rstan (version 2.7.0-1)

plot-methods: plot: plot an overview of summaries for the fitted model

Description

Drawn an overview of parameter summaries for the fitted model. In the overview plot, we also indicate the values of Rhats for all parameters of interest using differnt colors. In addition to all the parameters, the log-posterior is also plotted.

Usage

## S3 method for class 'stanfit,missing':
plot(x, pars, display_parallel = FALSE, 
  ask = TRUE, npars_per_page = 6, include = TRUE)

Arguments

x

An instance of class stanfit.

pars

A vector of character string specifying the parameters to be plotted. If not specified, all parameters are used. If include = FALSE, then the parameters are excluded from the plot.

display_parallel

TRUE or FALSE, indicating whether to plot the intervals with one line for each chain or one line for all chains. The default is FALSE so that only one interval line is drawn for each scalar parameter.

ask

TRUE or FALSE, to control (for the current device) whether the user is prompted before starting a new page of output in the case there are a lot of parameters (see devA

npars_per_page

An integer to specify the number of parameters that would be plotted per page.

include

Logical scalar indicating whether to include (the default) or exclude the parameters given by the pars argument from the plot.

Value

• NULL

Examples

library(rstan) 
fit <- stan(model_code = "parameters {real y;} model {y ~ normal(0,1);}") 
plot(fit)

# Create a stanfit object from reading CSV files of samples (saved in rstan
# package) generated by funtion stan for demonstration purpose from model as follows. 
# 
excode <- '
  transformed data {
    real y[20];
    y[1] <- 0.5796;  y[2]  <- 0.2276;   y[3] <- -0.2959; 
    y[4] <- -0.3742; y[5]  <- 0.3885;   y[6] <- -2.1585;
    y[7] <- 0.7111;  y[8]  <- 1.4424;   y[9] <- 2.5430; 
    y[10] <- 0.3746; y[11] <- 0.4773;   y[12] <- 0.1803; 
    y[13] <- 0.5215; y[14] <- -1.6044;  y[15] <- -0.6703; 
    y[16] <- 0.9459; y[17] <- -0.382;   y[18] <- 0.7619;
    y[19] <- 0.1006; y[20] <- -1.7461;
  }
  parameters {
    real mu;
    real<lower=0, upper=10> sigma;
    vector[2] z[3];
    real<lower=0> alpha;
  } 
  model {
    y ~ normal(mu, sigma);
    for (i in 1:3) 
      z[i] ~ normal(0, 1);
    alpha ~ exponential(2);
  } 
'

# exfit <- stan(model_code = excode, save_dso = FALSE, iter = 200, 
#               sample_file = "rstan_doc_ex.csv")
# 
exfit <- read_stan_csv(dir(system.file('misc', package = 'rstan'),
                       pattern='rstan_doc_ex_[[:digit:]].csv',
                       full.names = TRUE))

print(exfit)
plot(exfit)