add.dates: Add dates to age-depth plots

In rbacon: Age-Depth Modelling using Bayesian Statistics

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,
  set = get("info"),
  above = 1e-06,
  postbomb = 0,
  normal = TRUE,
  delta.R = set$delta.R,
  delta.STD = set$delta.STD,
  t.a = set$t.a,
  t.b = set$t.b,
  date.res = 100,
  height = 0.1,
  calheight = 1,
  agesteps = 1,
  cutoff = 0.005,
  col = rgb(1, 0, 0, 0.5),
  border = rgb(1, 0, 0, 0.5),
  rotate.axes = FALSE,
  mirror = TRUE,
  up = TRUE,
  BCAD = FALSE,
  pch = 4,
  cc.dir = c()
)

Arguments

mn	Reported mean of the date. Can be multiple dates. Negative numbers indicate postbomb dates (if cc > 0).
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=0 for none (dates that are already on the cal BP scale).
set	Detailed information of the current run, stored within this session's memory as variable info.
above	Threshold for plotting of probability values. Defaults to above=1e-3.
postbomb	Use a postbomb curve for negative (i.e. postbomb) 14C ages. 0 = none, 1 = NH1, 2 = NH2, 3 = NH3, 4 = SH1-2, 5 = SH3
normal	By default, Bacon uses the t-distribution (Christen and Perez 2009) to treat the dates. Use normal=TRUE to use the normal/Gaussian distribution. This will generally give higher weight to the dates.
delta.R	Mean of core-wide age offsets (e.g., regional marine offsets).
delta.STD	Error of core-wide age offsets (e.g., regional marine offsets).
t.a	The dates are treated using the t distribution by default (normal=FALSE). The t model 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 t distribution by default (normal=FALSE). The 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.
date.res	Resolution of the date's distribution. Defaults to date.res=100.
height	The heights of the distributions of the dates. See also normalise.dists.
calheight	Multiplier for the heights of the distributions of dates on the calendar scale. Defaults to calheight=1.
agesteps	Step size for age units of the distribution. Default agesteps=1.
cutoff	Avoid plotting very low probabilities of date distributions (default cutoff=0.005).
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.
pch	The shape of any marker to be added to the date. Defaults to a cross, pch=4. To leave empty, use pch=NA.
cc.dir	Directory where the calibration curves for C14 dates cc are located. By default cc.dir=c().

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. Calls rice's draw.dates function.

Value

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

Author(s)

Maarten Blaauw, J. Andres Christen

Examples

  Bacon(run=FALSE, coredir=tempfile())
  agedepth()
  add.dates(5000, 100, 60)

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