densplot.Rd
The function plots a set of densities (per chain and coefficient) from the MCMC sample of an object of class "JointAI".
densplot(object, ...) # S3 method for mcmc.list densplot(object, start = NULL, end = NULL, thin = NULL, ...) # S3 method for JointAI densplot(object, start = NULL, end = NULL, thin = NULL, subset = c(analysis_main = TRUE), exclude_chains = NULL, vlines = NULL, nrow = NULL, ncol = NULL, joined = FALSE, use_ggplot = FALSE, keep_aux = FALSE, warn = TRUE, mess = TRUE, ...)
object  object inheriting from class 'JointAI' 

...  additional parameters passed to 
start  the first iteration of interest (see 
end  the last iteration of interest (see 
thin  thinning interval (see 
subset  subset of parameters/variables/nodes (columns in the MCMC sample).
Uses the same logic as the argument 
exclude_chains  optional vector of the index numbers of chains that should be excluded 
vlines  list, where each element is a named list of parameters that
can be passed to 
nrow  optional number of rows and columns in the plot layout; automatically chosen if unspecified 
ncol  optional number of rows and columns in the plot layout; automatically chosen if unspecified 
joined  logical; should the chains be combined before plotting? 
use_ggplot  logical; Should ggplot be used instead of the base graphics? 
keep_aux  logical; Should constant effects of auxiliary variables be kept in the output? 
warn  logical; should warnings be given? Default is

mess  logical; should messages be given? Default is

The vignette Parameter Selection
contains some examples how to specify the argument subset
.
# fit a JointAI object: mod < lm_imp(y ~ C1 + C2 + M1, data = wideDF, n.iter = 100) # Example 1: basic densityplot densplot(mod)densplot(mod, exclude_chains = 2)# Example 2: use vlines to mark zero densplot(mod, col = c("darkred", "darkblue", "darkgreen"), vlines = list(list(v = rep(0, nrow(summary(mod)$stats)), col = grey(0.8))))# Example 3: use vlines to visualize the posterior mean and 2.5% and 97.5% quantiles densplot(mod, vlines = list(list(v = summary(mod)$stats[, "Mean"], lty = 1, lwd = 2), list(v = summary(mod)$stats[, "2.5%"], lty = 2), list(v = summary(mod)$stats[, "97.5%"], lty = 2)))# Example 4: ggplot version densplot(mod, use_ggplot = TRUE)# Example 5: changing how the ggplot version looks (using standard ggplot syntax) library(ggplot2) densplot(mod, use_ggplot = TRUE) + xlab("value") + theme(legend.position = 'bottom') + scale_color_brewer(palette = 'Dark2', name = 'chain')