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Replace RSI with SIR

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This commit is contained in:
Dr. Matthijs Berends
2023-01-21 23:47:20 +01:00
committed by GitHub
parent 24b12024ce
commit 98e62c9af2
127 changed files with 1746 additions and 1648 deletions
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10
R/mic.R
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@ -77,7 +77,7 @@ valid_mic_levels <- c(
#' @param x a [character] or [numeric] vector
#' @param na.rm a [logical] indicating whether missing values should be removed
#' @param ... arguments passed on to methods
#' @details To interpret MIC values as RSI values, use [as.rsi()] on MIC values. It supports guidelines from EUCAST (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`) and CLSI (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`).
#' @details To interpret MIC values as SIR values, use [as.sir()] on MIC values. It supports guidelines from EUCAST (`r min(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`) and CLSI (`r min(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "CLSI")$guideline)))`).
#'
#' This class for MIC values is a quite a special data type: formally it is an ordered [factor] with valid MIC values as [factor] levels (to make sure only valid MIC values are retained), but for any mathematical operation it acts as decimal numbers:
#'
@ -123,13 +123,13 @@ valid_mic_levels <- c(
#' @return Ordered [factor] with additional class [`mic`], that in mathematical operations acts as decimal numbers. Bare in mind that the outcome of any mathematical operation on MICs will return a [numeric] value.
#' @aliases mic
#' @export
#' @seealso [as.rsi()]
#' @seealso [as.sir()]
#' @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:
#' # this can also coerce combined MIC/SIR values:
#' as.mic("<=0.002; S")
#'
#' # mathematical processing treats MICs as numeric values
@ -138,13 +138,13 @@ valid_mic_levels <- c(
#' all(mic_data < 512)
#'
#' # interpret MIC values
#' as.rsi(
#' as.sir(
#' x = as.mic(2),
#' mo = as.mo("Streptococcus pneumoniae"),
#' ab = "AMX",
#' guideline = "EUCAST"
#' )
#' as.rsi(
#' as.sir(
#' x = as.mic(c(0.01, 2, 4, 8)),
#' mo = as.mo("Streptococcus pneumoniae"),
#' ab = "AMX",