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(v2.1.1.9095) Python support

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dr. M.S. (Matthijs) Berends
2024-10-15 17:12:55 +02:00
parent 94501371cd
commit 5c4d8fcd2a
18 changed files with 513 additions and 435 deletions
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8
R/disk.R
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@ -29,13 +29,13 @@
#' Transform Input to Disk Diffusion Diameters
#'
#' This transforms a vector to a new class [`disk`], which is a disk diffusion growth zone size (around an antibiotic disk) in millimetres between 6 and 50.
#' This transforms a vector to a new class [`disk`], which is a disk diffusion growth zone size (around an antibiotic disk) in millimetres between 0 and 50.
#' @rdname as.disk
#' @param x vector
#' @param na.rm a [logical] indicating whether missing values should be removed
#' @details Interpret disk values as SIR values with [as.sir()]. It supports guidelines from EUCAST and CLSI.
#'
#' Disk diffusion growth zone sizes must be between 6 and 50 millimetres. Values higher than 50 but lower than 100 will be maximised to 50. All others input values outside the 6-50 range will return `NA`.
#' Disk diffusion growth zone sizes must be between 0 and 50 millimetres. Values higher than 50 but lower than 100 will be maximised to 50. All others input values outside the 0-50 range will return `NA`.
#' @return An [integer] with additional class [`disk`]
#' @aliases disk
#' @export
@ -108,8 +108,8 @@ as.disk <- function(x, na.rm = FALSE) {
# round up and make it an integer
x <- as.integer(ceiling(clean_double2(x)))
# disks can never be less than 6 mm (size of smallest disk) or more than 50 mm
x[x < 6 | x > 99] <- NA_integer_
# disks can never be less than 0 mm or more than 50 mm
x[x < 0 | x > 99] <- NA_integer_
x[x > 50] <- 50L
na_after <- length(x[is.na(x)])