add.dates: Add dates to age-depth plots

View source: R/calibrate.R

add.datesR Documentation

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 = 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,
  ccdir = ""
)

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 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.

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 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.

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.

ccdir

Directory where the calibration curves for C14 dates cc are located. By default ccdir="".

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


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


rbacon documentation built on March 29, 2022, 5:05 p.m.