R/plot.R

In aedseo: Automated and Early Detection of Seasonal Epidemic Onset and Burden Levels

#' Create a complete 'ggplot' appropriate to a particular data type
#'
#' @description
#'
#' This function generates a complete 'ggplot' object suitable for visualizing time series data in
#' `tsd`, `tsd_onset`, `tsd_onset_and_burden` or `tsd_growth_warning` objects.
#'
#' @param x An `tsd`, `tsd_onset`, `tsd_onset_and_burden` or `tsd_growth_warning` object
#' @param ... Additional arguments passed to `autoplot()`.
#'
#' @return A 'ggplot' object for visualizing output from desired method.
#'
#' @aliases plot
#'
#' @seealso [autoplot()]
#'
#' @examples
#' # set.seed(321)
#' # Create and plot `tsd` object
#' tsd_obj <- generate_seasonal_data(
#'   years = 3,
#'   phase = 1,
#'   start_date = as.Date("2021-10-18")
#' )
#' plot(tsd_obj)
#'
#' disease_threshold <- 150
#'
#' # Create and plot `tsd_onset` object
#' tsd_onset_obj <- seasonal_onset(
#'   tsd = tsd_obj,
#'   k = 3,
#'   level = 0.95,
#'   disease_threshold = disease_threshold,
#'   family = "quasipoisson"
#' )
#' plot(tsd_onset_obj)
#'
#' # Create a `tsd_onset_and_burden` object
#' tsd_onset_burden_obj <- combined_seasonal_output(
#'   tsd = tsd_obj,
#'   disease_threshold = disease_threshold
#' )
#' plot(tsd_onset_burden_obj,
#'      y_lower_bound = ifelse(disease_threshold < 10, 1, 5))
#'
#' # Create a `tsd_growth_warning` object
#' tsd_onset_seasons <- seasonal_onset(
#'   tsd = tsd_obj,
#'   season_start = 21,
#'   family = "quasipoisson",
#'   only_current_season = FALSE
#' )
#' tsd_gr_w <- consecutive_growth_warnings(tsd_onset_seasons)
#' plot(tsd_gr_w)
#'
#' @importFrom graphics plot
#' @rdname plot
#' @method plot tsd
#' @export
plot.tsd <- function(x, ...) {
  suppressWarnings(print(autoplot(x, ...)))
}
#' @rdname plot
#' @method plot tsd_onset
#' @export
plot.tsd_onset <- function(x, ...) {
  plot_list <- autoplot(object = x, ...)
  suppressWarnings(print(plot_list$observed))
  suppressWarnings(print(plot_list$growth_rate))
}
#' @rdname plot
#' @method plot tsd_onset_and_burden
#' @export
plot.tsd_onset_and_burden <- function(x, ...) {
  suppressWarnings(print(autoplot(x, ...)))
}

#' @rdname plot
#' @method plot tsd_growth_warning
#' @export
plot.tsd_growth_warning <- function(x, ...) {
  suppressWarnings(print(autoplot(x, ...)))
}