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WHO update, antibiotics update

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dr. M.S. (Matthijs) Berends
2019-01-25 13:18:41 +01:00
parent 3ec44b6e0c
commit f4ff98b470
99 changed files with 1363 additions and 737 deletions
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17
R/age.R
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@ -29,6 +29,9 @@
#' @importFrom dplyr if_else
#' @inheritSection AMR Read more on our website!
#' @export
#' @examples
#' df <- data.frame(birth_date = Sys.Date() - runif(100) * 25000)
#' df$age <- age(df$birth_date)
age <- function(x, reference = Sys.Date()) {
if (length(x) != length(reference)) {
if (length(reference) == 1) {
@ -39,17 +42,21 @@ age <- function(x, reference = Sys.Date()) {
}
x <- base::as.POSIXlt(x)
reference <- base::as.POSIXlt(reference)
if (any(reference < x)) {
stop("`reference` cannot be lower (older) than `x`.")
}
years_gap <- reference$year - x$year
# 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))
if (any(ages > 120)) {
if (any(ages < 0, na.rm = TRUE)) {
warning("NAs introduced for ages below 0.")
ages[ages < 0] <- NA_integer_
}
if (any(ages > 120, na.rm = TRUE)) {
warning("Some ages are > 120.")
}
ages
}