Plots a set of densities (per MC 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), vlines = NULL,
nrow = NULL, ncol = NULL, joined = FALSE, use_ggplot = FALSE,
keep_aux = FALSE, warn = TRUE, mess = TRUE, ...)

## Arguments

object object inheriting from class 'JointAI' additional parameters passed to plot the first iteration of interest (see window.mcmc) the last iteration of interest (see window.mcmc) thinning interval (see window.mcmc) subset of parameters/variables/nodes (columns in the MCMC sample). Uses the same logic as the argument monitor_params in lm_imp, glm_imp, clm_imp, lme_imp, glme_imp, survreg_imp and coxph_imp. list, where each element is a named list of parameters that can be passed to abline to create vertical lines. Each of the list elements needs to contain at least v = , where is a vector of the same length as the number of plots (see examples). optional number of rows and columns in the plot layout; automatically chosen if unspecified optional number of rows and columns in the plot layout; automatically chosen if unspecified logical; should the chains be combined before plotting? logical; Should ggplot be used instead of the base graphics? logical; Should constant effects of auxiliary variables be kept in the output? logical; should warnings be given? Default is TRUE. Note: this applies only to warnings given directly by JointAI. logical; should messages be given? Default is TRUE. Note: this applies only to messages given directly by JointAI.

The vignette Parameter Selection contains some examples how to specify the argument subset.

## Examples


# fit a JointAI object:
mod <- lm_imp(y ~ C1 + C2 + M2, data = wideDF, n.iter = 100)#> This is new software. Please report any bugs to the package maintainer.
# Example 1: basic densityplot
densplot(mod)

# 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)#> Registered S3 methods overwritten by 'ggplot2':
#>   method         from
#>   [.quosures     rlang
#>   c.quosures     rlang
#>   print.quosures rlang

# 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')