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Replace RSI with SIR

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This commit is contained in:
Dr. Matthijs Berends
2023-01-21 23:47:20 +01:00
committed by GitHub
parent 24b12024ce
commit 98e62c9af2
127 changed files with 1746 additions and 1648 deletions
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6
data-raw/read_EUCAST.R
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@@ -230,7 +230,7 @@ read_EUCAST <- function(sheet, file, guideline_name) {
mo = ifelse(mo == "", mo_sheet, mo)
) %>%
filter(!(is.na(breakpoint_S) & is.na(breakpoint_R))) %>%
# comply with rsi_translation for now
# comply with clinical_breakpoints for now
transmute(guideline,
method,
site = case_when(
@@ -285,7 +285,7 @@ for (i in 2:length(sheets_to_analyse)) {
}
# 2021-07-12 fix for Morganellaceae (check other lines too next time)
morg <- rsi_translation %>%
morg <- clinical_breakpoints %>%
as_tibble() %>%
filter(
ab == "IPM",
@@ -298,7 +298,7 @@ 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 %>%
clinical_breakpoints <- clinical_breakpoints %>%
bind_rows(morg) %>%
bind_rows(morg %>%
mutate(guideline = "EUCAST 2020")) %>%