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(v2.1.1.9225) fix geom_hline()/_vline() in MIC plotting, add EUCAT 1.2 in full, add London contribs, fix mo codes, add Kleb pneu complex

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dr. M.S. (Matthijs) Berends
2025-03-26 17:19:17 +01:00
parent 8deaf2c8eb
commit e6f88241b2
53 changed files with 552 additions and 334 deletions
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5
R/custom_eucast_rules.R
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@@ -69,7 +69,7 @@
#' #> 1 Escherichia coli R S S
#' #> 2 Klebsiella pneumoniae R S S
#'
#' eucast_rules(df, rules = "custom", custom_rules = x, info = FALSE)
#' eucast_rules(df, rules = "custom", custom_rules = x, info = FALSE, overwrite = TRUE)
#' #> mo TZP ampi cipro
#' #> 1 Escherichia coli R R S
#' #> 2 Klebsiella pneumoniae R R S
@@ -83,7 +83,7 @@
#' y <- custom_eucast_rules(TZP == "S" & genus == "Klebsiella" ~ aminopenicillins == "S",
#' TZP == "R" & genus == "Klebsiella" ~ aminopenicillins == "R")
#'
#' eucast_rules(df, rules = "custom", custom_rules = y, info = FALSE)
#' eucast_rules(df, rules = "custom", custom_rules = y, info = FALSE, overwrite = TRUE)
#' #> mo TZP ampi cipro
#' #> 1 Escherichia coli R S S
#' #> 2 Klebsiella pneumoniae R R S
@@ -121,6 +121,7 @@
#' rules = "custom",
#' custom_rules = x,
#' info = FALSE,
#' overwrite = TRUE,
#' verbose = TRUE
#' )
#'