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(v2.1.1.9141) new AMR selectors, eucast overwrite arg

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dr. M.S. (Matthijs) Berends
2025-02-07 18:01:22 +01:00
parent baea4323c7
commit 8ba2e4ed94
42 changed files with 282 additions and 197 deletions
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4
data-raw/reproduction_of_clinical_breakpoints.R
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@@ -269,8 +269,8 @@ breakpoints_new <- breakpoints %>%
) %>%
# Greek symbols and EM dash symbols are not allowed by CRAN, so replace them with ASCII:
mutate(disk_dose = disk_dose %>%
gsub("μ", "u", ., fixed = TRUE) %>% # this is 'mu', \u03bc
gsub("µ", "u", ., fixed = TRUE) %>% # this is 'micro', u00b5 (yes, they look the same)
gsub("μ", "mc", ., fixed = TRUE) %>% # this is 'mu', \u03bc
gsub("µ", "mc", ., fixed = TRUE) %>% # this is 'micro', \u00b5 (yes, they look the same)
gsub("–", "-", ., fixed = TRUE)) %>%
arrange(desc(guideline), mo, ab, type, method) %>%
filter(!(is.na(breakpoint_S) & is.na(breakpoint_R)) & !is.na(mo) & !is.na(ab)) %>%