PPCdistributions.Rd
Compare the empirical distribution of the data y
to the distributions
of simulated/replicated data yrep
from the posterior predictive
distribution. See the Plot Descriptions section, below,
for details.
ppc_data(y, yrep, group = NULL) ppc_hist(y, yrep, ..., binwidth = NULL, breaks = NULL, freq = TRUE) ppc_boxplot(y, yrep, ..., notch = TRUE, size = 0.5, alpha = 1) ppc_freqpoly(y, yrep, ..., binwidth = NULL, freq = TRUE, size = 0.25, alpha = 1) ppc_freqpoly_grouped(y, yrep, group, ..., binwidth = NULL, freq = TRUE, size = 0.25, alpha = 1) ppc_dens(y, yrep, ..., trim = FALSE, size = 0.5, alpha = 1) ppc_dens_overlay(y, yrep, ..., size = 0.25, alpha = 0.7, trim = FALSE, bw = "nrd0", adjust = 1, kernel = "gaussian", n_dens = 1024) ppc_ecdf_overlay(y, yrep, ..., discrete = FALSE, pad = TRUE, size = 0.25, alpha = 0.7) ppc_violin_grouped(y, yrep, group, ..., probs = c(0.1, 0.5, 0.9), size = 1, alpha = 1, y_draw = c("violin", "points", "both"), y_size = 1, y_alpha = 1, y_jitter = 0.1)
y  A vector of observations. See Details. 

yrep  An \(S\) by \(N\) matrix of draws from the posterior
predictive distribution, where \(S\) is the size of the posterior sample
(or subset of the posterior sample used to generate 
group  A grouping variable (a vector or factor) the same length as

...  Currently unused. 
binwidth  Passed to 
breaks  Passed to 
freq  For histograms, 
notch  A logical scalar passed to 
size, alpha  Passed to the appropriate geom to control the appearance of
the 
trim  A logical scalar passed to 
bw, adjust, kernel, n_dens  Optional arguments passed to

discrete  For 
pad  A logical scalar passed to 
probs  A numeric vector passed to 
y_draw  For 
y_jitter, y_size, y_alpha  For 
A ggplot object that can be further customized using the
ggplot2 package. The _data
functions return the data that
would have been drawn by the plotting function.
For Binomial data, the plots will typically be most useful if
y
and yrep
contain the "success" proportions (not discrete
"success" or "failure" counts).
ppc_hist, ppc_freqpoly, ppc_dens, ppc_boxplot
A separate histogram, shaded frequency polygon, smoothed kernel density
estimate, or box and whiskers plot is displayed for y
and each
dataset (row) in yrep
. For these plots yrep
should therefore
contain only a small number of rows. See the Examples section.
ppc_freqpoly_grouped
A separate frequency polygon is plotted for each level of a grouping
variable for y
and each dataset (row) in yrep
. For this plot
yrep
should therefore contain only a small number of rows. See the
Examples section.
ppc_dens_overlay, ppc_ecdf_overlay
Kernel density or empirical CDF estimates of each dataset (row) in
yrep
are overlaid, with the distribution of y
itself on top
(and in a darker shade). When using ppc_ecdf_overlay
with discrete
data set the discrete
argument to TRUE
for better results.
ppc_violin_grouped
The density estimate of yrep
within each level of a grouping
variable is plotted as a violin with horizontal lines at notable
quantiles. y
is overlaid on the plot either as a violin, points, or
both, depending on the y_draw
argument.
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)
Other PPCs: PPCdiscrete
,
PPCerrors
, PPCintervals
,
PPCloo
, PPCoverview
,
PPCscatterplots
,
PPCteststatistics
#> [1] 500 434ppc_dens_overlay(y, yrep[1:25, ])ppc_ecdf_overlay(y, yrep[sample(nrow(yrep), 25), ])# for ppc_hist,dens,freqpoly,boxplot definitely use a subset yrep rows so # only a few (instead of nrow(yrep)) histograms are plotted ppc_hist(y, yrep[1:8, ])#>ppc_freqpoly(y, yrep[1:3,], alpha = 0.1, size = 1, binwidth = 5)# if groups are different sizes then the 'freq' argument can be useful group < example_group_data() ppc_freqpoly_grouped(y, yrep[1:3,], group) + yaxis_text()#>#># don't need to only use small number of rows for ppc_violin_grouped # (as it pools yrep draws within groups) color_scheme_set("gray") ppc_violin_grouped(y, yrep, group, size = 1.5)ppc_violin_grouped(y, yrep, group, alpha = 0)# change how y is drawn ppc_violin_grouped(y, yrep, group, alpha = 0, y_draw = "points", y_size = 1.5)ppc_violin_grouped(y, yrep, group, alpha = 0, y_draw = "both", y_size = 1.5, y_alpha = 0.5, y_jitter = 0.33)