R/stat_dailyAQCategory.R

In MazamaScience/AirMonitorPlots: Plot Utilities for the AirMonitor Package

#' @title Add daily average air quality categories to a plot
#'
#' @description
#' This function calculates the daily averaged AQI PM25 categories for the data
#' and colors the data by AQI cateogry when it is added to a plot. The default
#' is to add them as bars.
#'
#' @param mapping Set of aesthetic mappings created by \code{aes()}. If
#'   specified and \code{inherit.aes = TRUE} (the default), it is combined with
#'   the default mapping at the top level of the plot. You must supply
#'   \code{mapping} if there is no plot mapping.
#' @param data The data to be displayed in this layer. There are three options:
#'   if \code{NULL}, the default, the data is inherited from the plot data. A
#'   \code{data.frame} or other object, will override the plot data. A
#'   \code{function} will be called witha  single argument, the plot data. The
#'   return value must be a \code{data.frame}, and will be used as the layer
#'   data.
#' @param mv4Colors If \code{TRUE}, use the colors used in the monitoring v4
#'   site. Otherwise, use the "official" AQI colors.
#' @param timezone timezone for day start and end for averaging. If \code{NULL},
#'   uses the timezone used by the x-axis datetime scale. If the x-axis datetime
#'   scale has no timezone, it defaults to UTC.
#' @param minHours Minimum number oof valid data hours required to calculate
#'   each daily statistic
#' @param width bar width in units of days.
#' @param adjustylim if \code{TRUE}, the ylim of the plot will automatically be
#'   adjusted for the range of the daily means.
#' @param missingDataBar if \code{TRUE}, a transparent gray bar will be plotted
#'   where data is missing.
#' @param geom The geometic object to display the data
#' @param position Position adjustment, either as a string, or the result of a
#'   call to a position adjustment function.
#' @param na.rm remove NA values from data
#' @param show.legend logical indicating whether this layer should be included
#'   in legends.
#' @param inherit.aes if \code{FALSE}, overrides the default aesthetics, rather
#'   than combining with them. This is most useful for helper functions that
#'   define both data and the aesthetics and shouldn't inherit behaviour from
#'   the default plot specificatino, eg \code{borders()}.
#' @param ... additional arguments passed on to \code{layer()}, such as
#'   aesthetics.
#'
#' @import ggplot2
#' @export
#'
#' @examples
#' \dontrun{
#' library(AirMonitorPlots)
#'
#' monitor <- airsis_loadLatest()
#'
#' ggplot_pm25Timeseries(monitor) +
#'   stat_AQCategory(color = NA, width = 3000) +
#'   stat_dailyAQCategory(alpha = .5, missingDataBar = FALSE, width = 1, size = 1) +
#'   facet_wrap(~deviceDeploymentID)
#'
#' monitor <-
#'   airnow_loadLatest() %>%
#'   monitor_filter(id = "a18dacf2eabb6c79_160590004_04")
#'
#' ggplot_pm25Timeseries(mts_monitor) +
#'   stat_dailyAQCategory()
#' }
stat_dailyAQCategory <- function(
  mapping = NULL,
  data = NULL,
  mv4Colors = FALSE,
  timezone = NULL,
  minHours = 18,
  width = .8,
  adjustylim = FALSE,
  missingDataBar = TRUE,
  geom = "bar",
  position = "identity",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE,
  ...
) {

  width <- 86400 * width

  list(
    layer(
      stat = StatDailyAQILevel,
      data = data,
      mapping = mapping,
      geom = geom,
      position = position,
      show.legend = show.legend,
      inherit.aes = inherit.aes,
      params = list(
        mv4Colors = mv4Colors,
        timezone = timezone,
        minHours = minHours,
        na.rm = na.rm,
        adjustylim = adjustylim,
        width = width,
        missingDataBar = missingDataBar,
        ...
      )
    )
  )
}


StatDailyAQILevel <- ggproto(
  "StatDailyAQILevel",
  Stat,
  # BEGIN compute_group function
  compute_group = function(data,
                           scales,
                           params,
                           mv4Colors,
                           timezone,
                           minHours,
                           na.rm,
                           adjustylim,
                           missingDataBar) {

    # Get timezone
    if (is.null(timezone)) {
      if (!is.null(attr(scales$x$breaks, "tzone"))) {
        timezone <- attr(scales$x$breaks, "tzone")
      } else {
        timezone <- "UTC"
      }
    }

    ## STEPS:
    #  * Get date from numeric to POSIXct
    #  * Get Daily Mean

    dailyMeans <- data %>%
      dplyr::mutate(
        datetime = as.POSIXct(.data$x, tz = timezone, origin = "1970-01-01"),
        date = strftime(.data$datetime, "%Y%m%d", tz = timezone)
      ) %>%
      dplyr::group_by(date) %>%
      dplyr::summarise(
        dailyMean = mean(.data$y),
        count = sum(!is.na(.data$y))
      ) %>%
      dplyr::mutate(
        dailyMean = dplyr::if_else(.data$count < minHours, NA_real_, .data$dailyMean),
        datetime = .data$date %>%
          strptime("%Y%m%d", tz = timezone) %>%
          as.POSIXct(tz = timezone) %>%
          magrittr::add(lubridate::dhours(12)) %>%
          as.numeric()
      )

    data <- dplyr::select(
      dailyMeans,
      x = .data$datetime,
      y = .data$dailyMean
    )

    # Add column for AQI level
    data$aqi <- .bincode(data$y, AirMonitor::US_AQI$breaks_PM2.5, include.lowest = TRUE)

    if (!"colour" %in% names(data)) {
      if (mv4Colors) {
        data$colour <- AirMonitor::US_AQI$colors_subdued[data$aqi]
      } else {
        data$colour <- AirMonitor::US_AQI$colors_EPA[data$aqi]
      }
    }

    if (!"fill" %in% names(data)) {
      if (mv4Colors) {
        data$fill <- AirMonitor::US_AQI$colors_subdued[data$aqi]
      } else {
        data$fill <- AirMonitor::US_AQI$colors_EPA[data$aqi]
      }
    }

    if (adjustylim) {

      ymax <- max(data$y, na.rm = TRUE)

      yhi <- dplyr::case_when(
        ymax <= 50   ~ 50,
        ymax <= 100  ~ 100,
        ymax <= 200  ~ 200,
        ymax <= 400  ~ 400,
        ymax <= 600  ~ 600,
        ymax <= 1000 ~ 1000,
        ymax <= 1500 ~ 1500,
        TRUE         ~ 1.05 * ymax
      )

      scales$y$limits <- c(0, yhi)
    }

    # Add missing data bars
    if (missingDataBar) {

      # Extend data to full extent
      max_x <- max(data$x)
      while (max_x < scales$x$get_limits()[2]) {
        max_x <- max_x + 86400
        data <- dplyr::bind_rows(data, tibble::tibble(
          x = max_x,
          y = NA,
          aqi = NA,
          colour = NA,
          fill = NA
        ))
      }

      min_x <- min(data$x)
      while (min_x > scales$x$get_limits()[2]) {
        min_x <- min_x - 86400
        data <- dplyr::bind_rows(data, tibble::tibble(
          x = min_x,
          y = NA,
          aqi = NA,
          colour = NA,
          fill = NA
        ))
      }

      # Add gray bars
      for (missingRow in which(is.na(data$y))) {
        data[missingRow, "y"] <- scales$y$get_limits()[2]
      }
    }

    # Make sure there is no mean for today
    date <- strftime(as.POSIXct(data$x, tz = timezone, origin = "1970-01-01"), "%Y%m%d", tz = timezone)
    if (strftime(lubridate::now(tzone = timezone), "%Y%m%d", tz = timezone) %in% date) {
      data$y[which(date == strftime(lubridate::now(tzone = timezone), "%Y%m%d", tz = timezone))] <- NA
      data$fill[which(date == strftime(lubridate::now(tzone = timezone), "%Y%m%d", tz = timezone))] <- NA
    }

    return(data)

  },
  # END compute_group function

  required_aes = c("x", "y"),
  finish_layer = function(self, data, params) {
    # remove outline from missing data bars
    data$colour <- ifelse(is.na(data$aqi), NA, data$colour)
    data$fill <- ifelse(is.na(data$aqi), "#7F7F7F", data$fill)
    data$alpha <- ifelse(is.na(data$aqi), 0.3, data$alpha)
    data
  }

)