mcmc_areas() fixes

[tjmahr]

From the NEWS.md

• mcmc_areas()
  gains an argument area_method which controls how to draw the density
  curves. The default "equal area" constrains the heights so that the curves
  have the same area. As a result, a narrow interval will appear as a spike
  of density, while a wide, uncertain interval is spread thin over the x axis.
  Alternatively "equal height" will set the maximum height on each curve to
  the same value. This works well when the intervals are about the same width.
  Otherwise, that wide, uncertain interval will dominate the visual space
  compared to a narrow, less uncertain interval. A compromise between the two is
  "scaled height" which scales the curves from "equal height" using
  height * sqrt(height). (support for equal-height curves mcmc_areas() #163, mcmc_areas() fixes #169)

• mcmc_areas() correctly plots density curves where the point estimate
  does not include the highest point of the density curve.
  (Point estimate plotted weirdly in mcmc_areas() #168, mcmc_areas() fixes #169, @jtimonen)

• mcmc_areas_ridges() draws the vertical line at x = 0 over the curves so
  that it is always visible.

• mcmc_intervals() and mcmc_areas() raise a warning if prob_outer is ever
  less than prob. It sorts these two values into the correct order. (prob_outer ignored in mcmc_areas_ridges() #138)

Not in NEWS.md

• Updated all reference images in the visual unit tests.

Here are examples of the three plotting styles.

library(bayesplot)
library(tidyverse)

set.seed(123)

K <- 4
N <- 1000
X <- array(0,c(N,1,K))
for(k in 1:K) {
  x <- rgamma(N, c(1, 2, 4, 5)[k], c(3, 5, 5, 6)[k])
  X[,1,k] <- x
}
X[,1,4] <- runif(1000, min = min(X), max = max(X))
dimnames(X)[[3]] <- as.list(paste("x", 1:K, sep="_"))
x <- X

p1 <- mcmc_areas(X, area_method = "equal area") + ggtitle("equal area")
p2 <- mcmc_areas(X, area_method = "equal height") + ggtitle("equal height")
p3 <- mcmc_areas(X, area_method = "scaled height") + ggtitle("scaled height")

library(patchwork)
p1 + p2 + p3 + plot_layout(ncol = 1)

[tjmahr]

Closes #163. Closes #168. Closes #138.

[jgabry]

@tjmahr These changes are great! And I love the examples you added to the mcmc_areas doc where the titles/subtitles of the plots in the examples clearly explain the difference between the area_method options. Thanks!

[jgabry]

@avehtari I know you were interested in this, so just tagging you so you know it's merged now. thanks to @tjmahr the master branch of bayesplot should now have mcmc_areas with an argument area_method.

[avehtari]

Great!