R/imp2list.R

In slamballais/QDECR: Vertex-wise statistical analysis

#'Convert imputation output to \code{list}
#'
#'Converts known imputation objects containing datasets to a \code{list} of
#'datasets
#'
#'This function attempts to unify imputation object formats in supplying
#'datasets. This is done by extracting the imputed datasets from the imputation
#'object and assembling them into a \code{list}. If an unknown object is
#'supplied, the function will throw an error with the request to supply a list
#'of data frames instead.
#'
#'@param obj The imputation object that contains the imputed datasets
#'@return Outputs a list of imputed datasets
#'@author Sander Lamballais, 2018.
#'@export

imp2list <- function(obj) UseMethod("imp2list", obj)

imp2list.amelia <- function(obj) obj$imputations

imp2list.aregImpute <- function(obj) stop("The aregImpute format is not supported, ",
                                        "as it does not include the raw dataset. ",
                                        "Please create your own design matrices.")

imp2list.data.frame <- function(obj) list(obj)

imp2list.default <- function(obj) {
  x <- class(obj)[1]
  stop("The provided data seems of class `", x, "`. Please create a list object of ",
       "your imputed datasets and supply that instead.")
}

imp2list.list <- function(obj) {
  if(length(obj) > 1){
    s <- t(sapply(obj, names))
    if (all(is.null(s))) stop("The provided datasets (in the list) do not have column names")
    if (any(is.null(s))) stop("Some provided datasets (in the list) do not have column names")
    count <- sum(!duplicated(s))
    if (count == 1) s else stop("The supplied datasets (in the list) do not share column names.")
  }
  obj
}

imp2list.matrix <- function(obj) imp2list(as.data.frame(obj))

imp2list.mi <- function(obj) {
  if (!requireNamespace("mi", quietly = TRUE))
    stop("You are trying to load in an `mi` output object, but `mi` is not installed.")
  mi::complete(obj)
}

imp2list.mids <- function(obj) {
  if (!requireNamespace("mice", quietly = TRUE))
    stop("You are trying to load in an `mice` output object (class `mids`), but `mice` is not installed.")
  lapply(seq_len(obj$m), function(y) mice::complete(obj, y))
}

imp2list.missForest <- function(obj) list(obj$objimp)