f084d819
17 files changed
+47 -43
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R/mdro.R
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@@ -805,6 +805,7 @@ mdro <- function(x,
x[which(x$genus == "Escherichia" & x$species == "hermannii"), ab_NA(c(TCC, TZP))] <- NA
x[which((x$genus == "Citrobacter" & x$species == "freundii")
| (x$genus == "Enterobacter" & x$species == "aerogenes")
| (x$genus == "Klebsiella" & x$species == "aerogenes") # new name (2017)
| (x$genus == "Enterobacter" & x$species == "cloacae")
| (x$genus == "Hafnia" & x$species == "alvei")
| (x$genus == "Morganella" & x$species == "morganii")
@@ -824,6 +825,7 @@ mdro <- function(x,
x[which((x$genus == "Citrobacter" & x$species == "koseri")
| (x$genus == "Citrobacter" & x$species == "freundii")
| (x$genus == "Enterobacter" & x$species == "aerogenes")
| (x$genus == "Klebsiella" & x$species == "aerogenes") # new name (2017)
| (x$genus == "Enterobacter" & x$species == "cloacae")
| (x$genus == "Escherichia" & x$species == "hermannii")
| (x$genus == "Hafnia" & x$species == "alvei")
@@ -836,6 +838,7 @@ mdro <- function(x,
| (x$genus == "Serratia" & x$species == "marcescens")), ab_NA(AMP)] <- NA
x[which((x$genus == "Citrobacter" & x$species == "freundii")
| (x$genus == "Enterobacter" & x$species == "aerogenes")
| (x$genus == "Klebsiella" & x$species == "aerogenes") # new name (2017)
| (x$genus == "Enterobacter" & x$species == "cloacae")
| (x$genus == "Hafnia" & x$species == "alvei")
| (x$genus == "Morganella" & x$species == "morganii")
@@ -845,6 +848,7 @@ mdro <- function(x,
x[which((x$genus == "Citrobacter" & x$species == "freundii")
| (x$genus == "Citrobacter" & x$species == "koseri")
| (x$genus == "Enterobacter" & x$species == "aerogenes")
| (x$genus == "Klebsiella" & x$species == "aerogenes") # new name (2017)
| (x$genus == "Enterobacter" & x$species == "cloacae")
| (x$genus == "Hafnia" & x$species == "alvei")
| (x$genus == "Providencia" & x$species == "rettgeri")