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breakpoints UTI interpretation fix

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dr. M.S. (Matthijs) Berends
2023-07-10 13:41:52 +02:00
parent 3829311dd3
commit 70c601ca11
28 changed files with 605 additions and 150 deletions
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24
data-raw/reproduction_of_clinical_breakpoints.R
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@@ -133,8 +133,11 @@ organisms <- organisms %>%
select(-group) %>%
distinct()
# 2023-07-08 SGM must be Slowly-growing Mycobacterium, not Strep Gamma, not sure why this went wrong
# 2023-07-08 SGM is also Strep gamma in WHONET, must only be Slowly-growing Mycobacterium
organisms <- organisms %>%
filter(!(code == "SGM" & name %like% "Streptococcus"))
# this must be empty:
organisms$code[organisms$code %>% duplicated()]
saveRDS(organisms, "data-raw/organisms.rds", version = 2)
@@ -223,7 +226,7 @@ breakpoints %>%
filter(!WHONET_ABX_CODE %in% whonet_antibiotics$WHONET_ABX_CODE) %>%
pull(WHONET_ABX_CODE) %>%
unique()
# they are at the moment all old codes that have right replacements in `antibiotics`, so we can use as.ab()
# they are at the moment all old codes that have the right replacements in `antibiotics`, so we can use as.ab()
## Build new breakpoints table ----
@@ -260,7 +263,7 @@ breakpoints_new <- breakpoints %>%
gsub("–", "-", ., fixed = TRUE)) %>%
arrange(desc(guideline), mo, ab, type, method) %>%
filter(!(is.na(breakpoint_S) & is.na(breakpoint_R)) & !is.na(mo) & !is.na(ab)) %>%
distinct(guideline, ab, mo, method, site, breakpoint_S, .keep_all = TRUE)
distinct(guideline, type, ab, mo, method, site, breakpoint_S, .keep_all = TRUE)
# check the strange duplicates
breakpoints_new %>%
@@ -268,7 +271,7 @@ breakpoints_new %>%
filter(id %in% .$id[which(duplicated(id))])
# remove duplicates
breakpoints_new <- breakpoints_new %>%
distinct(guideline, ab, mo, method, site, .keep_all = TRUE)
distinct(guideline, type, ab, mo, method, site, .keep_all = TRUE)
# fix reference table names
breakpoints_new %>% filter(guideline %like% "EUCAST", is.na(ref_tbl)) %>% View()
@@ -289,10 +292,10 @@ breakpoints_new[which(breakpoints_new$method == "MIC" &
breakpoints_new[which(breakpoints_new$method == "MIC" &
is.na(breakpoints_new$breakpoint_R)), "breakpoint_R"] <- max(m)
# raise these one higher valid MIC factor level:
breakpoints_new[which(breakpoints_new$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$breakpoint_R == 1025), "breakpoint_R"] <- m[which(m == 1024) + 1]
breakpoints_new[which(breakpoints_new$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"] <- 513
breakpoints_new[which(breakpoints_new$breakpoint_R == 1025), "breakpoint_R"] <- 1024
# WHONET adds one log2 level to the R breakpoint for their software, e.g. in AMC in Enterobacterales:
# EUCAST 2022 guideline: S <= 8 and R > 8
@@ -319,6 +322,9 @@ breakpoints_new %>% filter(guideline == "EUCAST 2023", ab == "AMC", mo == "B_[OR
# compare with current version
clinical_breakpoints %>% filter(guideline == "EUCAST 2022", 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")
# check dimensions
dim(breakpoints_new)
dim(clinical_breakpoints)