Produce a plot of the dated depths and their dates
calib.plot(set = get("info"), BCAD = set$BCAD, cc = set$cc,
rotate.axes = FALSE, rev.d = FALSE, rev.age = FALSE,
rev.yr = rev.age, age.lim = c(), yr.lim = age.lim,
date.res = 100, d.lab = c(), age.lab = c(), yr.lab = age.lab,
height = 15, calheight = 1, 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), dates.col = c(), slump.col = grey(0.8),
new.plot = TRUE, plot.dists = TRUE, same.heights = FALSE,
normalise.dists = TRUE)Detailed information of the current run, stored within this session's memory as variable info.
The calendar scale of graphs is in cal BP by default, but can be changed to BC/AD using BCAD=TRUE.
Calibration curve to be used (defaults to info$cc)
The default of plotting age on the horizontal axis and event probability on the vertical one can be changed with rotate.axes=TRUE.
The direction of the depth axis can be reversed from the default (rev.d=TRUE).
The direction of the calendar age axis can be reversed from the default (rev.age=TRUE)
Deprecated - use rev.age instead
Minimum and maximum calendar age ranges, calculated automatically by default (age.lim=c()).
Deprecated - use age.lim instead
Date distributions are plotted using date.res=100 points by default.
The labels for the depth axis. Default d.lab="Depth (cm)".
The labels for the calendar axis (default yr.lab="cal BP" or "BC/AD" if BCAD=TRUE).
Deprecated - use age.lab instead
The heights of the distributions of the dates. See also normalise.dists.
Multiplier for the heights of the distributions of dates on the calendar scale. Defaults to calheight=1.
Plot the dates as 'blobs'. Set to mirror=FALSE to plot simple distributions.
Directions of distributions if they are plotted non-mirrored. Default up=TRUE.
Avoid plotting very low probabilities of date distributions (default cutoff=0.001).
Colour of the calibrated distributions of the dates. Default is semi-transparent blue: rgb(0,0,1,.35).
Colours of the borders of calibrated 14C dates. Default is transparent dark blue: cal.col
Colour of the non-14C dates in the age-depth plot: default semi-transparent blue-green: rgb(0,.5,.5,.35).
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).
As an alternative to colouring dates based on whether they are 14C or not, sets of dates can be coloured as, e.g., dates.col=colours()[2:100].
Colour of slumps. Defaults to slump.col=grey(0.8).
Start a new plot (new.plot=TRUE) or plot over an existing plot (new.plot=FALSE).
Plot the distributions of the dates (default plot.dists=TRUE).
Plot the distributions of the dates all at the same maximum height (default same.height=FALSE).
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.
NA
This function is generally called internally to produce the age-depth graph. It can be used to produce custom-built graphs.
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/euclid.ba/1339616472
# NOT RUN {
Bacon(run=FALSE, coredir=tempfile())
calib.plot()
# }
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