multi_marginal_plot {ArchaeoPhases}R Documentation

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, Anne.Philippe@univ-nantes.fr;

Marie-Anne Vibet, Marie-Anne.Vibet@univ-nantes.fr; and

Thomas S. Dye, tsd@tsdye.online

Examples

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


[Package ArchaeoPhases version 1.5 Index]