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(v1.7.1.9019) Morganella MIC in EUCAST 2021

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dr. M.S. (Matthijs) Berends
2021-07-12 12:28:41 +02:00
parent 5ccb330b42
commit fc946564d1
30 changed files with 112 additions and 74 deletions
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data-raw/read_EUCAST.R
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@ -118,7 +118,7 @@ read_EUCAST <- function(sheet, file, guideline_name) {
seq(from = 41, to = 49, by = 1),
seq(from = 81, to = 89, by = 1))
has_superscript <- function(x) {
# because due to floating point error 0.1252 is not in:
# because due to floating point error, 0.1252 is not in:
# seq(from = 0.1251, to = 0.1259, by = 0.0001)
sapply(x, function(x) any(near(x, MICs_with_trailing_superscript)))
}
@ -242,3 +242,21 @@ for (i in 2:length(sheets_to_analyse)) {
guideline_name = guideline_name))
, error = function(e) message(e$message))
}
# 2021-07-12 fix for Morganellaceae (check other lines too next time)
morg <- rsi_translation %>%
as_tibble() %>%
filter(ab == "IPM",
guideline == "EUCAST 2021",
mo == as.mo("Enterobacterales")) %>%
mutate(mo = as.mo("Morganellaceae"))
morg[which(morg$method == "MIC"), "breakpoint_S"] <- 0.001
morg[which(morg$method == "MIC"), "breakpoint_R"] <- 4
morg[which(morg$method == "DISK"), "breakpoint_S"] <- 50
morg[which(morg$method == "DISK"), "breakpoint_R"] <- 19
rsi_translation <- rsi_translation %>%
bind_rows(morg) %>%
bind_rows(morg %>%
mutate(guideline = "EUCAST 2020")) %>%
arrange(desc(guideline), ab, mo, method)

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@ -1 +1 @@
1a7fe52f8185c9bb2c470712863d1887
67a83b234f25a303c7944222bea47d73

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data-raw/rsi_translation.txt
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@ -754,6 +754,8 @@
"EUCAST 2021" "MIC" "Staphylococcus saccharolyticus" "Imipenem/relebactam" "Anaerobes, Grampositive" 2 2 FALSE
"EUCAST 2021" "MIC" "Viridans Group Streptococcus (VGS)" "Imipenem/relebactam" "Viridans group streptococci" 2 2 FALSE
"EUCAST 2021" "MIC" "(unknown name)" "Imipenem/relebactam" "PK PD breakpoints" 2 2 FALSE
"EUCAST 2021" "DISK" "Morganellaceae" "Imipenem" "Enterobacterales" "10ug" 50 19 FALSE
"EUCAST 2021" "MIC" "Morganellaceae" "Imipenem" "Enterobacterales" 0.001 4 FALSE
"EUCAST 2021" "DISK" "Enterobacterales" "Imipenem" "Enterobacterales" "10ug" 22 19 FALSE
"EUCAST 2021" "MIC" "Enterobacterales" "Imipenem" "Enterobacterales" 2 4 FALSE
"EUCAST 2021" "DISK" "Acinetobacter" "Imipenem" "Acinetobacter" "10ug" 24 21 FALSE
@ -2542,6 +2544,8 @@
"EUCAST 2020" "MIC" "Staphylococcus saccharolyticus" "Imipenem/relebactam" "Anaerobes, Grampositive" 2 2 FALSE
"EUCAST 2020" "MIC" "Viridans Group Streptococcus (VGS)" "Imipenem/relebactam" "Viridans group streptococci" 2 2 FALSE
"EUCAST 2020" "MIC" "(unknown name)" "Imipenem/relebactam" "PK PD breakpoints" 2 2 FALSE
"EUCAST 2020" "DISK" "Morganellaceae" "Imipenem" "Enterobacterales" "10ug" 50 19 FALSE
"EUCAST 2020" "MIC" "Morganellaceae" "Imipenem" "Enterobacterales" 0.001 4 FALSE
"EUCAST 2020" "DISK" "Enterobacterales" "Imipenem" "Enterobacterales" "10ug" 22 17 FALSE
"EUCAST 2020" "MIC" "Enterobacterales" "Imipenem" "Enterobacterales" 2 4 FALSE
"EUCAST 2020" "DISK" "Acinetobacter" "Imipenem" "Acinetobacter" "10ug" 24 21 FALSE