R/fix_zeros.R

In oslerinhealth/SummarizedActigraphy: Coerce Actigraphy to Summarized Experiments

#' Fix Zeros from Idle Sleep Mode
#'
#' @param df An object with columns `X`, `Y`, and `Z` or an
#' object of class `AccData`
#' @param fill_in Should the zeros be filled in with the last
#' observation carried forward?
#'
#' @return A data set with the zeros filled in
#' @export
#' @importFrom zoo na.locf
#' @examples
#' df = data.frame(
#'   X = c(0.3/sqrt(0.5), rep(0, 3)),
#'   Y = c(0.4/sqrt(0.5), rep(0, 3)),
#'   Z = c(0.5/sqrt(0.5), rep(0, 3)),
#'   stringsAsFactors = FALSE)
#' fix_zeros(df)
#' fix_zeros(df, fill_in = FALSE)
fix_zeros = function(df, fill_in = TRUE) {
  acc_data = is.AccData(df)
  if (acc_data) {
    xdf = df
    df = df$data.out
  }
  zero = rowSums(df[, c("X", "Y", "Z")] == 0) == 3
  names(zero) = NULL
  df$X[zero] = NA
  df$Y[zero] = NA
  df$Z[zero] = NA
  if (fill_in) {
    df =  idle_na_locf(df)
  }
  if (acc_data) {
    xdf$data.out = df
    df = xdf
  }
  df
}

#' @rdname fix_zeros
#' @export
idle_na_locf = function(df) {
  acc_data = is.AccData(df)
  if (acc_data) {
    xdf = df
    df = df$data.out
  }
  df$X = zoo::na.locf(df$X, na.rm = FALSE)
  df$Y = zoo::na.locf(df$Y, na.rm = FALSE)
  df$Z = zoo::na.locf(df$Z, na.rm = FALSE)

  df$X[ is.na(df$X)] = 0
  df$Y[ is.na(df$Y)] = 0
  df$Z[ is.na(df$Z)] = 0
  if (acc_data) {
    xdf$data.out = df
    df = xdf
  }
  df
}