P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-12 12:21:58 +02:00
Code Releases Activity

check for 2.0

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2023-03-12 13:02:37 +01:00
parent 9179e98e12
commit 80cfc503c2
25 changed files with 127 additions and 134 deletions
Download Patch File Download Diff File Expand all files Collapse all files

6
R/sir.R
View File

@ -999,7 +999,7 @@ as_sir_method <- function(method_short,
}
if (method == "mic") {
new_sir <- quick_case_when(
new_sir <- case_when_AMR(
is.na(values) ~ NA_sir_,
values <= breakpoints_current$breakpoint_S ~ as.sir("S"),
guideline_coerced %like% "EUCAST" & values > breakpoints_current$breakpoint_R ~ as.sir("R"),
@ -1010,7 +1010,7 @@ as_sir_method <- function(method_short,
TRUE ~ NA_sir_
)
} else if (method == "disk") {
new_sir <- quick_case_when(
new_sir <- case_when_AMR(
is.na(values) ~ NA_sir_,
as.double(values) >= as.double(breakpoints_current$breakpoint_S) ~ as.sir("S"),
guideline_coerced %like% "EUCAST" & as.double(values) < as.double(breakpoints_current$breakpoint_R) ~ as.sir("R"),
@ -1023,7 +1023,7 @@ as_sir_method <- function(method_short,
}
# write to verbose output
AMR_env$sir_interpretation_history <- rbind2(
AMR_env$sir_interpretation_history <- rbind_AMR(
AMR_env$sir_interpretation_history,
# recycling 1 to 2 rows does not seem to work, which is why rep() was added
data.frame(