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(v1.5.0.9025) big plot and ggplot generics update

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dr. M.S. (Matthijs) Berends
2021-02-25 10:33:08 +01:00
parent 31ceba5441
commit a673407904
42 changed files with 1058 additions and 842 deletions
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10
R/random.R
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@ -25,7 +25,7 @@
#' Random MIC Values/Disk Zones/RSI Generation
#'
#' These functions can be used for generating random MIC values and disk diffusion diameters, for AMR data analysis practice.
#' These functions can be used for generating random MIC values and disk diffusion diameters, for AMR data analysis practice. By providing a microorganism and antimicrobial agent, the generated results will reflect reality as much as possible.
#' @inheritSection lifecycle Maturing Lifecycle
#' @param size desired size of the returned vector
#' @param mo any character that can be coerced to a valid microorganism code with [as.mo()]
@ -111,8 +111,8 @@ random_exec <- function(type, size, mo = NULL, ab = NULL) {
if (log(set_range_max, 2) %% 1 == 0) {
# return powers of 2
valid_range <- unique(as.double(valid_range))
# add one higher MIC level to set_range_max
set_range_max <- 2 ^ (log(set_range_max, 2) + 1)
# add 1-3 higher MIC levels to set_range_max
set_range_max <- 2 ^ (log(set_range_max, 2) + sample(c(1:3), 1))
set_range <- as.mic(valid_range[log(valid_range, 2) %% 1 == 0 & valid_range <= set_range_max])
} else {
# no power of 2, return factors of 2 to left and right side
@ -121,8 +121,8 @@ random_exec <- function(type, size, mo = NULL, ab = NULL) {
}
return(as.mic(sample(set_range, size = size, replace = TRUE)))
} else if (type == "DISK") {
set_range <- seq(from = as.integer(min(df$breakpoint_R)),
to = as.integer(max(df$breakpoint_S)),
set_range <- seq(from = as.integer(min(df$breakpoint_R) / 1.25),
to = as.integer(max(df$breakpoint_S) * 1.25),
by = 1)
out <- sample(set_range, size = size, replace = TRUE)
out[out < 6] <- sample(c(6:10), length(out[out < 6]), replace = TRUE)