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(v2.1.1.9194) new argument for missing R breakpoints - updated from WHONET

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dr. M.S. (Matthijs) Berends
2025-03-12 16:24:38 +01:00
parent e1b7252ff6
commit a7ef22a21e
27 changed files with 15755 additions and 15399 deletions
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16
data-raw/reproduction_of_clinical_breakpoints.R
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@@ -271,7 +271,8 @@ breakpoints_new <- breakpoints %>%
mutate(disk_dose = disk_dose %>%
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)) %>%
gsub("–", "-", ., fixed = TRUE) %>%
gsub("(?<=\\d)(?=[a-zA-Z])", " ", ., perl = TRUE)) %>% # make sure we keep a space after a number, e.g. "1mcg" to "1 mcg"
arrange(desc(guideline), mo, ab, type, method) %>%
filter(!(is.na(breakpoint_S) & is.na(breakpoint_R)) & !is.na(mo) & !is.na(ab)) %>%
distinct(guideline, type, host, ab, mo, method, site, breakpoint_S, .keep_all = TRUE)
@@ -299,7 +300,7 @@ breakpoints_new <- breakpoints_new %>%
m <- unique(as.double(as.mic(levels(as.mic(1)))))
# WHONET has no >1024 but instead uses 1025, 513, etc, so as.mic() cannot be used to clean.
# instead, clean based on MIC factor levels
# instead, raise these one higher valid MIC factor level:
breakpoints_new[which(breakpoints_new$breakpoint_R == 129), "breakpoint_R"] <- m[which(m == 128) + 1]
breakpoints_new[which(breakpoints_new$breakpoint_R == 257), "breakpoint_R"] <- m[which(m == 256) + 1]
breakpoints_new[which(breakpoints_new$breakpoint_R == 513), "breakpoint_R"] <- m[which(m == 512) + 1]
@@ -316,9 +317,9 @@ breakpoints_new %>%
values_fill = list(n = 0)) |>
View()
breakpoints_new[which(breakpoints_new$method == "MIC" &
is.na(breakpoints_new$breakpoint_R)), "breakpoint_R"] <- max(m)
# raise these one higher valid MIC factor level:
# 2025-03-12 don't do this anymore - we now use as.sir(..., substitute_missing_r_breakpoint = TRUE/FALSE, ...)
# breakpoints_new[which(breakpoints_new$method == "MIC" &
# is.na(breakpoints_new$breakpoint_R)), "breakpoint_R"] <- max(m)
# fix streptococci in WHONET table of EUCAST: Strep A, B, C and G must only include these groups and not all streptococci:
@@ -373,7 +374,8 @@ breakpoints_new <- breakpoints_new %>%
breakpoint_R
))
# fill missing R breakpoint where there is an S breakpoint
breakpoints_new[which(is.na(breakpoints_new$breakpoint_R)), "breakpoint_R"] <- breakpoints_new[which(is.na(breakpoints_new$breakpoint_R)), "breakpoint_S"]
# 2025-03-12 don't do this anymore - we now use as.sir(..., substitute_missing_r_breakpoint = TRUE/FALSE, ...)
# breakpoints_new[which(is.na(breakpoints_new$breakpoint_R)), "breakpoint_R"] <- breakpoints_new[which(is.na(breakpoints_new$breakpoint_R)), "breakpoint_S"]
# check the strange duplicates
@@ -392,7 +394,7 @@ breakpoints_new <- breakpoints_new %>%
# check again
breakpoints_new %>% filter(guideline == "EUCAST 2024", ab == "AMC", mo == "B_[ORD]_ENTRBCTR", method == "MIC")
# compare with current version
clinical_breakpoints %>% filter(guideline == "EUCAST 2023", ab == "AMC", mo == "B_[ORD]_ENTRBCTR", method == "MIC")
clinical_breakpoints %>% filter(guideline == "EUCAST 2024", ab == "AMC", mo == "B_[ORD]_ENTRBCTR", method == "MIC")
# must have "human" and "ECOFF"
breakpoints_new %>% filter(mo == "B_STRPT_PNMN", ab == "AMP", guideline == "EUCAST 2020", method == "MIC")