#' Only patients presenting within a specific delay
#'
#' Keeps only the patients whom presented within a specific delay, where delay
#' refers to the time between injury and arrival to hospital.
#'
#' @param study.sample Data frame. The study sample. No default.
#' @param delay.variable.name Character vector of length 1. The name of the
#' delay variable. Defaults to "delay".
#' @param delay.cutoff Numeric vector of length 1. The delay cutoff in
#' hours. Defaults to 6, i.e. only observations with an delay less than 6
#' hours are kept in the sample.
#' @param remove.missing Logical vector of length 1. If TRUE all observations
#' with missing delay, as detected by is.na, are removed from the
#' sample. Defaults to TRUE.
#' @export
OnlyPatientsPresentingBefore <- function(study.sample, delay.variable.name = "delay", delay.cutoff = 6, remove.missing = TRUE) {
## Error handling
if (!is.data.frame(study.sample))
stop("study.sample has to be a data frame")
if (!is.character(delay.variable.name) | !IsLength1(delay.variable.name))
stop("delay.variable.name has to be a character vector of length 1")
if (!is.numeric(delay.cutoff) | !IsLength1(delay.cutoff))
stop("delay.cutoff has to be a numeric vector of length 1")
if (!is.logical(remove.missing) | !IsLength1(remove.missing))
stop("remove.missing has to be a logical vector of length 1")
## Make delay numeric
subsample <- study.sample
subsample[, delay.variable.name] <- as.numeric(subsample[, delay.variable.name])
## Remove missing
n.missing <- 0
if (remove.missing) {
subsample <- subsample[!is.na(subsample[, delay.variable.name]), ]
n.missing <- nrow(study.sample) - nrow(subsample)
}
## Remove those with too long delay
subsample <- subsample[subsample[, delay.variable.name] < delay.cutoff, ]
n.excluded <- nrow(study.sample) - nrow(subsample) - n.missing
## Collate return list
total.n.excluded <- n.excluded
if (remove.missing)
total.n.excluded <- total.n.excluded + n.missing
exclusion.text <- paste0(total.n.excluded, " had a delay of ", delay.cutoff, " hours or more.")
if (remove.missing) {
exclusion.text <- paste0(total.n.excluded, " excluded: \n\n",
"- ", n.missing, " had missing delay \n\n",
"- ", n.excluded, " had a delay of ", delay.cutoff, " hours or more. \n\n")
}
return.list <- list(exclusion.text = exclusion.text,
subsample = subsample)
return(return.list)
}
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