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(v2.1.1.9196) fix eucast, unit tests

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dr. M.S. (Matthijs) Berends
2025-03-13 15:38:39 +01:00
parent 9aab129ea6
commit 861331b1df
25 changed files with 114 additions and 97 deletions
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8
data-raw/reproduction_of_clinical_breakpoints.R
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@@ -343,6 +343,14 @@ breakpoints_new$mo[breakpoints_new$mo == "B_STPHY" & breakpoints_new$ab == "NIT"
# WHONET sets the 2023 breakpoints for SAM to MIC of 16/32 for Enterobacterales, should be MIC 8/32 like AMC (see issue #123 on github.com/msberends/AMR)
# UPDATE 2024-02-22: fixed now
# There's a problem with C. diff in EUCAST where breakpoint_R is missing - they are listed as normal human breakpoints but are ECOFF
rows <- which(breakpoints_new$guideline %like% "EUCAST" & breakpoints_new$mo == "B_CRDDS_DFFC" & is.na(breakpoints_new$breakpoint_R) & !is.na(breakpoints_new$breakpoint_S))
breakpoints_new$type[rows] <- "ECOFF"
breakpoints_new$host[rows] <- "ECOFF"
breakpoints_new$ref_tbl[rows] <- "ECOFF"
breakpoints_new$breakpoint_R[rows] <- breakpoints_new$breakpoint_S[rows]
breakpoints_new <- distinct(breakpoints_new, .keep_all = TRUE)
# determine rank again now that some changes were made on taxonomic level (genus -> species)
breakpoints_new <- breakpoints_new %>%
mutate(rank_index = case_when(