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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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14
R/mean_amr_distance.R
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@ -30,14 +30,14 @@
#' Calculate the Mean AMR Distance
#'
#' Calculates a normalised mean for antimicrobial resistance between multiple observations, to help to identify similar isolates without comparing antibiograms by hand.
#' @param x a vector of class [rsi][as.rsi()], [mic][as.mic()] or [disk][as.disk()], or a [data.frame] containing columns of any of these classes
#' @param x a vector of class [sir][as.sir()], [mic][as.mic()] or [disk][as.disk()], or a [data.frame] containing columns of any of these classes
#' @param ... variables to select (supports [tidyselect language][tidyselect::language] such as `column1:column4` and `where(is.mic)`, and can thus also be [antibiotic selectors][ab_selector()]
#' @param combine_SI a [logical] to indicate whether all values of S and I must be merged into one, so the input only consists of S+I vs. R (susceptible vs. resistant), defaults to `TRUE`
#' @details The mean AMR distance is effectively [the Z-score](https://en.wikipedia.org/wiki/Standard_score); a normalised numeric value to compare AMR test results which can help to identify similar isolates, without comparing antibiograms by hand.
#'
#' MIC values (see [as.mic()]) are transformed with [log2()] first; their distance is thus calculated as `(log2(x) - mean(log2(x))) / sd(log2(x))`.
#'
#' R/SI values (see [as.rsi()]) are transformed using `"S"` = 1, `"I"` = 2, and `"R"` = 3. If `combine_SI` is `TRUE` (default), the `"I"` will be considered to be 1.
#' SIR values (see [as.sir()]) are transformed using `"S"` = 1, `"I"` = 2, and `"R"` = 3. If `combine_SI` is `TRUE` (default), the `"I"` will be considered to be 1.
#'
#' For data sets, the mean AMR distance will be calculated per column, after which the mean per row will be returned, see *Examples*.
#'
@ -46,9 +46,9 @@
#' Isolates with distances less than 0.01 difference from each other should be considered similar. Differences lower than 0.025 should be considered suspicious.
#' @export
#' @examples
#' rsi <- random_rsi(10)
#' rsi
#' mean_amr_distance(rsi)
#' sir <- random_sir(10)
#' sir
#' mean_amr_distance(sir)
#'
#' mic <- random_mic(10)
#' mic
@ -62,7 +62,7 @@
#'
#' y <- data.frame(
#' id = LETTERS[1:10],
#' amox = random_rsi(10, ab = "amox", mo = "Escherichia coli"),
#' amox = random_sir(10, ab = "amox", mo = "Escherichia coli"),
#' cipr = random_disk(10, ab = "cipr", mo = "Escherichia coli"),
#' gent = random_mic(10, ab = "gent", mo = "Escherichia coli"),
#' tobr = random_mic(10, ab = "tobr", mo = "Escherichia coli")
@ -115,7 +115,7 @@ mean_amr_distance.disk <- function(x, ...) {
#' @rdname mean_amr_distance
#' @export
mean_amr_distance.rsi <- function(x, ..., combine_SI = TRUE) {
mean_amr_distance.sir <- function(x, ..., combine_SI = TRUE) {
meet_criteria(combine_SI, allow_class = "logical", has_length = 1, .call_depth = -1)
if (isTRUE(combine_SI)) {
x[x == "I"] <- "S"