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(v2.1.1.9193) new antimicrobials for screening

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dr. M.S. (Matthijs) Berends
2025-03-12 15:09:28 +01:00
parent 067a8aca66
commit e1b7252ff6
30 changed files with 319 additions and 174 deletions
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33
data-raw/reproduction_of_clinical_breakpoints.R
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@@ -222,7 +222,7 @@ unknown <- breakpoints %>%
breakpoints %>%
filter(code %in% unknown) %>%
count(GUIDELINES, YEAR, ORGANISM_CODE, BREAKPOINT_TYPE, sort = TRUE)
# 2024-06-14: these codes are currently: clu, kma, fso, tyi. No clue (are not in MO list of WHONET), and they are only ECOFFs, so remove them:
# 2025-03-11: these codes are currently: clu, kma, fso, tyi. No clue (are not in MO list of WHONET), and they are only ECOFFs, so remove them:
breakpoints <- breakpoints %>%
filter(!is.na(mo))
@@ -235,7 +235,7 @@ breakpoints %>%
filter(!WHONET_ABX_CODE %in% whonet_antibiotics$WHONET_ABX_CODE) %>%
pull(WHONET_ABX_CODE) %>%
unique()
# they are at the moment all old codes that have the right replacements in `antimicrobials`, so we can use as.ab()
# they are at the moment all old codes ("CFC", "ROX", "FIX") that have the right replacements in `antimicrobials`, so we can use as.ab()
## Build new breakpoints table ----
@@ -290,25 +290,36 @@ breakpoints_new[which(breakpoints_new$method == "DISK"), "breakpoint_R"] <- as.d
# regarding animal breakpoints, CLSI has adults and foals for horses, but only for amikacin - only keep adult horses
breakpoints_new %>%
filter(host %like% "foal") %>%
View()
count(guideline, host)
breakpoints_new <- breakpoints_new %>%
filter(host %unlike% "foal") %>%
mutate(host = ifelse(host %like% "horse", "horse", host))
# FIXES FOR WHONET ERRORS ----
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
m <- unique(as.double(as.mic(levels(as.mic(1)))))
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$breakpoint_R == 513), "breakpoint_R"] <- m[which(m == 512) + 1]
breakpoints_new[which(breakpoints_new$breakpoint_R == 1025), "breakpoint_R"] <- m[which(m == 1024) + 1]
# a lot of R breakpoints are missing, though none of the S breakpoints are missing:
anyNA(breakpoints_new$breakpoint_S)
breakpoints_new %>%
filter(is.na(breakpoint_R)) %>%
count(guideline, host) |>
pivot_wider(names_from = host,
values_from = n,
values_fill = list(n = 0)) |>
View()
breakpoints_new[which(breakpoints_new$method == "MIC" &
is.na(breakpoints_new$breakpoint_S)), "breakpoint_S"] <- min(m)
breakpoints_new[which(breakpoints_new$method == "MIC" &
is.na(breakpoints_new$breakpoint_R)), "breakpoint_R"] <- max(m)
is.na(breakpoints_new$breakpoint_R)), "breakpoint_R"] <- max(m)
# raise these one higher valid MIC factor level:
breakpoints_new[which(breakpoints_new$breakpoint_R == 129), "breakpoint_R"] <- 128
breakpoints_new[which(breakpoints_new$breakpoint_R == 257), "breakpoint_R"] <- 256
breakpoints_new[which(breakpoints_new$breakpoint_R == 513), "breakpoint_R"] <- 512
breakpoints_new[which(breakpoints_new$breakpoint_R == 1025), "breakpoint_R"] <- 1024
# fix streptococci in WHONET table of EUCAST: Strep A, B, C and G must only include these groups and not all streptococci:
breakpoints_new$mo[breakpoints_new$mo == "B_STRPT" & breakpoints_new$ref_tbl %like% "^strep.* a.* b.*c.*g"] <- as.mo("B_STRPT_ABCG")