R/stat-smooth.r

In duthedd/ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics

#' @param method smoothing method (function) to use, eg. "lm", "glm",
#'   "gam", "loess", "rlm".
#'
#'   For \code{method = "auto"} the smoothing method is chosen based on the
#'   size of the largest group (across all panels). \code{\link{loess}} is
#'   used for less than 1,000 observations; otherwise \code{\link[mgcv]{gam}} is
#'   used with \code{formula = y ~ s(x, bs = "cs")}. Somewhat anecdotally,
#'   \code{loess} gives a better appearance, but is O(n^2) in memory, so does
#'   not work for larger datasets.
#' @param formula formula to use in smoothing function, eg. \code{y ~ x},
#'   \code{y ~ poly(x, 2)}, \code{y ~ log(x)}
#' @param se display confidence interval around smooth? (TRUE by default, see
#'   level to control
#' @param fullrange should the fit span the full range of the plot, or just
#'   the data
#' @param level level of confidence interval to use (0.95 by default)
#' @param span Controls the amount of smoothing for the default loess smoother.
#'   Smaller numbers produce wigglier lines, larger numbers produce smoother
#'   lines.
#' @param n number of points to evaluate smoother at
#' @param method.args List of additional arguments passed on to the modelling
#'   function defined by \code{method}.
#' @section Computed variables:
#' \describe{
#'   \item{y}{predicted value}
#'   \item{ymin}{lower pointwise confidence interval around the mean}
#'   \item{ymax}{upper pointwise confidence interval around the mean}
#'   \item{se}{standard error}
#' }
#' @export
#' @rdname geom_smooth
stat_smooth <- function(mapping = NULL, data = NULL,
                        geom = "smooth", position = "identity",
                        ...,
                        method = "auto",
                        formula = y ~ x,
                        se = TRUE,
                        n = 80,
                        span = 0.75,
                        fullrange = FALSE,
                        level = 0.95,
                        method.args = list(),
                        na.rm = FALSE,
                        show.legend = NA,
                        inherit.aes = TRUE) {
  layer(
    data = data,
    mapping = mapping,
    stat = StatSmooth,
    geom = geom,
    position = position,
    show.legend = show.legend,
    inherit.aes = inherit.aes,
    params = list(
      method = method,
      formula = formula,
      se = se,
      n = n,
      fullrange = fullrange,
      level = level,
      na.rm = na.rm,
      method.args = method.args,
      span = span,
      ...
    )
  )
}

#' @rdname ggplot2-ggproto
#' @format NULL
#' @usage NULL
#' @export
StatSmooth <- ggproto("StatSmooth", Stat,

  setup_params = function(data, params) {
    if (identical(params$method, "auto")) {
      # Use loess for small datasets, gam with a cubic regression basis for
      # larger. Based on size of the _largest_ group to avoid bad memory
      # behaviour of loess
      max_group <- max(table(interaction(data$group, data$PANEL, drop = TRUE)))

      if (max_group < 1000) {
        params$method <- "loess"
      } else {
        params$method <- "gam"
        params$formula <- y ~ s(x, bs = "cs")
      }
      message("`geom_smooth()` using method = '", params$method, 
              "' and formula '", deparse(params$formula), "'")
    }
    if (identical(params$method, "gam")) {
      params$method <- mgcv::gam
    }

    params
  },

  compute_group = function(data, scales, method = "auto", formula = y~x,
                           se = TRUE, n = 80, span = 0.75, fullrange = FALSE,
                           xseq = NULL, level = 0.95, method.args = list(),
                           na.rm = FALSE) {
    if (length(unique(data$x)) < 2) {
      # Not enough data to perform fit
      return(data.frame())
    }

    if (is.null(data$weight)) data$weight <- 1

    if (is.null(xseq)) {
      if (is.integer(data$x)) {
        if (fullrange) {
          xseq <- scales$x$dimension()
        } else {
          xseq <- sort(unique(data$x))
        }
      } else {
        if (fullrange) {
          range <- scales$x$dimension()
        } else {
          range <- range(data$x, na.rm = TRUE)
        }
        xseq <- seq(range[1], range[2], length.out = n)
      }
    }
    # Special case span because it's the most commonly used model argument
    if (identical(method, "loess")) {
      method.args$span <- span
    }

    if (is.character(method)) method <- match.fun(method)

    base.args <- list(quote(formula), data = quote(data), weights = quote(weight))
    model <- do.call(method, c(base.args, method.args))

    predictdf(model, xseq, se, level)
  },

  required_aes = c("x", "y")
)