ggplot2 for RStan
Visual posterior analysis using ggplot2.
stan_plot(object, pars, include = TRUE, unconstrain = FALSE, ...)
stan_trace(object, pars, include = TRUE, unconstrain = FALSE,
inc_warmup = FALSE, nrow = NULL, ncol = NULL, ...,
window = NULL)
stan_scat(object, pars, unconstrain = FALSE,
inc_warmup = FALSE, nrow = NULL, ncol = NULL, ...)
stan_hist(object, pars, include = TRUE, unconstrain = FALSE,
inc_warmup = FALSE, nrow = NULL, ncol = NULL, ...)
stan_dens(object, pars, include = TRUE, unconstrain = FALSE,
inc_warmup = FALSE, nrow = NULL, ncol = NULL, ...,
separate_chains = FALSE)
stan_ac(object, pars, include = TRUE, unconstrain = FALSE,
inc_warmup = FALSE, nrow = NULL, ncol = NULL, ...,
separate_chains = FALSE, lags = 25, partial = FALSE)
quietgg(gg)object |
A stanfit or stanreg object. |
pars |
Optional character vector of parameter names.
If |
include |
Should the parameters given by the |
unconstrain |
Should parameters be plotted on the unconstrained space?
Defaults to |
inc_warmup |
Should warmup iterations be included? Defaults to
|
nrow,ncol |
Passed to |
... |
Optional additional named arguments passed to geoms
(e.g. for |
window |
For |
separate_chains |
For |
lags |
For |
partial |
For |
gg |
A ggplot object or an expression that creates one. |
For stan_plot, there are additional arguments that can be specified in
.... The optional arguments and their default values are:
point_est = "median"The point estimate to show. Either "median" or "mean".
show_density = FALSEShould kernel density estimates be plotted above the intervals?
ci_level = 0.8The posterior uncertainty interval to highlight.
Central 100*ci_level% intervals are computed from the quantiles of
the posterior draws.
outer_level = 0.95An outer interval to also draw as a line
(if show_outer_line is TRUE) but not highlight.
show_outer_line = TRUEShould the outer_level interval
be shown or hidden? Defaults to = TRUE (to plot it).
fill_color, outline_color, est_color
Colors to override the defaults for the highlighted interval, the outer interval (and density outline), and the point estimate.
A ggplot object that can be further customized
using the ggplot2 package.
Because the rstan plotting functions use ggplot2 (and thus the
resulting plots behave like ggplot objects), when calling a plotting
function within a loop or when assigning a plot to a name
(e.g., graph <- plot(fit, plotfun = "rhat")),
if you also want the side effect of the plot being displayed you
must explicity print it (e.g., (graph <- plot(fit, plotfun = "rhat")),
print(graph <- plot(fit, plotfun = "rhat"))).
## Not run:
example("read_stan_csv")
stan_plot(fit)
stan_trace(fit)
library(gridExtra)
fit <- stan_demo("eight_schools")
stan_plot(fit)
stan_plot(fit, point_est = "mean", show_density = TRUE, fill_color = "maroon")
# histograms
stan_hist(fit)
# suppress ggplot2 messages about default bindwidth
quietgg(stan_hist(fit))
quietgg(h <- stan_hist(fit, pars = "theta", binwidth = 5))
# juxtapose histograms of tau and unconstrained tau
tau <- stan_hist(fit, pars = "tau")
tau_unc <- stan_hist(fit, pars = "tau", unconstrain = TRUE) +
xlab("tau unconstrained")
grid.arrange(tau, tau_unc)
# kernel density estimates
stan_dens(fit)
(dens <- stan_dens(fit, fill = "skyblue", ))
dens <- dens + ggtitle("Kernel Density Estimates\n") + xlab("")
dens
(dens_sep <- stan_dens(fit, separate_chains = TRUE, alpha = 0.3))
dens_sep + scale_fill_manual(values = c("red", "blue", "green", "black"))
(dens_sep_stack <- stan_dens(fit, pars = "theta", alpha = 0.5,
separate_chains = TRUE, position = "stack"))
# traceplot
trace <- stan_trace(fit)
trace +
scale_color_manual(values = c("red", "blue", "green", "black"))
trace +
scale_color_brewer(type = "div") +
theme(legend.position = "none")
facet_style <- theme(strip.background = ggplot2::element_rect(fill = "white"),
strip.text = ggplot2::element_text(size = 13, color = "black"))
(trace <- trace + facet_style)
# scatterplot
(mu_vs_tau <- stan_scat(fit, pars = c("mu", "tau"), color = "blue", size = 4))
mu_vs_tau +
ggplot2::coord_flip() +
theme(panel.background = ggplot2::element_rect(fill = "black"))
## End(Not run)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.