BchronCalibrate: Fast radiocarbon calibration

In Bchron: Radiocarbon Dating, Age-Depth Modelling, Relative Sea Level Rate Estimation, and Non-Parametric Phase Modelling

Description

A fast function for calibrating large numbers of radiocarbon dates involving multiple calibration curves

Usage

BchronCalibrate(
  ages,
  ageSds,
  calCurves = rep("intcal20", length(ages)),
  ids = NULL,
  positions = NULL,
  pathToCalCurves = system.file("data", package = "Bchron"),
  allowOutside = FALSE,
  eps = 1e-05,
  dfs = rep(100, length(ages))
)

Arguments

ages	A vector of ages provided in years before 1950.
ageSds	A vector of 1-sigma values for the ages given above
calCurves	A vector of values containing either intcal20, shcal20, marine20, or normal (older calibration curves are supposed such as intcal13). Should be the same length the number of ages supplied. Non-standard calibration curves can be used provided they are supplied in the same format as those previously mentioned and are placed in the same directory. Normal indicates a normally-distributed (non-14C) age.
ids	ID names for each age
positions	Position values (e.g. depths) for each age. In the case of layers of non-zero thickness, this should be the middle value of the slice
pathToCalCurves	File path to where the calibration curves are located. Defaults to the system directory where the 3 standard calibration curves are stored.
allowOutside	Whether to allow calibrations to run outside the range of the calibration curve. By default this is turned off as calibrations outside of the range of the calibration curve can cause severe issues with probability ranges of calibrated dates
eps	Cut-off point for density calculation. A value of eps>0 removes ages from the output which have negligible probability density
dfs	Degrees-of-freedom values for the t-distribution associated with the calibration calculation. A large value indicates Gaussian distributions assumed for the 14C ages

Details

This function provides a direct numerical integration strategy for computing calibrated radiocarbon ages. The steps for each 14C age are approximately as follows: 1) Create a grid of ages covering the range of the calibration curve 2) Calculate the probability of each age according to the 14C age, the standard deviation supplied and the calibration curve 3) Normalise the probabilities so that they sum to 1 4) Remove any probabilities that are less than the value given for eps Multiple calibration curves can be specified so that each 14C age can have a different curve. For ages that are not 14C, use the 'normal' calibration curve which treats the ages as normally distributed with given standard deviation

Value

A list of lists where each element corresponds to a single age. Each element contains:

ages	The original age supplied
ageSds	The original age standard deviation supplied
positions	The position of the age (usually the depth)
calCurves	The calibration curve used for that age
ageGrid	A grid of age values over which the density was created
densities	A vector of probability values indicating the probability value for each element in ageGrid
ageLab	The label given to the age variable
positionLab	The label given to the position variable

See Also

Bchronology, BchronRSL, BchronDensity, BchronDensityFast, createCalCurve

Examples

# Calibrate a single age
ages1 <- BchronCalibrate(
  ages = 11553,
  ageSds = 230,
  calCurves = "intcal20",
  ids = "Date-1"
)
summary(ages1)
plot(ages1)

# Or plot with Calibration curve
plot(ages1, includeCal = TRUE)

# Calibrate multiple ages with different calibration curves
ages2 <- BchronCalibrate(
  ages = c(3445, 11553, 7456),
  ageSds = c(50, 230, 110),
  calCurves = c("intcal20", "intcal20", "shcal20")
)
summary(ages2)
plot(ages2)

# Calibrate multiple ages with multiple calibration curves and including depth
ages3 <- BchronCalibrate(
  ages = c(3445, 11553),
  ageSds = c(50, 230),
  positions = c(100, 150),
  calCurves = c("intcal20", "normal")
)
summary(ages3)
plot(ages3, withPositions = TRUE)

Example output

95% Highest density regions for Date-1
$`0.4%`
[1] 13004 13025

$`77.9%`
[1] 13059 13874

$`16.4%`
[1] 13923 14012


95% Highest density regions for Date1
$`94.4%`
[1] 3572 3834


95% Highest density regions for Date2
$`0.4%`
[1] 13004 13025

$`77.9%`
[1] 13059 13874

$`16.4%`
[1] 13923 14012


95% Highest density regions for Date3
$`94.6%`
[1] 8015 8409


[[1]]

[[2]]

[[3]]

95% Highest density regions for Date1
$`94.4%`
[1] 3572 3834


95% Highest density regions for Date2
$`94.7%`
[1] 11100 12005

Bchron documentation built on June 10, 2021, 9:10 a.m.