occurrence_plot {ArchaeoPhases}

R Documentation

Plot occurrences

Description

A statistical graphic designed for the archaeological study of when events of a specified kind occurred

Usage

occurrence_plot(
  data,
  position = 1:ncol(data),
  name = list("All"),
  level = 0.95,
  plot_result = TRUE,
  intervals = "CI",
  title = "Occurrence plot",
  subtitle = NULL,
  caption = "ArchaeoPhases",
  x_label = "Calendar year",
  y_label = NULL,
  language = "English",
  occurrence = "occurrence",
  height = 7,
  width = 7,
  unit = "in",
  x_min = NULL,
  x_max = NULL,
  x_scale = "calendar",
  elapsed_origin_position = NULL,
  dumbbell_size = 1,
  dot_guide = FALSE,
  dot_guide_size = 0.25,
  y_grid = FALSE,
  columns = 1,
  file = NULL,
  new_window = TRUE
)

Arguments

data	Data frame containing the output of the MCMC algorithm.
position	A list, each member of which is either a numeric vector containing the positions of the columns corresponding to the MCMC chains of interest, or a vector of column names. For convenience, a vector can be substituted for the singleton list.
name	A list, each member of which is a string that names the kind of event in the corresponding element of position. For convenience, a string can be substituted for the singleton list.
level	Probability corresponding to the level of confidence.
plot_result	If TRUE, then draw a plot on the display, else suppress drawing.
intervals	One of "CI" for credible intervals or "HPD" for highest posterior density intervals.
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.
language	String indicating a language recognized by the toOrdinal package.
occurrence	String to append to each y-axis tic label.
height	Plot height in unit.
width	Plot width in unit.
unit	String recognized by the ggsave() function, one of "in", "cm", "mm".
x_min	Minimum x-axis value.
x_max	Maximum x-axis value.
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.
dumbbell_size	Size of the plot symbol.
dot_guide	Switch for a horizontal guide from the y axis.
dot_guide_size	Size of the dot guide.
y_grid	Switch for horizontal grid lines.
columns	Number of columns for facet.
file	Name of the file that will be saved if specified. If NULL no plot will be saved.
new_window	Whether or not the plot is drawn within a new window.

Details

If we have k events, then we can estimate the calendar date t corresponding to the smallest date such that the number of events observed before t is equal to k. The OccurrencePlot() estimates these occurrences and gives the credible interval or the highest posterior density (HPD) region with a desired level of confidence.

Value

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

Author(s)

Anne Philippe, Anne.Philippe@univ-nantes.fr,

Thomas S. Dye, tsd@tsdye.online, and

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

Examples

  data(Events);
  OccurrencePlot(Events[1:1000, ], c(2:5),  print.data.result = FALSE)


## Not run: 
# Read from connection
ox <- read_oxcal("http://tsdye.online/AP/ox.csv")
# Plot all the columns
op <- occurrence_plot(ox, position = 1:ncol(ox))
# Plot again
plot(op)
# View metadata
str(op)

## End(Not run)

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