mirror of https://github.com/msberends/AMR.git
197 lines
8.0 KiB
R
Executable File
197 lines
8.0 KiB
R
Executable File
# ==================================================================== #
|
|
# TITLE #
|
|
# Antimicrobial Resistance (AMR) Analysis #
|
|
# #
|
|
# SOURCE #
|
|
# https://gitlab.com/msberends/AMR #
|
|
# #
|
|
# LICENCE #
|
|
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
|
# #
|
|
# 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. #
|
|
# #
|
|
# This R package was created for academic research and was publicly #
|
|
# released in the hope that it will be useful, but it comes WITHOUT #
|
|
# ANY WARRANTY OR LIABILITY. #
|
|
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
|
|
# ==================================================================== #
|
|
|
|
#' Age in years of individuals
|
|
#'
|
|
#' Calculates age in years based on a reference date, which is the sytem date at default.
|
|
#' @param x date(s), will be coerced with \code{\link{as.POSIXlt}}
|
|
#' @param reference reference date(s) (defaults to today), will be coerced with \code{\link{as.POSIXlt}} and cannot be lower than \code{x}
|
|
#' @param exact a logical to indicate whether age calculation should be exact, i.e. with decimals. It divides the number of days of \href{https://en.wikipedia.org/wiki/Year-to-date}{year-to-date} (YTD) of \code{x} by the number of days in a year of \code{reference} (either 365 or 366).
|
|
#' @param na.rm a logical to indicate whether missing values should be removed
|
|
#' @return An integer (no decimals) if \code{exact = FALSE}, a double (with decimals) otherwise
|
|
#' @seealso To split ages into groups, use the \code{\link{age_groups}} function.
|
|
#' @importFrom dplyr if_else
|
|
#' @inheritSection AMR Read more on our website!
|
|
#' @export
|
|
#' @examples
|
|
#' # 10 random birth dates
|
|
#' df <- data.frame(birth_date = Sys.Date() - runif(10) * 25000)
|
|
#' # add ages
|
|
#' df$age <- age(df$birth_date)
|
|
#' # add exact ages
|
|
#' df$age_exact <- age(df$birth_date, exact = TRUE)
|
|
#'
|
|
#' df
|
|
age <- function(x, reference = Sys.Date(), exact = FALSE, na.rm = FALSE) {
|
|
if (length(x) != length(reference)) {
|
|
if (length(reference) == 1) {
|
|
reference <- rep(reference, length(x))
|
|
} else {
|
|
stop("`x` and `reference` must be of same length, or `reference` must be of length 1.")
|
|
}
|
|
}
|
|
x <- as.POSIXlt(x)
|
|
reference <- as.POSIXlt(reference)
|
|
|
|
# from https://stackoverflow.com/a/25450756/4575331
|
|
years_gap <- reference$year - x$year
|
|
ages <- if_else(reference$mon < x$mon | (reference$mon == x$mon & reference$mday < x$mday),
|
|
as.integer(years_gap - 1),
|
|
as.integer(years_gap))
|
|
|
|
# add decimals
|
|
if (exact == TRUE) {
|
|
# get dates of `x` when `x` would have the year of `reference`
|
|
x_in_reference_year <- as.POSIXlt(paste0(format(reference, "%Y"), format(x, "-%m-%d")))
|
|
# get differences in days
|
|
n_days_x_rest <- as.double(difftime(reference, x_in_reference_year, units = "days"))
|
|
# get numbers of days the years of `reference` has for a reliable denominator
|
|
n_days_reference_year <- as.POSIXlt(paste0(format(reference, "%Y"), "-12-31"))$yday + 1
|
|
# add decimal parts of year
|
|
mod <- n_days_x_rest / n_days_reference_year
|
|
# negative mods are cases where `x_in_reference_year` > `reference` - so 'add' a year
|
|
mod[mod < 0] <- 1 + mod[mod < 0]
|
|
# and finally add to ages
|
|
ages <- ages + mod
|
|
}
|
|
|
|
if (any(ages < 0, na.rm = TRUE)) {
|
|
ages[ages < 0] <- NA
|
|
warning("NAs introduced for ages below 0.")
|
|
}
|
|
if (any(ages > 120, na.rm = TRUE)) {
|
|
warning("Some ages are above 120.")
|
|
}
|
|
|
|
if (isTRUE(na.rm)) {
|
|
ages <- ages[!is.na(ages)]
|
|
}
|
|
|
|
ages
|
|
}
|
|
|
|
#' Split ages into age groups
|
|
#'
|
|
#' Split ages into age groups defined by the \code{split} parameter. This allows for easier demographic (antimicrobial resistance) analysis.
|
|
#' @param x age, e.g. calculated with \code{\link{age}}
|
|
#' @param split_at values to split \code{x} at, defaults to age groups 0-11, 12-24, 25-54, 55-74 and 75+. See Details.
|
|
#' @param na.rm a logical to indicate whether missing values should be removed
|
|
#' @details To split ages, the input can be:
|
|
#' \itemize{
|
|
#' \item{A numeric vector. A vector of e.g. \code{c(10, 20)} will split on 0-9, 10-19 and 20+. A value of only \code{50} will split on 0-49 and 50+.
|
|
#' The default is to split on young children (0-11), youth (12-24), young adults (25-54), middle-aged adults (55-74) and elderly (75+).}
|
|
#' \item{A character:}
|
|
#' \itemize{
|
|
#' \item{\code{"children"} or \code{"kids"}, equivalent of: \code{c(0, 1, 2, 4, 6, 13, 18)}. This will split on 0, 1, 2-3, 4-5, 6-12, 13-17 and 18+.}
|
|
#' \item{\code{"elderly"} or \code{"seniors"}, equivalent of: \code{c(65, 75, 85)}. This will split on 0-64, 65-74, 75-84, 85+.}
|
|
#' \item{\code{"fives"}, equivalent of: \code{1:20 * 5}. This will split on 0-4, 5-9, 10-14, ..., 90-94, 95-99, 100+.}
|
|
#' \item{\code{"tens"}, equivalent of: \code{1:10 * 10}. This will split on 0-9, 10-19, 20-29, ... 80-89, 90-99, 100+.}
|
|
#' }
|
|
#' }
|
|
#' @keywords age_group age
|
|
#' @return Ordered \code{\link{factor}}
|
|
#' @seealso To determine ages, based on one or more reference dates, use the \code{\link{age}} function.
|
|
#' @export
|
|
#' @inheritSection AMR Read more on our website!
|
|
#' @examples
|
|
#' ages <- c(3, 8, 16, 54, 31, 76, 101, 43, 21)
|
|
#'
|
|
#' # split into 0-49 and 50+
|
|
#' age_groups(ages, 50)
|
|
#'
|
|
#' # split into 0-19, 20-49 and 50+
|
|
#' age_groups(ages, c(20, 50))
|
|
#'
|
|
#' # split into groups of ten years
|
|
#' age_groups(ages, 1:10 * 10)
|
|
#' age_groups(ages, split_at = "tens")
|
|
#'
|
|
#' # split into groups of five years
|
|
#' age_groups(ages, 1:20 * 5)
|
|
#' age_groups(ages, split_at = "fives")
|
|
#'
|
|
#' # split specifically for children
|
|
#' age_groups(ages, "children")
|
|
#' # same:
|
|
#' age_groups(ages, c(1, 2, 4, 6, 13, 17))
|
|
#'
|
|
#' \dontrun{
|
|
#' # resistance of ciprofloxacine per age group
|
|
#' library(dplyr)
|
|
#' example_isolates %>%
|
|
#' filter_first_isolate() %>%
|
|
#' filter(mo == as.mo("E. coli")) %>%
|
|
#' group_by(age_group = age_groups(age)) %>%
|
|
#' select(age_group, CIP) %>%
|
|
#' ggplot_rsi(x = "age_group")
|
|
#' }
|
|
age_groups <- function(x, split_at = c(12, 25, 55, 75), na.rm = FALSE) {
|
|
if (!is.numeric(x)) {
|
|
stop("`x` and must be numeric, not a ", paste0(class(x), collapse = "/"), ".")
|
|
}
|
|
if (any(x < 0, na.rm = TRUE)) {
|
|
x[x < 0] <- NA
|
|
warning("NAs introduced for ages below 0.")
|
|
}
|
|
if (is.character(split_at)) {
|
|
split_at <- split_at[1L]
|
|
if (split_at %like% "^(child|kid|junior)") {
|
|
split_at <- c(0, 1, 2, 4, 6, 13, 18)
|
|
} else if (split_at %like% "^(elder|senior)") {
|
|
split_at <- c(65, 75, 85)
|
|
} else if (split_at %like% "^five") {
|
|
split_at <- 1:20 * 5
|
|
} else if (split_at %like% "^ten") {
|
|
split_at <- 1:10 * 10
|
|
}
|
|
}
|
|
split_at <- sort(unique(as.integer(split_at)))
|
|
if (!split_at[1] == 0) {
|
|
# add base number 0
|
|
split_at <- c(0, split_at)
|
|
}
|
|
split_at <- split_at[!is.na(split_at)]
|
|
if (length(split_at) == 1) {
|
|
# only 0 is available
|
|
stop("invalid value for `split_at`.")
|
|
}
|
|
|
|
# turn input values to 'split_at' indices
|
|
y <- x
|
|
labs <- split_at
|
|
for (i in seq_len(length(split_at))) {
|
|
y[x >= split_at[i]] <- i
|
|
# create labels
|
|
labs[i - 1] <- paste0(unique(c(split_at[i - 1], split_at[i] - 1)), collapse = "-")
|
|
}
|
|
|
|
# last category
|
|
labs[length(labs)] <- paste0(split_at[length(split_at)], "+")
|
|
|
|
agegroups <- factor(labs[y], levels = labs, ordered = TRUE)
|
|
|
|
if (isTRUE(na.rm)) {
|
|
agegroups <- agegroups[!is.na(agegroups)]
|
|
}
|
|
|
|
agegroups
|
|
}
|