R: Marginal posterior densities of several events

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 1.8 Index]