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MO group fixes

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dr. M.S. (Matthijs) Berends
2023-07-12 15:04:48 +01:00
parent 9cf054903b
commit 0c46f61260
28 changed files with 1822 additions and 861 deletions
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18
data-raw/reproduction_of_clinical_breakpoints.R
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@@ -297,8 +297,22 @@ 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")
# fix streptococci in WHONET table of EUCAST: Strep A, B, C and G must only include these groups and not all streptococci:
clinical_breakpoints$mo[clinical_breakpoints$mo == "B_STRPT" & clinical_breakpoints$ref_tbl %like% "^strep.* a.* b.*c.*g"] <- as.mo("B_STRPT_ABCG")
# Haemophilus same error (must only be H. influenzae)
clinical_breakpoints$mo[clinical_breakpoints$mo == "B_HMPHL" & clinical_breakpoints$ref_tbl %like% "^h.* influenzae"] <- as.mo("B_HMPHL_INFL")
# EUCAST says that for H. parainfluenzae the H. influenza rules can be used, so add them
clinical_breakpoints <- clinical_breakpoints %>%
bind_rows(
clinical_breakpoints %>%
filter(guideline %like% "EUCAST", mo == "B_HMPHL_INFL") %>%
mutate(mo = as.mo("B_HMPHL_PRNF"))
) %>%
arrange(desc(guideline), mo, ab, type, method)
# Achromobacter denitrificans is in WHONET included in their A. xylosoxidans table, must be removed
clinical_breakpoints <- clinical_breakpoints %>% filter(mo != as.mo("Achromobacter denitrificans"))
# WHONET contains gentamicin breakpoints for viridans streptocci, which are intrinsic R - they meant genta-high, which is ALSO in their table, so we just remove gentamicin in viridans streptococci
clinical_breakpoints <- clinical_breakpoints %>% filter(!(mo == as.mo("Streptococcus viridans") & ab == "GEN"))
# 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