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(v1.8.1.9005) as.rsi() fix for EUCAST

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dr. M.S. (Matthijs) Berends
2022-05-10 17:01:37 +02:00
parent d4e22069bc
commit 680e8e7a41
21 changed files with 7475 additions and 7454 deletions
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12
R/rsi.R
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@ -818,18 +818,20 @@ exec_as.rsi <- function(method,
if (is.na(x[i]) | (is.na(get_record$breakpoint_S) & is.na(get_record$breakpoint_R))) {
new_rsi[i] <- NA_character_
} else if (method == "mic") {
new_rsi[i] <- quick_case_when(isTRUE(conserve_capped_values) & x[i] %like% "^<[0-9]" ~ "S",
isTRUE(conserve_capped_values) & x[i] %like% "^>[0-9]" ~ "R",
new_rsi[i] <- quick_case_when(isTRUE(conserve_capped_values) & isTRUE(x[i] %like% "^<[0-9]") ~ "S",
isTRUE(conserve_capped_values) & isTRUE(x[i] %like% "^>[0-9]") ~ "R",
# these basically call `<=.mic()` and `>=.mic()`:
x[i] <= get_record$breakpoint_S ~ "S",
x[i] >= get_record$breakpoint_R ~ "R",
isTRUE(x[i] <= get_record$breakpoint_S) ~ "S",
guideline_coerced %like% "EUCAST" & isTRUE(x[i] > get_record$breakpoint_R) ~ "R",
guideline_coerced %like% "CLSI" & isTRUE(x[i] >= get_record$breakpoint_R) ~ "R",
# return "I" when not match the bottom or top
!is.na(get_record$breakpoint_S) & !is.na(get_record$breakpoint_R) ~ "I",
# and NA otherwise
TRUE ~ NA_character_)
} else if (method == "disk") {
new_rsi[i] <- quick_case_when(isTRUE(as.double(x[i]) >= as.double(get_record$breakpoint_S)) ~ "S",
isTRUE(as.double(x[i]) <= as.double(get_record$breakpoint_R)) ~ "R",
guideline_coerced %like% "EUCAST" & isTRUE(as.double(x[i]) < as.double(get_record$breakpoint_R)) ~ "R",
guideline_coerced %like% "CLSI" & isTRUE(as.double(x[i]) <= as.double(get_record$breakpoint_R)) ~ "R",
# return "I" when not match the bottom or top
!is.na(get_record$breakpoint_S) & !is.na(get_record$breakpoint_R) ~ "I",
# and NA otherwise