mirror of
https://github.com/msberends/AMR.git
synced 2024-12-25 19:26:13 +01:00
(v1.5.0.9035) quick test
This commit is contained in:
parent
450bbe5fb7
commit
2f0fc3cab7
@ -1,5 +1,5 @@
|
||||
Package: AMR
|
||||
Version: 1.5.0.9034
|
||||
Version: 1.5.0.9035
|
||||
Date: 2021-03-07
|
||||
Title: Antimicrobial Resistance Data Analysis
|
||||
Authors@R: c(
|
||||
|
1
R/ab.R
1
R/ab.R
@ -105,7 +105,6 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = TRUE, ...) {
|
||||
already_regex <- isTRUE(list(...)$already_regex)
|
||||
fast_mode <- isTRUE(list(...)$fast_mode)
|
||||
|
||||
|
||||
x_bak <- x
|
||||
x <- toupper(x)
|
||||
x_nonNA <- x[!is.na(x)]
|
||||
|
23
R/rsi.R
23
R/rsi.R
@ -774,6 +774,11 @@ exec_as.rsi <- function(method,
|
||||
|
||||
for (i in seq_len(length(x))) {
|
||||
is_intrinsic_r <- paste(mo[i], ab) %in% INTRINSIC_R
|
||||
if (is_intrinsic_r == TRUE) {
|
||||
print("====")
|
||||
print(paste(mo[i], ab))
|
||||
print("====")
|
||||
}
|
||||
any_is_intrinsic_resistant <- any_is_intrinsic_resistant | is_intrinsic_r
|
||||
|
||||
if (isTRUE(add_intrinsic_resistance) & is_intrinsic_r) {
|
||||
@ -814,14 +819,22 @@ exec_as.rsi <- function(method,
|
||||
if (is.na(x[i])) {
|
||||
new_rsi[i] <- NA_character_
|
||||
} else if (method == "mic") {
|
||||
print("----")
|
||||
print(str(get_record))
|
||||
print(x[i])
|
||||
print(x[i] <= get_record$breakpoint_S)
|
||||
print(x[i] > get_record$breakpoint_R)
|
||||
print(x[i] >= get_record$breakpoint_R)
|
||||
print(guideline_coerced %like% "EUCAST" & x[i] > get_record$breakpoint_R)
|
||||
print(guideline_coerced %like% "EUCAST" && x[i] > get_record$breakpoint_R)
|
||||
print(guideline_coerced %like% "EUCAST" & (x[i] > get_record$breakpoint_R))
|
||||
print("----")
|
||||
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",
|
||||
# start interpreting: EUCAST uses <= S and > R, CLSI uses <=S and >= 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$breakpoint_R) ~ "R",
|
||||
x[i] <= get_record$breakpoint_S ~ "S",
|
||||
guideline_coerced %like% "EUCAST" & x[i] > get_record$breakpoint_R ~ "R",
|
||||
guideline_coerced %like% "CLSI" & x[i] >= get_record$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
|
||||
|
Loading…
Reference in New Issue
Block a user