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(v1.3.0.9035) mdro() for EUCAST 3.2, examples cleanup

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dr. M.S. (Matthijs) Berends
2020-09-29 23:35:46 +02:00
parent 68e6e1e329
commit 4e0374af29
94 changed files with 1143 additions and 1165 deletions
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7
man/as.disk.Rd
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@@ -38,7 +38,7 @@ On our website \url{https://msberends.github.io/AMR} you can find \href{https://
}
\examples{
\dontrun{
\donttest{
# transform existing disk zones to the `disk` class
library(dplyr)
df <- data.frame(microorganism = "E. coli",
@@ -46,8 +46,9 @@ df <- data.frame(microorganism = "E. coli",
CIP = 14,
GEN = 18,
TOB = 16)
df <- df \%>\% mutate_at(vars(AMP:TOB), as.disk)
df
df[, 2:5] <- lapply(df[, 2:5], as.disk)
# same with dplyr:
# df \%>\% mutate(across(AMP:TOB, as.disk))
# interpret disk values, see ?as.rsi
as.rsi(x = as.disk(18),