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Update clinical breakpoints and fix some as.mo() bugs (#117)

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* Updates clinical breakpoints EUCAST/CLSI 2023, fixes #102, fixes #112, fixes #113, fixes #114, fixes #115
* docs
* implement ecoffs
* unit tests
This commit is contained in:
Dr. Matthijs Berends
2023-06-22 15:10:59 +02:00
committed by GitHub
parent 9591688811
commit f065945d7b
55 changed files with 43056 additions and 18400 deletions
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8
R/random.R
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@ -136,11 +136,11 @@ random_exec <- function(type, size, mo = NULL, ab = NULL) {
# get highest/lowest +/- random 1 to 3 higher factors of two
max_range <- mic_range[min(
length(mic_range),
which(mic_range == max(df$breakpoint_R)) + sample(c(1:3), 1)
which(mic_range == max(df$breakpoint_R, na.rm = TRUE)) + sample(c(1:3), 1)
)]
min_range <- mic_range[max(
1,
which(mic_range == min(df$breakpoint_S)) - sample(c(1:3), 1)
which(mic_range == min(df$breakpoint_S, na.rm = TRUE)) - sample(c(1:3), 1)
)]
mic_range_new <- mic_range[mic_range <= max_range & mic_range >= min_range]
@ -158,8 +158,8 @@ random_exec <- function(type, size, mo = NULL, ab = NULL) {
return(out)
} else if (type == "DISK") {
set_range <- seq(
from = as.integer(min(df$breakpoint_R) / 1.25),
to = as.integer(max(df$breakpoint_S) * 1.25),
from = as.integer(min(df$breakpoint_R, na.rm = TRUE) / 1.25),
to = as.integer(max(df$breakpoint_S, na.rm = TRUE) * 1.25),
by = 1
)
out <- sample(set_range, size = size, replace = TRUE)