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dplyr 0.8.0 support, fixes #7

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dr. M.S. (Matthijs) Berends
2018-12-22 22:39:34 +01:00
parent b937662a97
commit 0b8084871d
29 changed files with 555 additions and 479 deletions
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32
R/age.R
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@ -19,28 +19,28 @@
#' Age in years of individuals
#'
#' Calculates age in years based on a reference date, which is the sytem time at default.
#' @param x date(s) - will be coerced with \code{\link{as.POSIXlt}}
#' @param y reference date(s) - defaults to \code{\link{Sys.Date}} - will be coerced with \code{\link{as.POSIXlt}}
#' @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}}
#' @return Integer (no decimals)
#' @seealso age_groups
#' @seealso \code{\link{age_groups}} to splits age into groups
#' @importFrom dplyr if_else
#' @export
age <- function(x, y = Sys.Date()) {
if (length(x) != length(y)) {
if (length(y) == 1) {
y <- rep(y, length(x))
age <- function(x, reference = Sys.Date()) {
if (length(x) != length(reference)) {
if (length(reference) == 1) {
reference <- rep(reference, length(x))
} else {
stop("`x` and `y` must be of same length, or `y` must be of length 1.")
stop("`x` and `reference` must be of same length, or `reference` must be of length 1.")
}
}
x <- base::as.POSIXlt(x)
y <- base::as.POSIXlt(y)
if (any(y < x)) {
stop("`y` cannot be lower (older) than `x`.")
reference <- base::as.POSIXlt(reference)
if (any(reference < x)) {
stop("`reference` cannot be lower (older) than `x`.")
}
years_gap <- y$year - x$year
years_gap <- reference$year - x$year
# from https://stackoverflow.com/a/25450756/4575331
ages <- if_else(y$mon < x$mon | (y$mon == x$mon & y$mday < x$mday),
ages <- if_else(reference$mon < x$mon | (reference$mon == x$mon & reference$mday < x$mday),
as.integer(years_gap - 1),
as.integer(years_gap))
if (any(ages > 120)) {
@ -51,9 +51,9 @@ age <- function(x, y = Sys.Date()) {
#' Split ages into age groups
#'
#' Splits ages into groups defined by the \code{split} parameter.
#' 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}, defaults to 0-11, 12-24, 26-54, 55-74 and 75+. See Details.
#' @param split_at values to split \code{x} at, defaults to age groups 0-11, 12-24, 26-54, 55-74 and 75+. See Details.
#' @details To split ages, the input can be:
#' \itemize{
#' \item{A numeric vector. A vector of \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+.
@ -68,7 +68,7 @@ age <- function(x, y = Sys.Date()) {
#' }
#' @keywords age_group age
#' @return Ordered \code{\link{factor}}
#' @seealso age
#' @seealso \code{\link{age}} to determine ages based on one or more reference dates
#' @export
#' @examples
#' ages <- c(3, 8, 16, 54, 31, 76, 101, 43, 21)