rstan: stanfit-method-plot – R documentation

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stanfit-method-plot

Plots for stanfit objects

Description

The default plot shows posterior uncertainty intervals and point estimates for parameters and generated quantities. The plot method can also be used to call the other rstan plotting functions via the plotfun argument (see Examples).

Usage

## S4 method for signature 'stanfit,missing'
plot(x, ..., plotfun)

Arguments

`x`	An instance of class `stanfit`.
`plotfun`	A character string naming the plotting function to apply to the stanfit object. If `plotfun` is missing, the default is to call `stan_plot`, which generates a plot of credible intervals and point estimates. See `rstan-plotting-functions` for the names and descriptions of the other plotting functions. `plotfun` can be either the full name of the plotting function (e.g. `"stan_hist"`) or can be abbreviated to the part of the name following the underscore (e.g. `"hist"`).
`...`	Optional arguments to `plotfun`.

Value

A ggplot object that can be further customized using the ggplot2 package.

Note

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"))).

Examples

## Not run: 
library(rstan)
fit <- stan_demo("eight_schools")
plot(fit)
plot(fit, show_density = TRUE, ci_level = 0.5, fill_color = "purple")
plot(fit, plotfun = "hist", pars = "theta", include = FALSE)
plot(fit, plotfun = "trace", pars = c("mu", "tau"), inc_warmup = TRUE)
plot(fit, plotfun = "rhat") + ggtitle("Example of adding title to plot")

## End(Not run)

rstan

R Interface to Stan

v2.21.2

GPL (>= 3)

Authors

Jiqiang Guo [aut], Jonah Gabry [aut], Ben Goodrich [cre, aut], Sebastian Weber [aut], Daniel Lee [ctb], Krzysztof Sakrejda [ctb], Modrak Martin [ctb], Trustees of Columbia University [cph], Oleg Sklyar [cph] (R/cxxfunplus.R), The R Core Team [cph] (R/pairs.R, R/dynGet.R), Jens Oehlschlaegel-Akiyoshi [cph] (R/pairs.R), John Maddock [cph] (gamma.hpp), Paul Bristow [cph] (gamma.hpp), Nikhar Agrawal [cph] (gamma.hpp), Christopher Kormanyos [cph] (gamma.hpp), Bronder Steve [ctb]

Initial release

2020-07-27