R: Plot a marginal posterior density

marginal_plot {ArchaeoPhases}

R Documentation

Plot a marginal posterior density

Description

Draws a plot of the marginal posterior density for a single parameter, with an option to add the mean and the credible interval at the desired level

Usage

marginal_plot(
  data,
  position = 1,
  level = 0.95,
  grid_length = 1024,
  title = if (is.numeric(position)) names(data)[position] else position,
  subtitle = "Marginal posterior density",
  caption = paste(level * 100, "% credible interval", sep = ""),
  x_label = "Calendar year",
  y_label = "Density",
  y_grid = TRUE,
  x_scale = "calendar",
  elapsed_origin_position = NULL,
  x_min = NULL,
  x_max = NULL,
  height = 7,
  width = 7,
  units = "in",
  file = NULL,
  plot_result = TRUE,
  mean_linetype = "dashed",
  mean_color = "white",
  mean_size = 0.5,
  ci_linetype = "dotted",
  ci_color = mean_color,
  ci_size = mean_size,
  line_linetype = "solid",
  line_color = "black",
  line_size = 1,
  density_color = "gray30",
  fill_palette = NULL
)

Arguments

`data`	Data frame containing the output of the MCMC algorithm.
`position`	Index of the column corresponding to the MCMC chain of interest, or a column name.
`level`	Probability corresponding to the level of confidence.
`grid_length`	Length of the grid used to estimate the density.
`title`	Title of the graph. The default uses the `data` column name.
`subtitle`	Subtitle of the graph. The default is "Marginal posterior density".
`caption`	Caption of the graph. The default describes the confidence of the credible interval.
`x_label`	Label of the x-axis.
`y_label`	Label of the y-axis.
`y_grid`	Switch for horizontal grid lines.
`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.
`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". This parameter has no effect on the display plot.
`file`	Name of the file that will be saved if chosen, default = `NULL`.
`plot_result`	If `TRUE`, then draw a plot on the display, else suppress drawing.
`mean_linetype`	The `linetype` used to indicate the mean density.
`mean_color`	The color of the line used to indicate mean density.
`mean_size`	The width of the line used to indicate the mean density.
`ci_linetype`	The `linetype` used to indicate the credible intervals.
`ci_color`	The color of the lines used to indicate the credible intervals.
`ci_size`	The width of the lines used to indicate the credible intervals.
`line_linetype`	The `linetype` used to indicate the density.
`line_color`	The color of the line used to indicate the density.
`line_size`	The width of the line used to indicate the density.
`density_color`	Color to use if fill_palette is not specified.
`fill_palette`	Palette to use for fills.

Details

The plot is drawn with the current theme and color scales; the function does not alter or override theme elements.

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)
  mp <- marginal_plot(data = Events, position = 2, level = 0.95)
  ## View data and metadata
  str(mp)

[Package ArchaeoPhases version 1.8 Index]