R/find_epoch.R

In gipso/actverse: Tools for Actigraphy Data Analysis

#' Find the epochs/periodicities in a `tsibble`
#'
#' @description
#'
#' `r lifecycle::badge("experimental")`
#'
#' `find_epoch()` returns the different epochs/periodicities present in a
#' [`tsibble`][tsibble::tsibble()] object along with a best match epoch based
#' on a predefined threshold.
#'
#' @details
#'
#' In the rare cases that a [`tsibble`][tsibble::tsibble()] object have
#' periodicities with the same prevalence above the threshold, `best_match` will
#' return just one of those values.
#'
#' @param data A [tsibble][tsibble::tsibble()] object with a [`Date`][as.Date()]
#'   or [`POSIXt`][as.POSIXct()] vector as index.
#' @param threshold (optional) a number, from `0` to `1`, indicating the minimum
#'   proportion that an epoch must have to be considered valid. `threshold = 1`
#'   means that the regularity of the time series must be strict (i.e., have
#'   just 1 periodicity) (default: `0.9`).
#'
#' @return A [`list`][list()] object with the following elements:
#'
#' * `best_match`: A number indicating the epoch/periodicity above the
#' `threshold` with greater prevalence in seconds. If none is find, `best_match`
#' value will be equal as `as.numeric(NA)`.
#' * `prevalence`: a [`tibble`][tibble::tibble()] listing the unique
#' epochs/periodicities found in `data` along with its proportions.
#'
#' @family utility functions
#' @export
#'
#' @examples
#' data <- dplyr::tibble(
#'     index = c(
#'         as.POSIXct(seq(60, 5400, by = 60), origin = lubridate::origin),
#'         as.POSIXct(seq(5430, 5490, by = 30), origin = lubridate::origin),
#'         as.POSIXct(seq(5505, 5520, by = 15), origin = lubridate::origin),
#'         as.POSIXct(seq(5530, 5540, by = 10), origin = lubridate::origin),
#'         as.POSIXct(seq(5545, 5555, by = 5), origin = lubridate::origin)
#'         ),
#'     x = seq_along(timestamp)
#'     )
#' data <- tsibble::tsibble(data, index = index)
#'
#' find_epoch(data, 0.8)
find_epoch <- function(data, threshold = 0.9) {
    assert_tsibble(data, min.rows = 2, min.cols = 2)
    assert_index_class(data, c("Date", "POSIXt"))
    checkmate::assert_number(threshold, lower = 0.001, upper = 1)

    # R CMD Check variable bindings fix (see: https://bit.ly/3z24hbU)
    # nolint start: object_usage_linter.
    . <- .x <- proportion <- NULL
    # nolint end

    diff <- diff(data[[tsibble::index_var(data)]]) %>%
        `units<-`("secs") %>%
        as.numeric()

    prevalence <- unique(diff) %>%
        purrr::map(~ dplyr::tibble(
            epoch = .x,
            proportion = length(which(diff == .x)) / length(diff))) %>%
        purrr::reduce(dplyr::bind_rows) %>%
        dplyr::arrange(dplyr::desc(proportion))

    if (prevalence$proportion[1] >= threshold) {
        best_match <- prevalence$epoch[1]
    } else {
        best_match <- as.numeric(NA)
    }

    list(best_match = best_match, prevalence = prevalence)
}