Plot MCMC sample traces — trace

Takes as input a sefraModel object following a call to sampler and plots traces for desired parameters.

Usage

trace_plot(object, pars, labels, ...)

# S3 method for class 'CmdStanMCMC'
trace_plot(object, pars, labels = list(), ...)

# S3 method for class 'sefraModel'
trace_plot(object, pars, labels = list(), ...)

Arguments

object: sefraModel object.
pars: character vector of posterior parameter samples to be extracted.
labels: character or expression vector of labels
...: (not used)

Examples

library(cmdstanr)
library(ggplot2)
#> Warning: package 'ggplot2' was built under R version 4.5.2

CODE <- "data{ int n; vector[n] x; }  
   parameters{ real mu; }  
   model{ x ~ normal(mu, 1.0);} 
   generated quantities{ vector[n] x_sim; real x_sim_sum; 
   for (i in 1:n) x_sim[i] = normal_rng(mu, 1.0); x_sim_sum = sum(x_sim);}\n"
   
ff  <- write_stan_file(CODE)  
mdl <- cmdstan_model(stan_file = ff); rm(ff)

n <- 20
x <- rnorm(n, 0, 2)

mdl_fit <- mdl$sample(data = list(n = n, x = x), init = function() list(mu = 0), chains = 1)
#> Running MCMC with 1 chain...
#> 
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#> Chain 1 finished in 0.1 seconds.

trace_plot(mdl_fit, pars = "mu", labels = list(1)) + facet_wrap(~"mu", labeller = label_parsed)