add.dates: Add dates to age-depth plots

In clam: Classical Age-Depth Modelling of Cores from Deposits

Add dates to age-depth plots

Description

Add dated depths to plots, e.g. to show dates that weren't used in the age-depth model

Usage

add.dates(
  mn,
  sdev,
  depth,
  cc = 1,
  above = 0.001,
  exx = 50,
  normal = TRUE,
  normalise = TRUE,
  t.a = 3,
  t.b = 4,
  age.res = 100,
  times = 20,
  col = rgb(1, 0, 0, 0.5),
  border = rgb(1, 0, 0, 0.5),
  rotate.axes = FALSE,
  mirror = TRUE,
  up = TRUE,
  BCAD = FALSE
)

Arguments

mn	Reported mean of the date. Can be multiple dates.
sdev	Reported error of the date. Can be multiple dates.
depth	Depth of the date.
cc	The calibration curve to use: cc=1 for IntCal20 (northern hemisphere terrestrial), cc=2 for Marine20 (marine), cc=3 for SHcal20 (southern hemisphere terrestrial), cc=0 for none (dates that are already on the cal BP scale).
above	Threshold for plotting of probability values. Defaults to above=1e-3.
exx	Exaggeration of probability distribution plots. Defaults to exx=50.
normal	By default, Bacon uses the student's t-distribution to treat the dates. Use normal=TRUE to use the normal/Gaussian distribution. This will generally give higher weight to the dates.
normalise	By default, the date is normalised to an area of 1 (normalise=TRUE).
t.a	The dates are treated using the student's t distribution by default (normal=FALSE). The student's t-distribution has two parameters, t.a and t.b, set at 3 and 4 by default (see Christen and Perez, 2010). If you want to assign narrower error distributions (more closely resembling the normal distribution), set t.a and t.b at for example 33 and 34 respectively (e.g., for specific dates in your .csv file). For symmetry reasons, t.a must always be equal to t.b-1.
t.b	The dates are treated using the student's t distribution by default (normal=FALSE). The student's t-distribution has two parameters, t.a and t.b, set at 3 and 4 by default (see Christen and Perez, 2010). If you want to assign narrower error distributions (more closely resembling the normal distribution), set t.a and t.b at for example 33 and 34 respectively (e.g., for specific dates in your .csv file). For symmetry reasons, t.a must always be equal to t.b-1.
age.res	Resolution of the date's distribution. Defaults to date.res=100.
times	The extent of the range to be calculated for each date. Defaults to times=20.
col	The colour of the ranges of the date. Default is semi-transparent red: col=rgb(1,0,0,.5).
border	The colours of the borders of the date. Default is semi-transparent red: border=rgb(1,0,0,0.5).
rotate.axes	The default of plotting age on the horizontal axis and event probability on the vertical one can be changed with rotate.axes=TRUE.
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.
BCAD	The calendar scale of graphs is in cal BP by default, but can be changed to BC/AD using BCAD=TRUE.

Details

Sometimes it is useful to add additional dating information to age-depth plots, e.g., to show outliers or how dates calibrate with different estimated offsets.

Value

A date's distribution, added to an age-depth plot.

Author(s)

Maarten Blaauw, J. Andres Christen

Examples

  base_temp_dir <- tempdir()
  clam_dir <- file.path(base_temp_dir, "clam_runs")
  dir.create(clam_dir, recursive = TRUE, showWarnings = FALSE)
  clam(, coredir=clam_dir, ask=FALSE)
  add.dates(5000, 100, 60)

clam documentation built on April 4, 2025, 4:45 a.m.