clean: Simulate removing contamination from a radiocarbon age

In rice: Radiocarbon Equations

Simulate removing contamination from a radiocarbon age

Description

Given an observed radiocarbon age, remove the impact of contamination (for example, 1% contamination with modern carbon) to estimate the true/target age

Usage

clean(
  y,
  er = 0,
  percentage,
  percentage.error = 0,
  F.contam = 1,
  F.contam.er = 0,
  MC = TRUE,
  its = 10000,
  roundby = 1,
  decimals = 5,
  visualise = TRUE,
  talk = TRUE,
  eq.x = 5,
  eq.y = c(),
  eq.size = 0.75,
  true.col = "darkgreen",
  observed.col = "blue",
  contamination.col = "red",
  true.pch = 20,
  observed.pch = 18,
  contamination.pch = 17,
  true.name = "true",
  xlab = "contamination (%)",
  ylab = "F14C",
  ylim = c(),
  C14.axis = TRUE,
  bty = "u"
)

Arguments

y	The observed radiocarbon age
er	The error of the observed radiocarbon age
percentage	Relative amount of contamination. Must be between 0 and 100 (%)
percentage.error	Uncertainty of the contamination. Assumed to be normally distributed (which fails close to 0% or 100% contamination levels). Defaults to 0%.
F.contam	The F14C of the contamination. Set at 1 for carbon of modern radiocarbon age, at 0 for 14C-free carbon, or anywhere inbetween.
F.contam.er	The error of the contamination. Defaults to 0.
MC	Whether or not to use Monte Carlo iterations to estimate the values. Defaults to TRUE, because it treats uncertainties better than if set to FALSE.
its	Amount of iterations to use if MC=TRUE. Defaults to 10,000.
roundby	Rounding of the output for C14 ages. Defaults to 1 decimal.
decimals	Rounding of the output. Since details matter here, the default is to provide 5 decimals.
visualise	By default, a plot is made to visualise the target and observed F14C values, together with the inferred contamination.
talk	Whether or not to report the calculations made. Defaults to talk=TRUE.
eq.x	Leftmost location of the equation. Defaults to eq.x=5. Can be set to values outside of (0,100) to make the equation invisible.
eq.y	Vertical location of the equation. Defaults to the top of the graph.
eq.size	Size of the font of the equation. In case the equation gets jumbled up upon resizing of a graphical device, just issue the previous 'clean' command again. Defaults to eq.size=0.8.
true.col	Colour for the target/true values. Defaults to "darkgreen".
observed.col	Colour for the observed values. Defaults to blue.
contamination.col	Colour for the contamination values. Defaults to red.
true.pch	Icon for the true/target date. Defaults to a filled circle.
observed.pch	Icon for the observed. Defaults to a diamond
contamination.pch	Icon for the contamination. Defaults to a triangle.
true.name	Name of the label of the true/target date
xlab	Name of the x-axis. Defaults to 'contamination (%)'.
ylab	Name of the y-axis. Defaults to 'F14C'.
ylim	Limits of the y-axis. Calculated automatically by default.
C14.axis	Whether or not to draw a secondary vertical axis for C14 ages. Defaults to C14.axis=TRUE.
bty	Draw a box around a box of a certain shape. Defaults to bty="u".

Details

Whereas the function takes C14 ages and percentage contamination as input, internal calculations are done in the F14C realm and using fractions (between 0 and 1). The central calculation is 'F_true = ((1-frac)*F_obs) - (frac*F_contam)', where 'F_true' is the true or target age in F14C, 'frac' is the fraction of contamination, 'F_obs' is the F14C of the observed C14 age, and 'F_contam' is the F activity of the contamination. In some extreme cases, the calculations will spit out unexpected results. Messages will be provided in most of these cases.

Value

The true/target radiocarbon age and error

Author(s)

Maarten Blaauw

Examples

# 1% contamination with modern carbon (no uncertainties in contamination's percentage or F)
clean(5000, 20, 1, 0, 1, 0)
# now with errors:
clean(5000, 20, 1, 0.1, 1, 0.1)

rice documentation built on April 11, 2025, 5:53 p.m.