AMR/R/kurtosis.R

81 lines
4.0 KiB
R
Raw Normal View History

# ==================================================================== #
# TITLE: #
2022-10-05 09:12:22 +02:00
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE CODE: #
2020-07-08 14:48:06 +02:00
# https://github.com/msberends/AMR #
# #
# PLEASE CITE THIS SOFTWARE AS: #
2022-10-05 09:12:22 +02:00
# 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. #
2023-05-27 10:39:22 +02:00
# https://doi.org/10.18637/jss.v104.i03 #
2022-10-05 09:12:22 +02:00
# #
2022-12-27 15:16:15 +01:00
# 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. #
# #
2019-01-02 23:24:07 +01:00
# 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. #
2020-10-08 11:16:03 +02:00
# #
# 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
2018-07-08 22:14:55 +02:00
#'
#' @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.
2020-10-08 11:16:03 +02:00
#' @param x a vector of values, a [matrix] or a [data.frame]
2021-05-12 18:15:03 +02:00
#' @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()]
2018-07-08 22:14:55 +02:00
#' @rdname kurtosis
#' @export
2022-08-28 10:31:50 +02:00
#' @examples
2022-08-21 16:37:20 +02:00
#' 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)
2018-07-08 22:14:55 +02:00
UseMethod("kurtosis")
}
2020-05-28 16:48:55 +02:00
#' @method kurtosis default
2018-07-08 22:14:55 +02:00
#' @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)
2018-07-08 22:14:55 +02:00
x <- as.vector(x)
2022-11-14 15:20:39 +01:00
if (isTRUE(na.rm)) {
2018-07-08 22:14:55 +02:00
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)
2018-07-08 22:14:55 +02:00
}
2020-05-28 16:48:55 +02:00
#' @method kurtosis matrix
2018-07-08 22:14:55 +02:00
#' @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)
2018-07-08 22:14:55 +02:00
}
2020-05-28 16:48:55 +02:00
#' @method kurtosis data.frame
2018-07-08 22:14:55 +02:00
#' @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)
2018-07-08 22:14:55 +02:00
}