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website update

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dr. M.S. (Matthijs) Berends
2019-05-29 00:36:48 +02:00
parent 27380fa021
commit 62e6f41961
63 changed files with 414 additions and 482 deletions
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18
R/age.R
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@ -50,8 +50,8 @@ age <- function(x, reference = Sys.Date()) {
as.integer(years_gap))
if (any(ages < 0, na.rm = TRUE)) {
warning("NAs introduced for ages below 0.")
ages[ages < 0] <- NA_integer_
warning("NAs introduced for ages below 0.")
}
if (any(ages > 120, na.rm = TRUE)) {
warning("Some ages are > 120.")
@ -71,7 +71,7 @@ age <- function(x, reference = Sys.Date()) {
#' 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"}, 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{"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+.}
@ -107,17 +107,15 @@ age <- function(x, reference = Sys.Date()) {
#' # resistance of ciprofloxacine per age group
#' library(dplyr)
#' septic_patients %>%
#' mutate(first_isolate = first_isolate(.)) %>%
#' filter(first_isolate == TRUE,
#' mo == as.mo("E. coli")) %>%
#' filter_first_isolate) %>%
#' filter(mo == as.mo("E. coli")) %>%
#' group_by(age_group = age_groups(age)) %>%
#' select(age_group,
#' CIP) %>%
#' select(age_group, CIP) %>%
#' ggplot_rsi(x = "age_group")
age_groups <- function(x, split_at = c(12, 25, 55, 75)) {
if (is.character(split_at)) {
split_at <- split_at[1L]
if (split_at %like% "^(child|kid)") {
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)
@ -133,10 +131,12 @@ age_groups <- function(x, split_at = c(12, 25, 55, 75)) {
}
split_at <- sort(unique(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 available
# only 0 is available
stop("invalid value for `split_at`.")
}