#' Only polytrauma patients
#'
#' Keeps only the polytrauma patients. Polytrauma is here defined as at least
#' two injuries scored above a certain abbreviated injury scale (AIS) score
#' cutoff in at least two different body regions.
#' @param sample Data frame. The study sample. No default.
#' @param ais.variables Character vector. The names of the variables with AIS
#' scores for each body region. Defaults to c("head_and_neck", "face",
#' "chest", "extremities", "external").
#' @param ais.cutoff Integer vector of length 1 between 1 and 6. The cutoff
#' above which an injury is counted for polytrauma. Defaults to 2.
#' @param remove.missing Logical vector of length 1. If TRUE all observations
#' with missing AIS, as detected by is.na, are removed from the
#' sample. Defaults to FALSE.
#' @export
OnlyPolytraumaPatients <- function(sample,
ais.variables = c("head_and_neck",
"face", "chest",
"extremities",
"external"),
ais.cutoff = 2, remove.missing = FALSE) {
## Error handling
if (!is.data.frame(study.data))
stop("sample has to be a data frame")
if (!is.character(ais.variables))
stop("ais.variables has to be a character vector")
if (!is.numeric(ais.cutoff) | !IsLength1(ais.cutoff))
stop("ais.cutoff has to be an integer vector of length 1 between 1 and 6")
if (!is.logical(remove.missing) | !IsLength1(remove.missing))
stop("remove.missing has to be a logical vector of length 1")
## Remove missing
n.missing <- 0
subsample <- sample
if (remove.missing) {
subsample <- subsample[complete.cases(subsample[, ais.variables]), ]
n.missing <- nrow(sample) - nrow(subsample)
}
## Identify cases with polytrauma
valid.ais.values <- (ais.cutoff + 1):6
valid.ais.string <- paste0(valid.ais.values, collapse = "|")
ais.above.cutoff <- do.call(cbind, lapply(subsample[, ais.variables], function(column) {
new.column <- grepl(valid.ais.string, column)
return(new.column)
}))
polytrauma <- rowSums(ais.above.cutoff) > 1
subsample <- subsample[polytrauma, ]
n.excluded <- nrow(sample) - nrow(subsample) + n.missing
## Collate return list
total.n.excluded <- n.excluded + n.missing
exclusion.text <- paste0(total.n.excluded, " did not have polytrauma.")
if (remove.missing) {
exclusion.text <- paste0(total.n.excluded, " excluded: \n\n",
"- ", n.missing, " had missing AIS scores \n\n",
"- ", n.excluded, " did not have polytrauma \n\n")
}
return.list <- list(exclusion.text = exclusion.text,
subsample = subsample)
return(return.list)
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.