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add strep groups to ABCG

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dr. M.S. (Matthijs) Berends
2023-07-12 11:41:25 +01:00
parent 66eeeb4b88
commit 7cd9ca274c
7 changed files with 12 additions and 39 deletions
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data-raw/reproduction_of_clinical_breakpoints.R
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@@ -297,6 +297,9 @@ breakpoints_new[which(breakpoints_new$breakpoint_R == 257), "breakpoint_R"] <- 2
breakpoints_new[which(breakpoints_new$breakpoint_R == 513), "breakpoint_R"] <- 512
breakpoints_new[which(breakpoints_new$breakpoint_R == 1025), "breakpoint_R"] <- 1024
# fix streptococci in WHONET table of EUCAST: Strep A, B, C and G now includes all streptococci:
clinical_breakpoints$mo[clinical_breakpoints$mo == "B_STRPT" & clinical_breakpoints$ref_tbl %like% "strep.* a.* b.*c.*g"] <- as.mo("B_STRPT_ABCG")
# 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
# WHONET file: S <= 8 and R >= 16