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dr. M.S. (Matthijs) Berends
2022-08-21 16:37:20 +02:00
parent 7226b70c3d
commit 952d16de33
315 changed files with 839 additions and 34495 deletions
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R/mic.R
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@ -43,7 +43,6 @@ valid_mic_levels <- c(c(t(vapply(FUN.VALUE = character(9), ops,
#' Transform Input to Minimum Inhibitory Concentrations (MIC)
#'
#' This transforms vectors to a new class [`mic`], which treats the input as decimal numbers, while maintaining operators (such as ">=") and only allowing valid MIC values known to the field of (medical) microbiology.
#' @inheritSection lifecycle Stable Lifecycle
#' @rdname as.mic
#' @param x a [character] or [numeric] vector
#' @param na.rm a [logical] indicating whether missing values should be removed
@ -95,32 +94,35 @@ valid_mic_levels <- c(c(t(vapply(FUN.VALUE = character(9), ops,
#' @aliases mic
#' @export
#' @seealso [as.rsi()]
#' @inheritSection AMR Read more on Our Website!
#' @examples
#' mic_data <- as.mic(c(">=32", "1.0", "1", "1.00", 8, "<=0.128", "8", "16", "16"))
#' mic_data
#' is.mic(mic_data)
#'
#' # this can also coerce combined MIC/RSI values:
#' as.mic("<=0.002; S") # will return <=0.002
#' as.mic("<=0.002; S")
#'
#' # mathematical processing treats MICs as [numeric] values
#' # mathematical processing treats MICs as numeric values
#' fivenum(mic_data)
#' quantile(mic_data)
#' all(mic_data < 512)
#'
#' # interpret MIC values
#' as.rsi(x = as.mic(2),
#' mo = as.mo("S. pneumoniae"),
#' mo = as.mo("Streptococcus pneumoniae"),
#' ab = "AMX",
#' guideline = "EUCAST")
#' as.rsi(x = as.mic(4),
#' mo = as.mo("S. pneumoniae"),
#' as.rsi(x = as.mic(c(0.01, 2, 4, 8)),
#' mo = as.mo("Streptococcus pneumoniae"),
#' ab = "AMX",
#' guideline = "EUCAST")
#'
#' # plot MIC values, see ?plot
#' plot(mic_data)
#' plot(mic_data, mo = "E. coli", ab = "cipro")
#' autoplot(mic_data, mo = "E. coli", ab = "cipro")
#' autoplot(mic_data, mo = "E. coli", ab = "cipro", language = "nl") # Dutch
#' autoplot(mic_data, mo = "E. coli", ab = "cipro", language = "uk") # Ukrainian
as.mic <- function(x, na.rm = FALSE) {
meet_criteria(x, allow_class = c("mic", "character", "numeric", "integer", "factor"), allow_NA = TRUE)
meet_criteria(na.rm, allow_class = "logical", has_length = 1)