agedepth: Plot an age-depth model

In rbacon: Age-Depth Modelling using Bayesian Statistics

Plot an age-depth model

Description

Plot the age-depth model of a core.

Usage

agedepth(
  set = get("info"),
  BCAD = set$BCAD,
  depth.unit = set$depth.unit,
  age.unit = "yr",
  unit = depth.unit,
  d.lab = c(),
  age.lab = c(),
  yr.lab = age.lab,
  kcal = FALSE,
  acc.lab = c(),
  mem.lab = c(),
  d.min = c(),
  d.max = c(),
  d.by = c(),
  depths = set$depths,
  depths.file = FALSE,
  accordion = c(),
  plotatthesedepths = c(),
  age.min = c(),
  yr.min = age.min,
  age.max = c(),
  yr.max = age.max,
  hiatus.option = 1,
  dark = c(),
  prob = set$prob,
  rounded = c(),
  d.res = 400,
  age.res = 400,
  yr.res = age.res,
  date.res = 100,
  rotate.axes = FALSE,
  rev.age = FALSE,
  rev.yr = rev.age,
  rev.d = FALSE,
  maxcalc = 500,
  height = 1,
  calheight = 1,
  mirror = TRUE,
  up = TRUE,
  cutoff = 0.1,
  plot.range = TRUE,
  range.col = grey(0.5),
  range.lty = "12",
  range.lwd = 1,
  mn.col = "red",
  mn.lty = "12",
  mn.lwd = 1,
  med.col = NA,
  med.lty = "12",
  med.lwd = 1,
  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(),
  pb.background = 0.5,
  pbmodelled.col = function(x) rgb(0, 0, 1, 0.5 * x),
  pbmeasured.col = "blue",
  pb.lim = c(),
  supp.col = rgb(0.5, 0, 0.5, 0.5),
  remove.tail = TRUE,
  MCMC.resample = TRUE,
  hiatus.col = grey(0.5),
  hiatus.lty = "12",
  rgb.scale = c(0, 0, 0),
  rgb.res = 100,
  slump.col = grey(0.8),
  normalise.dists = TRUE,
  same.heights = FALSE,
  cc = set$cc,
  title = set$core,
  title.location = "topleft",
  title.size = 1.5,
  plot.labels = FALSE,
  labels = c(),
  label.age = 1,
  label.size = 0.8,
  label.col = "black",
  label.offset = c(0, 0),
  label.adj = c(0.5, 0),
  label.rot = 0,
  after = set$after,
  bty = "l",
  mar.left = c(3, 3, 1, 0.5),
  mar.middle = c(3, 0, 1, 0.5),
  mar.right = c(3, 0, 1, 0.5),
  mar.main = c(3, 3, 1, 1),
  righthand = 3,
  mgp = c(1.7, 0.7, 0),
  xaxs = "r",
  yaxs = "i",
  MCMC.col = grey(0.4),
  post.col = grey(0.8),
  post.border = grey(0.4),
  prior.col = 3,
  prior.lwd = 2,
  prior.fontcol = 2,
  prior.ticks = "n",
  prior.fontsize = 0.9,
  toppanel.fontsize = 0.9,
  mainpanel.tickfontsize = 1,
  mainpanel.labelfontsize = 1,
  acc.xlim = c(),
  acc.ylim = c(),
  mem.xlim = c(),
  mem.ylim = c(),
  hiatus.xlim = c(),
  hiatus.ylim = c(),
  phi.xlim = c(),
  phi.ylim = c(),
  supp.xlim = c(),
  supp.ylim = c(),
  xaxt = "s",
  yaxt = "s",
  plot.pb = TRUE,
  pb.lty = 1,
  plot.pdf = FALSE,
  dates.only = FALSE,
  model.only = FALSE,
  verbose = TRUE,
  save.info = TRUE
)

Arguments

set	Detailed information of the current run, stored within this session's memory as variable info.
BCAD	The calendar scale of graphs and age output-files is in cal BP by default, but can be changed to BC/AD using BCAD=TRUE.
depth.unit	Units of the depths. Defaults to the one provided in the Bacon() command, depth.unit=set$depth.unit.
age.unit	Units of the ages. Defaults to age.unit="yr".
unit	Deprecated and replaced by depth.unit.
d.lab	The labels for the depth axis. Default d.lab="Depth (cm)". See also depth.unit.
age.lab	The labels for the calendar axis (default age.lab="cal BP" or "BC/AD" if BCAD=TRUE).
yr.lab	Deprecated - use age.lab instead
kcal	Use kcal BP. Default is kcal=FALSE.
acc.lab	The labels for the accumulation rate plot (top middle). Default d.lab="Acc. rate (yr/cm)" (or whatever units you're using).
mem.lab	The labels for the memory plot (top right). Default d.lab="Memory".
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.d.by=0.5.
depths	By default, Bacon will calculate the ages for the depths d.min to d.max in steps of d.by. Alternative depths can be provided as, e.g., depths=seq(0, 100, length=500) or as a file, e.g., depths=read.table("CoreDepths.txt". See also depths.file.
depths.file	By default, Bacon will calculate the ages for the depths d.min to d.max in steps of d.by. If depths.file=TRUE, Bacon will read a file containing the depths for which you require ages. This file, containing the depths in a single column without a header, should be stored within coredir, and its name should start with the core's name and end with '_depths.txt'. Then specify depths.file=TRUE (default FALSE). See also depths.
accordion	An experimental option to squeeze and stretch depths below a boundary. Needs 2 parameters: boundary depth and compression ratio, e.g., accordion=c(25,20). Defaults to inactive, accordion=c().
plotatthesedepths	An option to plot ages at different depths (e.g., if a core has been compressed during a run). Use with extreme caution!
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, hiatus.option=1), use a w-weighted mix between the prior and posterior values for depths below the hiatus and prior information only for above the hiatus (hiatus.option=2), or use the originally calculated slopes (hiatus.option=0).
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 dark=c(). Lower values will result in lighter grey but values >1 are not allowed.
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 (1 digit for plum models).
d.res	Resolution or amount of greyscale pixels to cover the depth scale of the age-model plot. Default d.res=200.
age.res	Resolution or amount of greyscale pixels to cover the age scale of the age-model plot. Default yr.res=200.
yr.res	Deprecated - use age.res instead.
date.res	Date distributions are plotted using date.res=100 points by 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 rotate.axes=TRUE.
rev.age	The direction of the age axis, which can be reversed using rev.age=TRUE.
rev.yr	Deprecated - use rev.age instead.
rev.d	The direction of the depth axis, which can be reversed using rev.d=TRUE.
maxcalc	Number of depths to calculate ages for. If this is more than maxcalc=500, a warning will be shown that calculations will take time.
height	The maximum heights of the distributions of the dates on the plot. See also normalise.dists.
calheight	Multiplier for the heights of the distributions of dates on the calendar scale. Defaults to calheight=1.
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=0.1).
plot.range	Whether or not to plot the curves showing the confidence ranges of the age-model. Defaults to (plot.range=TRUE).
range.col	The colour of the curves showing the confidence ranges of the age-model. Defaults to medium grey (range.col=grey(0.5)).
range.lty	The line type of the curves showing the confidence ranges of the age-model. Defaults to range.lty=12.
range.lwd	Widths of the lines of the ranges of the age-depth model. Default range.lwd=1.
mn.col	The colour of the mean age-depth model: default mn.col="red".
mn.lty	The line type of the mean age-depth model. Default mn.lty=12.
mn.lwd	Width of the line of the mean age-depth model. Default mn.lwd=1.
med.col	The colour of the median age-depth model: not drawn by default med.col=NA.
med.lty	The line type of the median age-depth model. Default med.lty=12.
med.lwd	Width of the line of the median age-depth model. Default med.lwd=1.
C14.col	The colour of the calibrated ranges of the dates. Default is semi-transparent blue: C14.col=rgb(0,0,1,.35).
C14.border	The colours of the borders of calibrated 14C dates. Default is semi-transparent dark blue: C14.border=rgb(0, 0, 1, 0.5).
cal.col	The colour of the non-14C dates. Default is semi-transparent blue-green: cal.col=rgb(0,.5,.5,.35).
cal.border	The colour of the border of non-14C dates in the age-depth plot: default semi-transparent dark blue-green: cal.border=rgb(0,.5,.5,.5). Not used by default.
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., dates.col=colours()[2:100].
pb.background	Probability at which total Pb values are considered to have reached background values, or in other words, that their modelled values are at or below supported + detection limit (Al)). Setting this at 0.5 means that any depth with a Pb measurement, where at least half of the iterations model Pb values reaching background values, is flagged as having reached background. The age-model is not extended to any Pb measurements that have reached background.
pbmodelled.col	Colour of the modelled 210Pb values. Defaults to shades of blue: pbmodelled.col=function(x) rgb(0,0,1,x).
pbmeasured.col	Colour of the measured 210Pb values (default pbmeasured.col="blue"). Draws rectangles of the upper and lower depths as well as the Pb values with 95 percent error ranges.
pb.lim	Axis limits for the Pb-210 data. Calculated automatically by default (pblim=c()).
supp.col	Colour of supported Pb-210. Defaults to semi-transparent purple, because why not.
remove.tail	Whether or not to remove the tail measurements when plotting. Sometimes automated removal might go wrong, so then this option can be used to avoid removing the tail measurements.
MCMC.resample	After the MCMC run, if there are more MCMC iterations than requested, only the last 'ssize' iterations will be retained. Defaults to TRUE.
hiatus.col	The colour of the depths of any hiatuses. Default hiatus.col=grey(0.5).
hiatus.lty	The line type of the depths of any hiatuses. Default hiatus.lty=12.
rgb.scale	The function to produce a coloured representation of all age-models. Needs 3 values for the intensity of red, green and blue. Defaults to grey-scales: rgb.scale=c(0,0,0), but could also be, say, scales of red (rgb.scale=c(1,0,0)).
rgb.res	Resolution of the colour spectrum depicting the age-depth model. Default rgb.res=100.
slump.col	Colour of slumps. Defaults to slump.col=grey(0.8).
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.
same.heights	Plot the distributions of the dates all at the same maximum height (default same.height=FALSE).
cc	Calibration curve for 14C dates: cc=1 for IntCal20 (northern hemisphere terrestrial), cc=2 for Marine20 (marine), cc=3 for SHCal20 (southern hemisphere terrestrial). For dates that are already on the cal BP scale use cc=0.
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="".
title.location	Location of the title. Default title.location='topleft'.
title.size	Size of the title font. Defaults to title.size=1.5.
plot.labels	Whether or not to plot labels next to the dated depths. Defaults to FALSE.
labels	Add labels to the dates (as given by the first column of the .csv file). FALSE by default.
label.age	Position on the age axis of the date labels. By default draws them before the youngest age (1), but can also draw them after the oldest age (2), or above its mean (3).
label.size	Size of labels.
label.col	Colour of the labels. Defaults to the colour given to the borders of the dates.
label.offset	Offsets of the positions of the labels, giving the x and y offsets. Defaults to c(0,0).
label.adj	Justification of the labels. Follows R's adj option: A value of ‘0’ produces left-justified text, ‘0.5’ (the default) centered text and ‘1’ right-justified text.
label.rot	Rotation of the label. 0 by default (horizontal).
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 ("n" for none, and "l" (default), "7", "c", "u", or "o" for correspondingly shaped boxes).
mar.left	Plot margins for the topleft panel (amount of white space along edges of axes 1-4). Default mar.left=c(3,3,1,1).
mar.middle	Plot margins for the middle panel(s) at the top (amount of white space along edges of axes 1-4). Default mar.middle=c(3,3,1,1).
mar.right	Plot margins for the topright panel (amount of white space along edges of axes 1-4). Default mar.right=c(3,3,1,1).
mar.main	Plot margins for the main panel (amount of white space along edges of axes 1-4). Default mar.main=c(3,3,1,1).
righthand	Adapt the righthand margins by a certain amount (default 2) to allow a righthand axis to be plotted (for plum)
mgp	Axis text margins (where should titles, labels and tick marks be plotted). Defaults to mgp=c(1.7, 0.7, 0.0).
xaxs	Extension of x-axis. By default, add some extra white-space at both extremes (xaxs="r"). See ?par for other options.
yaxs	Extension of y-axis. By default, add no extra white-space at both extremes (yaxs="i"). See ?par for other options.
MCMC.col	Colour of the MCMC output. Defaults to post.col=grey(0.4)).
post.col	Colour of the posterior histogram. Defaults to post.col=grey(0.8)).
post.border	Colour of the posterior border. Defaults to post.border=grey(0.4)).
prior.col	Colour of the prior curve. Defaults to light green, prior.col=3).
prior.lwd	Line width of the prior curve. Defaults to prior.lwd=2).
prior.fontcol	Colour of the font accompanying the posterior histograms. Defaults to red, prior.fontcol=2).
prior.ticks	Plot tickmarks and values on the vertical axes for the prior and posterior distributions. Defaults to no tick marks (prior.ticks="n"). Set to prior.ticks="s" to plot the tick marks. Note that these values are of little practical use, as they correspond poorly to, e.g., the mean and strength values. All that matters is that the areas of both the prior and the posterior distributions sum to 1; wider distributions tend to give lower peaks, and narrower distributions higher peaks.
prior.fontsize	Font size of the prior, relative to R's standard size. Defaults to prior.fontsize=0.9.
toppanel.fontsize	Font size of the top panels, relative to R's standard size. Defaults to prior.fontsize=0.9.
mainpanel.tickfontsize	Font size of values at the tick marks in the main panel, relative to R's standard size. Defaults to mainpanel.tickfontsize=1.
mainpanel.labelfontsize	Font size of axis labels in the main panel, relative to R's standard size. Defaults to mainpanel.labelsize=1.
acc.xlim	Horizontal axis limits of the accumulation rate panel. Calculated automatically by default.
acc.ylim	Vertical axis limits of the accumulation rate panel. Calculated automatically by default.
mem.xlim	Horizontal axis limits of the memory panel. Calculated automatically by default.
mem.ylim	Vertical axis limits of the memory panel. Calculated automatically by default.
hiatus.xlim	Horizontal axis limits of the hiatus size panel. Calculated automatically by default.
hiatus.ylim	Vertical axis limits of the hiatus size panel. Calculated automatically by default.
phi.xlim	Horizontal axis limits of the phi panel. Calculated automatically by default.
phi.ylim	Vertical axis limits of the phi panel. Calculated automatically by default.
supp.xlim	Horizontal axis limits of the supported-Pb panel. Calculated automatically by default.
supp.ylim	Vertical axis limits of the supported-Pb panel. Calculated automatically by default.
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 (if present). Defaults to plot.pb=TRUE.
pb.lty	Line type of measured Pb-210 data.
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 dates.only=TRUE.
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 model.only=TRUE. Note however that this removes relevant information to evaluate the age-depth model, so we do recommend to present age-models together with these upper panels.
verbose	Provide a summary of the age ranges after producing the age-depth model graph; default verbose=FALSE.
save.info	By default, a variable called ‘info’ with relevant information about the run (e.g., core name, priors, settings, ages, output) is saved into the working directory. Note that this will overwrite any existing variable with the same name - as an alternative, one could run, e.g., myvar <- Bacon(), followed by supplying the variable myvar in any subsequent commands.

Details

After loading a previous run, or after running either the scissors or thinner command, plot the age-model again using the command agedepth().

Value

A plot of the age-depth model, and estimated ages incl. confidence ranges for each depth.

Author(s)

Maarten Blaauw, J. Andres Christen

Examples

  Bacon(ask=FALSE, coredir=tempfile())
  agedepth()

rbacon documentation built on Sept. 30, 2024, 9:40 a.m.