agedepth: Plot an age-depth model

View source: R/agedepth.R

agedepthR Documentation

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(),
  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 = 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",
  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(),
  pb.background = 0.5,
  pbmodelled.col = function(x) rgb(0, 0, 1, 0.5 * x),
  pbmeasured.col = "blue",
  pb.lim = c(),
  supp.col = "purple",
  plot.tail = TRUE,
  remove.tail = 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",
  prior.ticks = "n",
  prior.fontsize = 0.9,
  toppanel.fontsize = 0.9,
  xaxt = "s",
  yaxt = "s",
  plot.pb = TRUE,
  pb.lty = 1,
  plot.pdf = FALSE,
  dates.only = FALSE,
  model.only = FALSE,
  verbose = 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).

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.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.

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.

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.

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.

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 .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 purple, because why not.

plot.tail

The depth axis can extend to all Pb measurements (plot.tail=TRUE), or leave out the ones where background has been reached.

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. Quite similar to plot.tail.

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, .7, .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.

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.

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.

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 March 29, 2022, 5:05 p.m.