agedepth {rplum} | R Documentation |
Plot the age-depth model of a core.
agedepth( set = get("info"), BCAD = set$BCAD, depth.unit = "cm", age.unit = "yr", unit = depth.unit, d.lab = c(), age.lab = c(), yr.lab = age.lab, kcal = FALSE, acc.lab = c(), d.min = c(), d.max = c(), d.by = c(), depths = set$depths, depths.file = FALSE, age.min = c(), yr.min = age.min, age.max = c(), yr.max = age.max, hiatus.option = 1, dark = c(), prob = set$prob, rounded = 0, d.res = 400, age.res = 400, yr.res = age.res, date.res = 100, grey.res = 100, rotate.axes = FALSE, rev.age = FALSE, rev.yr = rev.age, rev.d = FALSE, maxcalc = 500, height = 15, calheight = 1, mirror = TRUE, up = TRUE, cutoff = 0.001, plot.range = TRUE, panels = layout(1), range.col = grey(0.5), range.lty = "12", mn.col = "red", mn.lty = "12", med.col = NA, med.lty = "12", C14.col = rgb(0, 0, 1, 0.35), C14.border = rgb(0, 0, 1, 0.5), cal.col = rgb(0, 0.5, 0.5, 0.35), cal.border = rgb(0, 0.5, 0.5, 0.5), dates.col = c(), pbmodelled.col = function(x) rgb(0, 0, 1, 0.5 * x), pbmeasured.col = "blue", pb.lim = c(), hiatus.col = grey(0.5), hiatus.lty = "12", greyscale = grey(seq(1, 0, length = grey.res)), slump.col = grey(0.8), normalise.dists = TRUE, same.heights = FALSE, cc = set$cc, title = set$core, title.location = "top", after = set$after, bty = "l", mar = c(3, 3, 1, 1), mgp = c(1.5, 0.7, 0), xaxs = "r", yaxs = "i", xaxt = "s", yaxt = "s", plot.pb = TRUE, plot.pdf = FALSE, dates.only = FALSE, model.only = FALSE, verbose = TRUE )
set |
Detailed information of the current run, stored within this session's memory as variable |
BCAD |
The calendar scale of graphs and age output-files is in |
depth.unit |
Units of the depths. Defaults to |
age.unit |
Units of the ages. Defaults to |
unit |
Deprecated and replaced by |
d.lab |
The labels for the depth axis. Default |
age.lab |
The labels for the calendar axis (default |
yr.lab |
Deprecated - use age.lab instead |
kcal |
Use kcal BP. Default is |
acc.lab |
The labels for the accumulation rate plot (top middle). Default |
d.min |
Minimum depth of age-depth model (use this to extrapolate to depths higher than the top dated depth). |
d.max |
Maximum depth of age-depth model (use this to extrapolate to depths below the bottom dated depth). |
d.by |
Depth intervals at which ages are calculated. Default 1. Alternative depth intervals can be provided using, e.g., d. |
depths |
By default, Bacon will calculate the ages for the depths |
depths.file |
By default, Bacon will calculate the ages for the depths |
age.min |
Minimum age of the age-depth plot. |
yr.min |
Deprecated - use age.min instead. |
age.max |
Maximum age of the age-depth plot. |
yr.max |
Deprecated - use age.min instead. |
hiatus.option |
How to calculate accumulation rates and ages for sections with hiatuses. Either extrapolate from surrounding sections (default, |
dark |
Darkness of the greyscale age-depth model. By default, the darkest grey value is calculated as 10 times the height of the lowest-precision age estimate |
prob |
Confidence interval to report (between 0 and 1, default 0.95 or 95%). |
rounded |
Rounding of years. Default is to round to single years. |
d.res |
Resolution or amount of greyscale pixels to cover the depth scale of the age-model plot. Default |
age.res |
Resolution or amount of greyscale pixels to cover the age scale of the age-model plot. Default |
yr.res |
Deprecated - use age.res instead. |
date.res |
Date distributions are plotted using |
grey.res |
Grey-scale resolution of the age-depth model. Default |
rotate.axes |
By default, the age-depth model is plotted with the depths on the horizontal axis and ages on the vertical axis. This can be changed with |
rev.age |
The direction of the age axis, which can be reversed using |
rev.yr |
Deprecated - use rev.age instead. |
rev.d |
The direction of the depth axis, which can be reversed using |
maxcalc |
Number of depths to calculate ages for. If this is more than |
height |
The maximum heights of the distributions of the dates on the plot. See also |
calheight |
Multiplier for the heights of the distributions of dates on the calendar scale. Defaults to |
mirror |
Plot the dates as 'blobs'. Set to |
up |
Directions of distributions if they are plotted non-mirrored. Default |
cutoff |
Avoid plotting very low probabilities of date distributions (default |
plot.range |
Whether or not to plot the curves showing the confidence ranges of the age-model. Defaults to ( |
panels |
Divide the graph panel. Defaults to 1 graph per panel, |
range.col |
The colour of the curves showing the confidence ranges of the age-model. Defaults to medium grey ( |
range.lty |
The line type of the curves showing the confidence ranges of the age-model. Defaults to |
mn.col |
The colour of the mean age-depth model: default |
mn.lty |
The line type of the mean age-depth model. Default |
med.col |
The colour of the median age-depth model: not drawn by default |
med.lty |
The line type of the median age-depth model. Default |
C14.col |
The colour of the calibrated ranges of the dates. Default is semi-transparent blue: |
C14.border |
The colours of the borders of calibrated 14C dates. Default is semi-transparent dark blue: |
cal.col |
The colour of the non-14C dates. Default is semi-transparent blue-green: |
cal.border |
The colour of the border of non-14C dates in the age-depth plot: default semi-transparent dark blue-green: |
dates.col |
As an alternative to colouring dates based on whether they are 14C or not, sets of dates can be coloured as, e.g., |
pbmodelled.col |
Colour of the modelled 210Pb values. Defaults to shades of blue: |
pbmeasured.col |
Colour of the measured 210Pb values (default |
pb.lim |
Axis limits for the Pb-210 data. Calculated automatically by default ( |
hiatus.col |
The colour of the depths of any hiatuses. Default |
hiatus.lty |
The line type of the depths of any hiatuses. Default |
greyscale |
The function to produce a coloured representation of all age-models. Defaults to grey-scales: |
slump.col |
Colour of slumps. Defaults to |
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 |
same.heights |
Plot the distributions of the dates all at the same maximum height (default |
cc |
Calibration curve for 14C dates: |
title |
The title of the age-depth model is plotted on the main panel. By default this is the core's name. To leave empty: |
title.location |
Location of the title. Default |
after |
Sets a short section above and below hiatus.depths within which to calculate ages. For internal calculations - do not change. |
bty |
Type of box to be drawn around plots ( |
mar |
Plot margins (amount of white space along edges of axes 1-4). Default |
mgp |
Axis text margins (where should titles, labels and tick marks be plotted). Defaults to |
xaxs |
Extension of x-axis. By default, add some extra white-space at both extremes ( |
yaxs |
Extension of y-axis. By default, add no extra white-space at both extremes ( |
xaxt |
Whether or not to plot the x-axis. Can be used to adapt axes after a plot. See ?par for other options. |
yaxt |
Whether or not to plot the y-axis. Can be used to adapt axes after a plot. See ?par for other options. |
plot.pb |
Plot the 210Pb data. Defaults to |
plot.pdf |
Produce a pdf file of the age-depth plot. |
dates.only |
By default, the age-depth model is plotted on top of the dates. This can be avoided by supplying |
model.only |
By default, panels showing the MCMC iterations and the priors and posteriors for accumulation rate and memory are plotted above the main age-depth model panel. This can be avoided by supplying |
verbose |
Provide a summary of the age ranges after producing the age-depth model graph; default |
After loading a previous run, or after running either the scissors or thinner command, plot the age-model
again using the command agedepth()
.
A plot of the age-depth model, and estimated ages incl. confidence ranges for each depth.
Maarten Blaauw, J. Andres Christen
Blaauw, M. and Christen, J.A., Flexible paleoclimate age-depth models using an autoregressive gamma process. Bayesian Analysis 6 (2011), no. 3, 457–474. https://projecteuclid.org/euclid.ba/1339616472
Plum(ssize=100, ask=FALSE, suggest=FALSE, coredir=tempfile(), date.sample=2018.5, radon.case=0, n.supp=3) agedepth()