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(v0.9.0.9005) as.mo for G. species

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dr. M.S. (Matthijs) Berends
2019-12-21 10:56:06 +01:00
parent cc8cd043e1
commit ba3ce77f02
21 changed files with 501 additions and 361 deletions
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8
R/disk.R
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@ -21,12 +21,12 @@
#' Class 'disk'
#'
#' This transforms a vector to a new class [`disk`], which is a growth zone size (around an antibiotic disk) in millimeters between 6 and 99.
#' This transforms a vector to a new class [`disk`], which is a growth zone size (around an antibiotic disk) in millimeters between 6 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 RSI values with [as.rsi()]. It supports guidelines from EUCAST and CLSI.
#' @return Ordered integer factor with new class [`disk`]
#' @return An [`integer`] with additional new class [`disk`]
#' @aliases disk
#' @export
#' @seealso [as.rsi()]
@ -56,8 +56,8 @@ as.disk <- function(x, na.rm = FALSE) {
# force it to be integer
x <- suppressWarnings(as.integer(x))
# disks can never be less than 9 mm (size of a disk) or more than 50 mm
x[x < 6 | x > 99] <- NA_integer_
# disks can never be less than 6 mm (size of smallest disk) or more than 50 mm
x[x < 6 | x > 50] <- NA_integer_
na_after <- length(x[is.na(x)])
if (na_before != na_after) {