PPC-test-statistics: PPC test statistics
In jgabry/bayesplot: Plotting for Bayesian Models

PPC-test-statistics

R Documentation

PPC test statistics

Description

The distribution of a (test) statistic T(yrep), or a pair of (test) statistics, over the simulated datasets in yrep, compared to the observed value T(y) computed from the data y. See the Plot Descriptions and Details sections, below, as well as Gabry et al. (2019).

NOTE: Although the default test statistic is the mean, this is unlikely to detect anything interesting in most cases. In general we recommend using some other test statistic as discussed in Section 5 of Gabry et al. (2019).

Usage

ppc_stat(
  y,
  yrep,
  stat = "mean",
  ...,
  binwidth = NULL,
  bins = NULL,
  breaks = NULL,
  freq = TRUE
)

ppc_stat_grouped(
  y,
  yrep,
  group,
  stat = "mean",
  ...,
  facet_args = list(),
  binwidth = NULL,
  bins = NULL,
  breaks = NULL,
  freq = TRUE
)

ppc_stat_freqpoly(
  y,
  yrep,
  stat = "mean",
  ...,
  facet_args = list(),
  binwidth = NULL,
  bins = NULL,
  freq = TRUE
)

ppc_stat_freqpoly_grouped(
  y,
  yrep,
  group,
  stat = "mean",
  ...,
  facet_args = list(),
  binwidth = NULL,
  bins = NULL,
  freq = TRUE
)

ppc_stat_2d(y, yrep, stat = c("mean", "sd"), ..., size = 2.5, alpha = 0.7)

ppc_stat_data(y, yrep, group = NULL, stat)

Arguments

`y`	A vector of observations. See Details.
`yrep`	An `S` by `N` matrix of draws from the posterior (or prior) predictive distribution. The number of rows, `S`, is the size of the posterior (or prior) sample used to generate `yrep`. The number of columns, `N` is the number of predicted observations (`length(y)`). The columns of `yrep` should be in the same order as the data points in `y` for the plots to make sense. See the Details and Plot Descriptions sections for additional advice specific to particular plots.
`stat`	A single function or a string naming a function, except for the 2D plot which requires a vector of exactly two names or functions. In all cases the function(s) should take a vector input and return a scalar statistic. If specified as a string (or strings) then the legend will display the function name(s). If specified as a function (or functions) then generic naming is used in the legend.
`...`	Currently unused.
`binwidth`	Passed to `ggplot2::geom_histogram()` to override the default binwidth.
`bins`	Passed to `ggplot2::geom_histogram()` to override the default binwidth.
`breaks`	Passed to `ggplot2::geom_histogram()` as an alternative to `binwidth`.
`freq`	For histograms, `freq=TRUE` (the default) puts count on the y-axis. Setting `freq=FALSE` puts density on the y-axis. (For many plots the y-axis text is off by default. To view the count or density labels on the y-axis see the `yaxis_text()` convenience function.)
`group`	A grouping variable of the same length as `y`. Will be coerced to factor if not already a factor. Each value in `group` is interpreted as the group level pertaining to the corresponding observation.
`facet_args`	A named list of arguments (other than `facets`) passed to `ggplot2::facet_wrap()` or `ggplot2::facet_grid()` to control faceting. Note: if `scales` is not included in `facet_args` then bayesplot may use `scales="free"` as the default (depending on the plot) instead of the ggplot2 default of `scales="fixed"`.
`size`, `alpha`	For the 2D plot only, arguments passed to `ggplot2::geom_point()` to control the appearance of scatterplot points.

Details

For Binomial data, the plots may be more useful if the input contains the "success" proportions (not discrete "success" or "failure" counts).

Value

The plotting functions return a ggplot object that can be further customized using the ggplot2 package. The functions with suffix ⁠_data()⁠ return the data that would have been drawn by the plotting function.

Plot Descriptions

ppc_stat(), ppc_stat_freqpoly(): A histogram or frequency polygon of the distribution of a statistic computed by applying stat to each dataset (row) in yrep. The value of the statistic in the observed data, stat(y), is overlaid as a vertical line. More details and example usage of ppc_stat() can be found in Gabry et al. (2019).
ppc_stat_grouped(),ppc_stat_freqpoly_grouped(): The same as ppc_stat() and ppc_stat_freqpoly(), but a separate plot is generated for each level of a grouping variable. More details and example usage of ppc_stat_grouped() can be found in Gabry et al. (2019).
ppc_stat_2d(): A scatterplot showing the joint distribution of two statistics computed over the datasets (rows) in yrep. The value of the statistics in the observed data is overlaid as large point.

References

Gabry, J. , Simpson, D. , Vehtari, A. , Betancourt, M. and Gelman, A. (2019), Visualization in Bayesian workflow. J. R. Stat. Soc. A, 182: 389-402. doi:10.1111/rssa.12378. (journal version, arXiv preprint, code on GitHub)

Gelman, A., Carlin, J. B., Stern, H. S., Dunson, D. B., Vehtari, A., and Rubin, D. B. (2013). Bayesian Data Analysis. Chapman & Hall/CRC Press, London, third edition. (Ch. 6)

Examples

y <- example_y_data()
yrep <- example_yrep_draws()
ppc_stat(y, yrep, stat = "median")
ppc_stat(y, yrep, stat = "sd") + legend_none()

# use your own function for the 'stat' argument
color_scheme_set("brightblue")
q25 <- function(y) quantile(y, 0.25)
ppc_stat(y, yrep, stat = "q25") # legend includes function name

# can define the function in the 'stat' argument instead of
# using its name but then the legend doesn't include the function name
ppc_stat(y, yrep, stat = function(y) quantile(y, 0.25))

# plots by group
color_scheme_set("teal")
group <- example_group_data()
ppc_stat_grouped(y, yrep, group, stat = "median")
ppc_stat_grouped(y, yrep, group, stat = "mad") + yaxis_text()

# force y-axes to have same scales, allow x axis to vary
ppc_stat_grouped(y, yrep, group, facet_args = list(scales = "free_x")) + yaxis_text()

# the freqpoly plots use frequency polygons instead of histograms
ppc_stat_freqpoly(y, yrep, stat = "median")
ppc_stat_freqpoly_grouped(y, yrep, group, stat = "median", facet_args = list(nrow = 2))

# ppc_stat_2d allows 2 statistics and makes a scatterplot
bayesplot_theme_set(ggplot2::theme_linedraw())
color_scheme_set("viridisE")
ppc_stat_2d(y, yrep, stat = c("mean", "sd"))

bayesplot_theme_set(ggplot2::theme_grey())
color_scheme_set("brewer-Paired")
ppc_stat_2d(y, yrep, stat = c("median", "mad"))

# reset aesthetics
color_scheme_set()
bayesplot_theme_set()

jgabry/bayesplot documentation built on Feb. 1, 2025, 3:04 a.m.