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mean AMR distance

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dr. M.S. (Matthijs) Berends
2022-10-21 15:59:31 +02:00
parent 4bebba3610
commit 178ab5e5ff
5 changed files with 13 additions and 13 deletions
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R/mean_amr_distance.R
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@ -41,7 +41,7 @@
#'
#' For data sets, the mean AMR distance will be calculated per variable, after which the mean of all columns will returned per row (using [rowMeans()]), see *Examples*.
#'
#' Use [distance_from_row()] to subtract distances from the distance of one row, see *Examples*.
#' Use [mean_distance_from_row()] to subtract distances from the distance of one row, see *Examples*.
#' @section Interpretation:
#' 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
@ -66,7 +66,7 @@
#' y %>%
#' mutate(
#' amr_distance = mean_amr_distance(., where(is.mic)),
#' check_id_C = distance_from_row(amr_distance, id == "C")
#' check_id_C = mean_distance_from_row(amr_distance, id == "C")
#' ) %>%
#' arrange(check_id_C)
#' }
@ -104,7 +104,7 @@ mean_amr_distance.disk <- function(x, ...) {
#' @rdname mean_amr_distance
#' @export
mean_amr_distance.rsi <- function(x, combine_SI = TRUE, ...) {
mean_amr_distance.rsi <- 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"
@ -157,7 +157,7 @@ mean_amr_distance.data.frame <- function(x, ..., combine_SI = TRUE) {
#' @param mean_distance the outcome of [mean_amr_distance()]
#' @param row an index, such as a row number
#' @export
distance_from_row <- function(mean_distance, row) {
mean_distance_from_row <- function(mean_distance, row) {
meet_criteria(mean_distance, allow_class = c("double", "numeric"), is_finite = TRUE)
meet_criteria(row, allow_class = c("logical", "double", "numeric"))
if (is.logical(row)) {