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(v2.1.1.9232) is.mic() iteration, documentation cleanup

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dr. M.S. (Matthijs) Berends
2025-03-31 10:51:31 +02:00
parent 5f5b77bfaf
commit 63099cd81e
93 changed files with 1001 additions and 990 deletions
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12
R/mean_amr_distance.R
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@ -30,9 +30,9 @@
#' 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 [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 [antimicrobial selectors][amr_selector()]
#' @param combine_SI a [logical] to indicate whether all values of S, SDD, and I must be merged into one, so the input only consists of S+I vs. R (susceptible vs. resistant) - the default is `TRUE`
#' @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 [antimicrobial selectors][amr_selector()]
#' @param combine_SI A [logical] to indicate whether all values of S, SDD, and I must be merged into one, so the input only consists of S+I vs. R (susceptible vs. resistant) - the default is `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))`.
@ -69,7 +69,7 @@
#' )
#' y
#' mean_amr_distance(y)
#' y$amr_distance <- mean_amr_distance(y, where(is.mic))
#' y$amr_distance <- mean_amr_distance(y, is.mic(y))
#' y[order(y$amr_distance), ]
#'
#' if (require("dplyr")) {
@ -171,8 +171,8 @@ mean_amr_distance.data.frame <- function(x, ..., combine_SI = TRUE) {
}
#' @rdname mean_amr_distance
#' @param amr_distance the outcome of [mean_amr_distance()]
#' @param row an index, such as a row number
#' @param amr_distance The outcome of [mean_amr_distance()]
#' @param row An index, such as a row number
#' @export
amr_distance_from_row <- function(amr_distance, row) {
meet_criteria(amr_distance, allow_class = "numeric", is_finite = TRUE)