multi_marginal_plot: Marginal posterior densities of several events

In ArchaeoPhases: Post-Processing of the Markov Chain Simulated by 'ChronoModel', 'Oxcal' or 'BCal'

Marginal posterior densities of several events

Description

Draws a plot of the estimated marginal posterior density for a parameter and adds the mean and the credible interval at the desired level

Usage

multi_marginal_plot(
  data,
  position = 1:ncol(data),
  level = 0.95,
  grid_length = 1024,
  x_scale = "calendar",
  elapsed_origin_position = NULL,
  title = "Characteristics of several dates",
  subtitle = "Marginal densities",
  caption = paste(level * 100, "% credible interval", sep = ""),
  x_label = "Calendar year",
  y_label = NULL,
  density_fill = "gray30",
  density_color = "black",
  density_alpha = 1,
  mean_color = "white",
  mean_linetype = "dashed",
  mean_size = 0.5,
  ci_color = mean_color,
  ci_linetype = "dotted",
  ci_size = mean_size,
  y_grid = TRUE,
  x_min = NULL,
  x_max = NULL,
  height = 7,
  width = 7,
  units = "in",
  file = NULL,
  new_window = TRUE,
  plot_result = TRUE,
  fill_palette = NULL,
  colors = NULL,
  color_legend_name = "Legend"
)

Arguments

data	Data frame containing the output of the MCMC algorithm.
position	Numeric vector containing the position of the column corresponding to the MCMC chains of interest, or a vector of column names.
level	Probability corresponding to the level of confidence.
grid_length	Number of equally spaced points at which the density is to be estimated (for density() function).
x_scale	One of "calendar" for calendar years, "BP" for years before present, or "elapsed" for time elapsed from a specified origin.
elapsed_origin_position	Position of the column to use as the origin for elapsed time calculations.
title	Title of the plot.
subtitle	Subtitle of the plot.
caption	Caption of the plot.
x_label	Label of the x-axis.
y_label	Label of the y-axis.
density_fill	A color specification for the fill under the density line.
density_color	A color specification for the density line.
density_alpha	A number between 0 for transparent and 1 for opaque.
mean_color	A color specification for the mean line.
mean_linetype	A line type specification for the mean line.
mean_size	A size specification for the mean line.
ci_color	A color specification for the credible interval lines.
ci_linetype	A line type specification for the credible interval lines.
ci_size	A size specification of the credible interval lines.
y_grid	Switch for horizontal grid lines.
x_min	Minimum x-axis value.
x_max	Maximum x-axis value.
height	Plot height in units.
width	Plot width in units.
units	String recognized by the ggsave() function, one of "in", "cm", "mm".
file	Name of the file that will be saved if specified, default = NULL.
new_window	Whether or not the plot is drawn within a new window.
plot_result	If TRUE, then draw a plot on the display, else suppress drawing.
fill_palette	A vector of colors for qualitative data.
colors	A vector of indices into palette keyed by position.
color_legend_name	A label for the legend.

Details

The density is estimated using density() function with n = grid_length. The input MCMC chains should either be in calendar years or converted to calendar years using x_scale vector or elapsed_origin_position.

Value

An archaeophases_plot object with the data and metadata needed to reproduce the plot.

Author(s)

Anne Philippe, [e-mail];

Marie-Anne Vibet, [e-mail]; and

Thomas S. Dye, [e-mail]

Examples

  data(Events);
  multi_marginal_plot(Events, position = c(2, 3, 4), level = 0.95)

ArchaeoPhases documentation built on March 18, 2022, 5:44 p.m.