rbacon (version 2.3.3)

calib.plot: Plot the dates

Description

Produce a plot of the dated depths and their dates

Usage

calib.plot(set = get("info"), BCAD = set$BCAD, rotate.axes = FALSE,
  rev.d = FALSE, rev.yr = FALSE, yr.lim = c(), date.res = 100,
  d.lab = c(), yr.lab = c(), height = 15, mirror = TRUE, up = TRUE,
  cutoff = 0.001, C14.col = rgb(0, 0, 1, 0.5), C14.border = rgb(0, 0, 1,
  0.75), cal.col = rgb(0, 0.5, 0.5, 0.5), cal.border = rgb(0, 0.5, 0.5,
  0.75), slump.col = grey(0.8), new.plot = TRUE, plot.dists = TRUE,
  normalise.dists = TRUE)

Arguments

set

Detailed information of the current run, stored within this session's memory as variable info.

BCAD

The calendar scale of graphs is in cal BP by default, but can be changed to BC/AD using BCAD=TRUE.

rotate.axes

The default of plotting age on the horizontal axis and event probability on the vertical one can be changed with rotate.axes=TRUE.

rev.d

The direction of the depth axis can be reversed from the default (rev.d=TRUE).

rev.yr

The direction of the calendar age axis can be reversed from the default (rev.yr=TRUE)

yr.lim

Minimum and maximum calendar age ranges, calculated automatically by default (yr.lim=c()).

date.res

Date distributions are plotted using date.res=100 points by default.

d.lab

The labels for the depth axis. Default d.lab="Depth (cm)".

yr.lab

The labels for the calendar axis (default yr.lab="cal BP" or "BC/AD" if BCAD=TRUE).

height

The heights of the distributions of the dates. See also normalise.dists.

mirror

Plot the dates as 'blobs'. Set to mirror=FALSE to plot simple distributions.

up

Directions of distributions if they are plotted non-mirrored. Default up=TRUE.

cutoff

Avoid plotting very low probabilities of date distributions (default cutoff=0.001).

C14.col

Colour of the calibrated distributions of the dates. Default is semi-transparent blue: rgb(0,0,1,.35).

C14.border

Colours of the borders of calibrated 14C dates. Default is transparent dark blue: cal.col

cal.col

Colour of the non-14C dates in the age-depth plot: default semi-transparent blue-green: rgb(0,.5,.5,.35).

cal.border

Colour of the of the border of non-14C dates in the age-depth plot: default semi-transparent dark blue-green: rgb(0,.5,.5,.5).

slump.col

Colour of slumps. Defaults to slump.col=grey(0.8).

new.plot

Start a new plot (new.plot=TRUE) or plot over an existing plot (new.plot=FALSE).

plot.dists

Plot the distributions of the dates (default plot.dists=TRUE).

normalise.dists

By default, the distributions of more precise dates will cover less time and will thus peak higher than less precise dates. This can be avoided by specifying normalise.dists=FALSE.

Value

NA

Details

This function is generally called internally to produce the age-depth graph. It can be used to produce custom-built graphs.

References

Blaauw, M. and Christen, J.A., Flexible paleoclimate age-depth models using an autoregressive gamma process. Bayesian Anal. 6 (2011), no. 3, 457--474. https://projecteuclid.org/download/pdf_1/euclid.ba/1339616472

See Also

http://www.chrono.qub.ac.uk/blaauw/manualBacon_2.3.pdf

Examples

# NOT RUN {
  Bacon(run=FALSE, coredir=tempfile())
  calib.plot()

# }