R/check.visitSequence.R

In stefvanbuuren/dsMice: DataSHIELD server-side functions for the mice package

#' Creates a \code{visitSequence} argument
#'
#' This helper function creates a valid \code{visitSequence}. The 
#' \code{visitSequence} is an argument to the \code{mice} function that 
#' specifies the sequence in which blocks are imputed.
#' @inheritParams mice
#' @return Vector containing block names
#' @seealso \code{\link{mice}}
#' @examples
#' make.visitSequence(nhanes)
#' @export
#' 

check.visitSequence <- function(visitSequence = NULL, 
                                data, where = NULL, blocks) {
  
  if (is.null(names(blocks)) || any(is.na(names(blocks))))
    stop("Missing names in `blocks`.")
  
  if (is.null(visitSequence)) return(make.visitSequence(data, blocks))
  
  if (is.null(where)) where <- is.na(data)
  nimp <- nimp(where, blocks)
  if (length(nimp) == 0) visitSequence <- nimp
  
  if (length(visitSequence) == 1 && is.character(visitSequence)) {
    code <- match.arg(visitSequence, c("roman", "arabic", "monotone",
                                       "revmonotone"))
    visitSequence <- switch(
      code, 
      roman = names(blocks)[nimp > 0],
      arabic = rev(names(blocks)[nimp > 0]),
      monotone = names(blocks)[order(nimp)],
      revmonotone = rev(names(blocks)[order(nimp)])
    )
  }
  
  # legacy handling
  if (is.numeric(visitSequence)) 
    visitSequence <- colnames(data)[visitSequence]
  
  # check against names(blocks)
  visitSequence <- visitSequence[is.element(visitSequence, names(blocks))]
  
  # remove any blocks without missing data
  visitSequence <- names((nimp > 0L)[visitSequence])
  visitSequence
}