R/diagnostic_plots.R

In spsanderson/healthyR.ts: The Time Series Modeling Companion to 'healthyR'

#' Get Random Walk `ggplot2` layers
#'
#' @author Steven P. Sanderson II, MPH
#'
#' @description
#' Get layers to add to a `ggplot` graph from the [ts_random_walk()] function.
#'
#' @details
#' - Set the intercept of the initial value from the random walk
#' - Set the max and min of the cumulative sum of the random walks
#'
#' @param .data The data passed to the function.
#'
#' @examples
#' library(ggplot2)
#'
#' df <- ts_random_walk()
#'
#' df %>%
#'   ggplot(
#'     mapping = aes(
#'       x = x
#'       , y = cum_y
#'       , color = factor(run)
#'       , group = factor(run)
#'    )
#'  ) +
#'  geom_line(alpha = 0.8) +
#'  ts_random_walk_ggplot_layers(df)
#'
#' @return
#' A `ggplot2` layers object
#' @name ts_random_walk_ggplot_layers
NULL

#' @export
#' @rdname ts_random_walk_ggplot_layers

# Function for obtaining ggplot layers to commonly apply to subsequent plots
ts_random_walk_ggplot_layers <- function(.data) {

  # Check
  if (!is.data.frame(.data)) {
    stop(call. = FALSE, "(.data) was not provided. Please supply.")
  }

  df <- dplyr::as_tibble(.data)

  gg_layers <- list(
    ggplot2::geom_hline(
      yintercept = attr(df, ".initial_value"),
      color = "black", linetype = "dotted"
    ),
    ggplot2::geom_hline(
      yintercept = max(subset(df, x == max(x))$cum_y),
      color = "steelblue", linetype = "dashed"
    ),
    ggplot2::geom_hline(
      yintercept = min(subset(df, x == max(x))$cum_y),
      color = "firebrick", linetype = "dashed"
    ),
    ggplot2::annotate(
      geom = "label",
      x = max(df$x), y = max(subset(df, x == max(x))$cum_y),
      label = prettyNum(round(max(subset(df, x == max(x))$cum_y), 0), big.mark = ","),
      size = 3, hjust = 1, color = "white", fill = "steelblue"
    ),
    ggplot2::annotate(
      geom = "label",
      x = max(df$x), y = min(subset(df, x == max(x))$cum_y),
      label = prettyNum(round(min(subset(df, x == max(x))$cum_y), 0), big.mark = ","),
      size = 3, hjust = 1, color = "white", fill = "firebrick"
    ),
    ggplot2::labs(
      title = "Random Walk Simulation",
      subtitle = paste(
        attr(df, ".num_walks"), "Random walks with",
        paste0("an initial value of: ", prettyNum(attr(df, ".initial_value"), big.mark = ",")),
        "and", paste0(round(attr(df, ".sd") * 100, 0), "%"),
        "volatility"
      ),
      x = "Days into future", y = "Value"
    ),
    ggplot2::theme_minimal(),
    ggplot2::theme(legend.position = "none")
  )
  return(gg_layers)
}

#' Quality Control Run Chart
#'
#' @author Steven P. Sanderson II, MPH
#'
#' @description
#' A control chart is a specific type of graph that shows data points between
#' upper and lower limits over a period of time. You can use it to understand
#' if the process is in control or not. These charts commonly have three types
#' of lines such as upper and lower specification limits, upper and lower limits
#' and planned value. By the help of these lines, Control Charts show the
#' process behavior over time.
#'
#' @details
#' - Expects a time-series tibble/data.frame
#' - Expects a date column and a value column
#'
#' @param .data The data.frame/tibble to be passed.
#' @param .date_col The column holding the timestamp.
#' @param .value_col The column with the values to be analyzed.
#' @param .interactive Default is FALSE, TRUE for an interactive plotly plot.
#' @param .median Default is TRUE. This will show the median line of the data.
#' @param .cl This is the first upper control line
#' @param .mcl This is the second sigma control line positive
#' @param .ucl This is the third sigma control line positive
#' @param .lc This is the first negative control line
#' @param .lmcl This is the second sigma negative control line
#' @param .llcl This si the thrid sigma negative control line
#'
#' @examples
#' library(dplyr)
#'
#' data_tbl <- ts_to_tbl(AirPassengers) %>%
#'   select(-index)
#'
#' data_tbl %>%
#'   ts_qc_run_chart(
#'     .date_col    = date_col
#'     , .value_col = value
#'     , .llcl      = TRUE
#'   )
#'
#' @return
#' A static ggplot2 graph or if .interactive is set to TRUE a plotly plot
#' @name ts_qc_run_chart
NULL

#' @export
#' @rdname ts_qc_run_chart

ts_qc_run_chart <- function(.data, .date_col, .value_col, .interactive = FALSE,
                            .median = TRUE, .cl = TRUE, .mcl = TRUE, .ucl = TRUE,
                            .lc = FALSE, .lmcl = FALSE, .llcl = FALSE) {

  # Tidyeval
  date_col_var_expr <- rlang::enquo(.date_col)
  value_col_var_expr <- rlang::enquo(.value_col)

  # Checks
  if (!is.data.frame(.data)) {
    stop(call. = FALSE, "(.data) is missing. Please supply.")
  }

  if (rlang::quo_is_missing(date_col_var_expr)) {
    stop(call. = FALSE, "(.date_col) is missing. Please supply.")
  }

  if (rlang::quo_is_missing(value_col_var_expr)) {
    stop(call. = FALSE, "(.value_col) is missing. Please supply.")
  }

  data_tbl <- tibble::as_tibble(.data)

  data_tbl <- data_tbl %>%
    dplyr::select({{ date_col_var_expr }}, {{ value_col_var_expr }}) %>%
    purrr::set_names("ds", "y")

  y <- data_tbl %>% dplyr::pull(y)
  max_ds <- data_tbl %>%
    dplyr::pull(ds) %>%
    base::max()

  # Construct control limit lines
  mean_alos <- base::mean(y, na.rm = TRUE)
  median_alos <- stats::median(y, na.rm = TRUE)
  std_dev <- stats::sd(y)
  cl_a <- mean_alos + std_dev
  cl_b <- mean_alos + (2 * std_dev)
  cl_c <- mean_alos + (3 * std_dev)
  cl_d <- mean_alos - std_dev
  cl_e <- mean_alos - (2 * std_dev)
  cl_f <- mean_alos - (3 * std_dev)

  # Plot
  p <- data_tbl %>%
    ggplot2::ggplot(
      mapping = ggplot2::aes(
        x = ds,
        y = y
      )
    ) +
    ggplot2::geom_line(size = .5, color = "#2C3E50") +
    ggplot2::theme_minimal()

  # Check if add median line
  if (.median) {
    p <- p +
      ggplot2::geom_line(
        mapping = ggplot2::aes(y = median_alos),
        linetype = "dashed",
        size = 1,
        color = "#6A3D9A"
      )
  }

  # Check if add cl
  if (.cl) {
    p <- p +
      ggplot2::geom_line(
        mapping = ggplot2::aes(y = cl_a),
        color = "#18BC9C",
        size = 1
      )
  }

  # Check if add mcl
  if (.mcl) {
    p <- p +
      ggplot2::geom_line(
        mapping = ggplot2::aes(y = cl_b),
        color = "#CCBE93",
        size = 1
      )
  }

  # Check if add ucl
  if (.ucl) {
    p <- p +
      ggplot2::geom_line(
        mapping = ggplot2::aes(y = cl_c),
        color = "#E31A1C",
        size = 1
      )
  }

  # Check if add lcl
  if (.lc) {
    p <- p +
      ggplot2::geom_line(
        mapping = ggplot2::aes(y = cl_d),
        color = "#18BC9C",
        size = 1
      )
  }

  # Check if add mcl
  if (.lmcl) {
    p <- p +
      ggplot2::geom_line(
        mapping = ggplot2::aes(y = cl_e),
        color = "#CCBE93",
        size = 1
      )
  }

  # Check if add ucl
  if (.llcl) {
    p <- p +
      ggplot2::geom_line(
        mapping = ggplot2::aes(y = cl_f),
        color = "#E31A1C",
        size = 1
      )
  }

  # * Interactive ----
  if (.interactive) {
    return(plotly::ggplotly(p))
  } else {
    p <- p +
      ggplot2::geom_text(
        mapping = ggplot2::aes(x = max_ds, y = cl_a),
        label = round(cl_a, 2),
        hjust = -.2,
        na.rm = TRUE
      ) +
      ggplot2::geom_text(
        mapping = ggplot2::aes(x = max_ds, y = cl_b),
        label = round(cl_b, 2),
        hjust = -.2,
        na.rm = TRUE
      ) +
      ggplot2::geom_text(
        mapping = ggplot2::aes(x = max_ds, y = cl_c),
        label = round(cl_c, 2),
        hjust = -.2,
        na.rm = TRUE
      ) +
      ggplot2::geom_text(
        mapping = ggplot2::aes(x = max_ds, y = cl_d),
        label = round(cl_a, 2),
        hjust = -.2,
        na.rm = TRUE
      ) +
      ggplot2::geom_text(
        mapping = ggplot2::aes(x = max_ds, y = cl_e),
        label = round(cl_b, 2),
        hjust = -.2,
        na.rm = TRUE
      ) +
      ggplot2::geom_text(
        mapping = ggplot2::aes(x = max_ds, y = cl_f),
        label = round(cl_c, 2),
        hjust = -.2,
        na.rm = TRUE
      ) +
      ggplot2::geom_text(
        mapping = ggplot2::aes(x = max_ds, y = median_alos),
        label = median_alos,
        hjust = -.2,
        na.rm = TRUE
      )
  }

  # * Return ----
  print(p)
}