highlight {broom} functions in examples

Author: teunbrand

R/fortify-lm.R

@@ -21,63 +21,22 @@
 #' @param ... not used by this method
 #' @keywords internal
 #' @export
-#' @examples
+#' @examplesIf require("broom")
 #' mod <- lm(mpg ~ wt, data = mtcars)
-#' head(fortify(mod))
-#' head(fortify(mod, mtcars))
-#'
-#' plot(mod, which = 1)
 #'
-#' ggplot(mod, aes(.fitted, .resid)) +
-#'   geom_point() +
-#'   geom_hline(yintercept = 0) +
-#'   geom_smooth(se = FALSE)
+#' # Show augmented model
+#' head(augment(mod))
+#' head(fortify(mod))
 #'
-#' ggplot(mod, aes(.fitted, .stdresid)) +
+#' # Using augment to convert model to ready-to-plot data
+#' ggplot(augment(mod), aes(.fitted, .resid)) +
 #'   geom_point() +
 #'   geom_hline(yintercept = 0) +
 #'   geom_smooth(se = FALSE)
 #'
-#' ggplot(fortify(mod, mtcars), aes(.fitted, .stdresid)) +
-#'   geom_point(aes(colour = factor(cyl)))
-#'
-#' ggplot(fortify(mod, mtcars), aes(mpg, .stdresid)) +
-#'   geom_point(aes(colour = factor(cyl)))
-#'
-#' plot(mod, which = 2)
-#' ggplot(mod) +
-#'   stat_qq(aes(sample = .stdresid)) +
-#'   geom_abline()
-#'
-#' plot(mod, which = 3)
-#' ggplot(mod, aes(.fitted, sqrt(abs(.stdresid)))) +
-#'   geom_point() +
-#'   geom_smooth(se = FALSE)
-#'
-#' plot(mod, which = 4)
-#' ggplot(mod, aes(seq_along(.cooksd), .cooksd)) +
-#'   geom_col()
-#'
-#' plot(mod, which = 5)
-#' ggplot(mod, aes(.hat, .stdresid)) +
-#'   geom_vline(linewidth = 2, colour = "white", xintercept = 0) +
-#'   geom_hline(linewidth = 2, colour = "white", yintercept = 0) +
-#'   geom_point() + geom_smooth(se = FALSE)
-#'
-#' ggplot(mod, aes(.hat, .stdresid)) +
-#'   geom_point(aes(size = .cooksd)) +
-#'   geom_smooth(se = FALSE, linewidth = 0.5)
-#'
-#' plot(mod, which = 6)
-#' ggplot(mod, aes(.hat, .cooksd)) +
-#'   geom_vline(xintercept = 0, colour = NA) +
-#'   geom_abline(slope = seq(0, 3, by = 0.5), colour = "white") +
-#'   geom_smooth(se = FALSE) +
+#' # Colouring by original data not included in the model
+#' ggplot(augment(mod, mtcars), aes(.fitted, .std.resid, colour = factor(cyl))) +
 #'   geom_point()
-#'
-#' ggplot(mod, aes(.hat, .cooksd)) +
-#'   geom_point(aes(size = .cooksd / .hat)) +
-#'   scale_size_area()
 fortify.lm <- function(model, data = model$model, ...) {
   lifecycle::deprecate_warn(
     "3.6.0", I("`fortify(<lm>)`"), I("`broom::augment(<lm>)`")

R/fortify-multcomp.R

@@ -11,28 +11,35 @@
 #' @param data,... other arguments to the generic ignored in this method.
 #' @name fortify-multcomp
 #' @keywords internal
-#' @examples
-#' if (require("multcomp")) {
+#' @examplesIf require("multcomp") && require("broom")
 #' amod <- aov(breaks ~ wool + tension, data = warpbreaks)
-#' wht <- glht(amod, linfct = mcp(tension = "Tukey"))
+#' wht <- multcomp::glht(amod, linfct = multcomp::mcp(tension = "Tukey"))
 #'
+#' tidy(wht) # recommended
 #' fortify(wht)
-#' ggplot(wht, aes(lhs, estimate)) + geom_point()
 #'
-#' CI <- confint(wht)
-#' fortify(CI)
-#' ggplot(CI, aes(lhs, estimate, ymin = lwr, ymax = upr)) +
+#' ggplot(tidy(wht), aes(contrast, estimate)) + geom_point()
+#'
+#' ci <- confint(wht)
+#' tidy(ci) # recommended
+#' fortify(ci)
+#'
+#' ggplot(tidy(confint(wht)),
+#'        aes(contrast, estimate, ymin = conf.low, ymax = conf.high)) +
 #'    geom_pointrange()
 #'
-#' fortify(summary(wht))
-#' ggplot(mapping = aes(lhs, estimate)) +
-#'    geom_linerange(aes(ymin = lwr, ymax = upr), data = CI) +
-#'    geom_point(aes(size = p), data = summary(wht)) +
+#' smry <- summary(wht)
+#' tidy(smry) # recommended
+#' fortify(smry)
+#'
+#' ggplot(mapping = aes(contrast, estimate)) +
+#'    geom_linerange(aes(ymin = conf.low, ymax = conf.high), data = tidy(ci)) +
+#'    geom_point(aes(size = adj.p.value), data = tidy(smry)) +
 #'    scale_size(transform = "reverse")
 #'
-#' cld <- cld(wht)
+#' cld <- multcomp::cld(wht)
+#' tidy(cld) # recommended
 #' fortify(cld)
-#' }
 NULL
 
 #' @method fortify glht