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Add marginal dist. to PPD plots#429

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Add marginal dist. to PPD plots#429
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@mattansb mattansb commented Mar 8, 2026 •
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Addresses #425

This PR adds the show_marginal argument (default FALSE) to the PPD-distributions and the PPD-test-statistics functions (the PPD-intervals functions de-facto show the marginal PPD(s)).

I think we need a better default PPD color - which?

Here are all of these functions (default plots -- show_marginal=FALSE -- are unchanged!):

library(bayesplot)
#> This is bayesplot version 1.15.0.9000
#> - Online documentation and vignettes at mc-stan.org/bayesplot
#> - bayesplot theme set to bayesplot::theme_default()
#>    * Does _not_ affect other ggplot2 plots
#>    * See ?bayesplot_theme_set for details on theme setting

ypred <- example_yrep_draws()[1:19,]
g <- example_group_data()

ppd-distributions

ppd_dens_overlay(ypred) # mid color

ppd_dens_overlay(ypred, show_marginal = TRUE) # light + dark colors

# ppd_ecdf_overlay(ypred)
ppd_ecdf_overlay(ypred, show_marginal = TRUE)

# ppd_dens(ypred)
ppd_dens(ypred, show_marginal = TRUE)

# ppd_hist(ypred)
ppd_hist(ypred, show_marginal = TRUE)
#> `stat_bin()` using `bins = 30`. Pick better value `binwidth`.
#> `stat_bin()` using `bins = 30`. Pick better value `binwidth`.

# ppd_dots(ypred)
ppd_dots(ypred, show_marginal = TRUE)

# ppd_freqpoly(ypred)
ppd_freqpoly(ypred, show_marginal = TRUE)
#> `stat_bin()` using `bins = 30`. Pick better value `binwidth`.
#> `stat_bin()` using `bins = 30`. Pick better value `binwidth`.

# ppd_freqpoly_grouped(ypred[1:4,], group = g)
ppd_freqpoly_grouped(ypred[1:4,], group = g, show_marginal = TRUE)
#> `stat_bin()` using `bins = 30`. Pick better value `binwidth`.
#> `stat_bin()` using `bins = 30`. Pick better value `binwidth`.

# ppd_boxplot(ypred[1:7,])
ppd_boxplot(ypred[1:7,], show_marginal = TRUE)

ppd-test-statistics

# ppd_stat_data returns marginal data too...
ppd_stat_data(ypred, g, var, show_marginal = TRUE) |>
  subset(variable == "PPD")
#> # A tibble: 2 × 3
#>   group  variable value
#>   <fct>  <fct>    <dbl>
#> 1 GroupA PPD       463.
#> 2 GroupB PPD       389.

# ppd_stat(ypred)
ppd_stat(ypred, show_marginal = TRUE)
#> `stat_bin()` using `bins = 30`. Pick better value `binwidth`.

# ppd_stat_grouped(ypred, g)
ppd_stat_grouped(ypred, g, show_marginal = TRUE)
#> `stat_bin()` using `bins = 30`. Pick better value `binwidth`.

# ppd_stat_freqpoly(ypred)
ppd_stat_freqpoly(ypred, show_marginal = TRUE)
#> `stat_bin()` using `bins = 30`. Pick better value `binwidth`.

# ppd_stat_freqpoly_grouped(ypred, g)
ppd_stat_freqpoly_grouped(ypred, g, show_marginal = TRUE)
#> `stat_bin()` using `bins = 30`. Pick better value `binwidth`.

# ppd_stat_2d(ypred)
ppd_stat_2d(ypred, show_marginal = TRUE)

Created on 2026-03-12 with reprex v2.1.1

@jgabry
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jgabry commented Mar 9, 2026

Thanks for the PR! I haven't had a chance to look at the code yet (I'm a bit swamped with work at the moment), but a couple quick comments:

  1. I just triggered the GHA workflows to run and it looks like there are some failures.

  2. Regarding the color issue you mentioned, this is my fault due to lack for foresight! When I added the PPD plots I was assuming no overlays since we wouldn't be comparing to data. So instead of the light and dark distinction used for the PPC plots, I went with a color somewhere in between. But now this makes it harder to find a good color for overlays.

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mattansb commented Mar 10, 2026

@jgabry I fixed the error that popped up.

Well the color "issue" can be resolved quite simply if we switch from "mid" to "light" for PPD, like PPC.
Or with some logic we can use "light"/"dark" only if show_marginal = TRUE and "mid" otherwise.
WDYT?

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jgabry commented Mar 10, 2026

Well the color "issue" can be resolved quite simply if we switch from "mid" to "light" for PPD, like PPC.
Or with some logic we can use "light"/"dark" only if show_marginal = TRUE and "mid" otherwise.
WDYT?

@tjmahr Any preference on this? The first option would keep the code simpler, but it would change the appearance of all the PPD plots (could we call this breaking visual backwards compatibility?). I would lean towards the second option but I'm not really sure.

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jgabry commented Mar 10, 2026

I just tried using this branch and show_marginal seems to work well for the plots I tried, but I don't think the new argument is documented yet.

@mattansb
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mattansb commented Mar 10, 2026

Sorry, it was only documented in PPD-distributions. Added to PPD-test-statistics now.

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mattansb commented Mar 12, 2026

Or with some logic we can use "light"/"dark" only if show_marginal = TRUE and "mid" otherwise.

I did this - wasn't too hard, and it actually made some of the code more simple. I've updated the examples above - I think it looks much better (note that the first ppd_dens_overlay(ypred) uses the mid color as it did before).

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jgabry commented Mar 13, 2026

Thanks, I agree it looks better!

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jgabry commented Mar 13, 2026

I think after that change there are now some visual tests that are failing. I checked one of the ppd_stat ones and it looks like it's the legend that's changed.

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mattansb commented Mar 14, 2026

Okay, should be fixed.

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@mattansb @jgabry