Bchronplot: Produce Bchron chronology plots

Description

Produces plots of chronologies and radiocarbon dates

Usage

Bchronplot(Bchrondata, plot = TRUE, dates = TRUE, datelabels = FALSE, chrons = TRUE, dateselect = NULL, limits = NULL, dateheight = mean(diff(Bchrondata$input[, 4]))/200, chronwidth = 0.95, datecolour = "black", chroncolour = "blue", outcolour = "red", transp = 0.5, outprob = 0.4, legendloc = "topleft", leghoriz = TRUE, ...)

Arguments

Bchrondata

A Bchron data object with fields for the the input and output files, the name of the core being used, the details of the calibration curve, and details of the model run required. See Bchronload and

plot

If true, will create a new plot, if false, will overlay on top of existing plot

dates

If true, will plot the individually calibrated dates.

datelabels

If true, will plot the date labels to the left of the individually calibrated dates.

chrons

If true, will plot the chronology.

dateselect

A vector or sequence giving the dates which are to be plotted. Useful for ignoring the dates of boundaries, or when many dates overlap.

limits

A vector of length 4 with dimensions as c(lowestdepth,oldestage,highestdepth,youngestage).

dateheight

The height of the date densities relative to the depth scale.

chronwidth

The desired probability range of the plotted chronology. Default is 0.95 of 95

datecolour

The colour of the radiocarbon dates as plotted.

chroncolour

The colour of the chronology.

outcolour

The colour of outlying dates.

transp

The degree of transparency of the chronology.

outprob

The threshold over which dates are considered outliers and coloured accordingly. Default is 0.4.

legendloc

The location of the legend. Can be given as any of "topleft", "top", etc, or locator(1) to position the legend manually.

leghoriz

If true, creates a horizontal rather than vertical legend.

...

Other arguments, such as width, height, of the plot created.

Details

The options allow for a wide variety of possible plotting scenarios, including black and white plots, overlayed densities, outlier idenitfication, etc, etc.

References

Haslett and Parnell (2008, JRSSC, 57:399-418) and Parnell et al (2008, QSR, 27(19-20):1872-1885)

Examples

Run this code

# For the example data, the following should run (when the files are placed in the default directory in windows; c:/Bchron)
# myrun <- Bchronload("Glendalough")
# Bchroncalibrate(myrun)
# BchronMCMC(myrun)
# Bchronpredict(myrun)
# Bchronplot(myrun)