(v1.3.0.9039) lifecycle updates, added excess kurtosis

R/ab.R

@@ -22,7 +22,7 @@
 #' Transform input to an antibiotic ID
 #'
 #' Use this function to determine the antibiotic code of one or more antibiotics. The data set [antibiotics] will be searched for abbreviations, official names and synonyms (brand names).
-#' @inheritSection lifecycle Maturing lifecycle
+#' @inheritSection lifecycle Stable lifecycle
 #' @param x character vector to determine to antibiotic ID
 #' @param flag_multiple_results logical to indicate whether a note should be printed to the console that probably more than one antibiotic code or name can be retrieved from a single input value.
 #' @param info logical to indicate whether a progress bar should be printed

R/guess_ab_col.R

@@ -22,7 +22,7 @@
 #' Guess antibiotic column
 #'
 #' This tries to find a column name in a data set based on information from the [antibiotics] data set. Also supports WHONET abbreviations.
-#' @inheritSection lifecycle Maturing lifecycle
+#' @inheritSection lifecycle Stable lifecycle
 #' @param x a [data.frame]
 #' @param search_string a text to search `x` for, will be checked with [as.ab()] if this value is not a column in `x`
 #' @param verbose a logical to indicate whether additional info should be printed

R/kurtosis.R

@@ -21,41 +21,43 @@
 
 #' Kurtosis of the sample
 #'
-#' @description Kurtosis is a measure of the "tailedness" of the probability distribution of a real-valued random variable.
-#' @inheritSection lifecycle Questioning lifecycle
+#' @description Kurtosis is a measure of the "tailedness" of the probability distribution of a real-valued random variable. A normal distribution has a kurtosis of 3 and a excess kurtosis of 0.
+#' @inheritSection lifecycle Stable lifecycle
 #' @param x a vector of values, a [`matrix`] or a [data.frame]
-#' @param na.rm a logical value indicating whether `NA` values should be stripped before the computation proceeds.
+#' @param na.rm a logical to indicate whether `NA` values should be stripped before the computation proceeds
+#' @param excess a logical to indicate whether the *excess kurtosis* should be returned, defined as the kurtosis minus 3.
 #' @seealso [skewness()]
 #' @rdname kurtosis
 #' @inheritSection AMR Read more on our website!
 #' @export
-kurtosis <- function(x, na.rm = FALSE) {
+kurtosis <- function(x, na.rm = FALSE, excess = FALSE) {
   UseMethod("kurtosis")
 }
 
 #' @method kurtosis default
 #' @rdname kurtosis
 #' @export
-kurtosis.default <- function(x, na.rm = FALSE) {
+kurtosis.default <- function(x, na.rm = FALSE, excess = FALSE) {
   x <- as.vector(x)
   if (na.rm == TRUE) {
     x <- x[!is.na(x)]
   }
   n <- length(x)
-  n * sum((x - mean(x, na.rm = na.rm))^4, na.rm = na.rm) /
+  k <- n * sum((x - mean(x, na.rm = na.rm))^4, na.rm = na.rm) /
     (sum((x - mean(x, na.rm = na.rm))^2, na.rm = na.rm)^2)
+  k - ifelse(excess, 3, 0)
 }
 
 #' @method kurtosis matrix
 #' @rdname kurtosis
 #' @export
-kurtosis.matrix <- function(x, na.rm = FALSE) {
-  apply(x, 2, kurtosis.default, na.rm = na.rm)
+kurtosis.matrix <- function(x, na.rm = FALSE, excess = FALSE) {
+  apply(x, 2, kurtosis.default, na.rm = na.rm, excess = excess)
 }
 
 #' @method kurtosis data.frame
 #' @rdname kurtosis
 #' @export
-kurtosis.data.frame <- function(x, na.rm = FALSE) {
-  sapply(x, kurtosis.default, na.rm = na.rm)
+kurtosis.data.frame <- function(x, na.rm = FALSE, excess = FALSE) {
+  sapply(x, kurtosis.default, na.rm = na.rm, excess = excess)
 }

R/mdro.R

@@ -22,7 +22,7 @@
 #' Determine multidrug-resistant organisms (MDRO)
 #'
 #' Determine which isolates are multidrug-resistant organisms (MDRO) according to international and national guidelines.
-#' @inheritSection lifecycle Maturing lifecycle
+#' @inheritSection lifecycle Stable lifecycle
 #' @param guideline a specific guideline to follow. When left empty, the publication by Magiorakos *et al.* (2012, Clinical Microbiology and Infection) will be followed, please see *Details*.
 #' @inheritParams eucast_rules
 #' @param pct_required_classes minimal required percentage of antimicrobial classes that must be available per isolate, rounded down. For example, with the default guideline, 17 antimicrobial classes must be available for *S. aureus*. Setting this `pct_required_classes` argument to `0.5` (default) means that for every *S. aureus* isolate at least 8 different classes must be available. Any lower number of available classes will return `NA` for that isolate.

R/skewness.R

@@ -23,10 +23,10 @@
 #'
 #' @description Skewness is a measure of the asymmetry of the probability distribution of a real-valued random variable about its mean.
 #'
-#' When negative: the left tail is longer; the mass of the distribution is concentrated on the right of the figure. When positive: the right tail is longer; the mass of the distribution is concentrated on the left of the figure.
-#' @inheritSection lifecycle Questioning lifecycle
+#' When negative ('left-skewed'): the left tail is longer; the mass of the distribution is concentrated on the right of a histogram. When positive ('right-skewed'): the right tail is longer; the mass of the distribution is concentrated on the left of a histogram. A normal distribution has a skewness of 0.
+#' @inheritSection lifecycle Stable lifecycle
 #' @param x a vector of values, a [`matrix`] or a [data.frame]
-#' @param na.rm a logical value indicating whether `NA` values should be stripped before the computation proceeds.
+#' @param na.rm a logical value indicating whether `NA` values should be stripped before the computation proceeds
 #' @seealso [kurtosis()]
 #' @rdname skewness
 #' @inheritSection AMR Read more on our website!