mirror of
https://github.com/msberends/AMR.git
synced 2024-12-27 22:46:11 +01:00
81 lines
4.0 KiB
R
Executable File
81 lines
4.0 KiB
R
Executable File
# ==================================================================== #
|
|
# TITLE: #
|
|
# AMR: An R Package for Working with Antimicrobial Resistance Data #
|
|
# #
|
|
# SOURCE CODE: #
|
|
# https://github.com/msberends/AMR #
|
|
# #
|
|
# PLEASE CITE THIS SOFTWARE AS: #
|
|
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
|
|
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
|
|
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
|
# https://doi.org/10.18637/jss.v104.i03 #
|
|
# #
|
|
# Developed at the University of Groningen and the University Medical #
|
|
# Center Groningen in The Netherlands, in collaboration with many #
|
|
# colleagues from around the world, see our website. #
|
|
# #
|
|
# This R package is free software; you can freely use and distribute #
|
|
# it for both personal and commercial purposes under the terms of the #
|
|
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
|
|
# the Free Software Foundation. #
|
|
# We created this package for both routine data analysis and academic #
|
|
# research and it was publicly released in the hope that it will be #
|
|
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
|
|
# #
|
|
# Visit our website for the full manual and a complete tutorial about #
|
|
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
|
|
# ==================================================================== #
|
|
|
|
#' Kurtosis of the Sample
|
|
#'
|
|
#' @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.
|
|
#' @param x a vector of values, a [matrix] or a [data.frame]
|
|
#' @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
|
|
#' @export
|
|
#' @examples
|
|
#' kurtosis(rnorm(10000))
|
|
#' kurtosis(rnorm(10000), excess = TRUE)
|
|
kurtosis <- function(x, na.rm = FALSE, excess = FALSE) {
|
|
meet_criteria(na.rm, allow_class = "logical", has_length = 1)
|
|
meet_criteria(excess, allow_class = "logical", has_length = 1)
|
|
UseMethod("kurtosis")
|
|
}
|
|
|
|
#' @method kurtosis default
|
|
#' @rdname kurtosis
|
|
#' @export
|
|
kurtosis.default <- function(x, na.rm = FALSE, excess = FALSE) {
|
|
meet_criteria(na.rm, allow_class = "logical", has_length = 1)
|
|
meet_criteria(excess, allow_class = "logical", has_length = 1)
|
|
x <- as.vector(x)
|
|
if (isTRUE(na.rm)) {
|
|
x <- x[!is.na(x)]
|
|
}
|
|
n <- length(x)
|
|
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, excess = FALSE) {
|
|
meet_criteria(na.rm, allow_class = "logical", has_length = 1)
|
|
meet_criteria(excess, allow_class = "logical", has_length = 1)
|
|
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, excess = FALSE) {
|
|
meet_criteria(na.rm, allow_class = "logical", has_length = 1)
|
|
meet_criteria(excess, allow_class = "logical", has_length = 1)
|
|
vapply(FUN.VALUE = double(1), x, kurtosis.default, na.rm = na.rm, excess = excess)
|
|
}
|