Package 'IntCal'

Calculate pMC values from C14 ages

Description

Calculate pMC values from radiocarbon ages

Usage

age.pMC(mn, sdev, ratio = 100, decimals = 3)

Arguments

mn	Reported mean of the 14C age.
sdev	Reported error of the 14C age.
ratio	Most modern-date values are reported against 100. If it is against 1 instead, use 1 here.
decimals	Amount of decimals required for the pMC value.

Details

Post-bomb dates are often reported as pMC or percent modern carbon. Since Bacon expects radiocarbon ages, this function can be used to calculate pMC values from radiocarbon ages. The reverse function of pMC.age.

Value

pMC values from C14 ages.

Examples

age.pMC(-2000, 20)
  age.pMC(-2000, 20, 1)

---

Find the 14C age and error belonging to a cal BP age.

Description

Given a calendar age, the calibration curve (default cc=1) is interpolated and the corresponding 14C age and error are returned.

Usage

calBP.14C(yr, cc = 1, postbomb = FALSE, rule = 1, ccdir = NULL)

Arguments

yr	The cal BP year.
cc	calibration curve for C14 (see caldist()).
postbomb	Whether or not to use a postbomb curve (see caldist()).
rule	How should R's approx function deal with extrapolation. If rule=1, the default, then NAs are returned for such points and if it is 2, the value at the closest data extreme is used.
ccdir	Directory of the calibration curves. Defaults to where the package's files are stored (system.file), but can be set to, e.g., ccdir="curves".

Details

Interpolation is used, and values outside the calibration curve are given as NA. For negative cal BP ages, a postbomb curve will have to be provided.

Author(s)

Maarten Blaauw

Examples

calBP.14C(100)

---

Calculate calibrated distribution

Description

Calculate the calibrated distribution of a radiocarbon date.

Usage

caldist(
  age,
  error,
  cc = 1,
  postbomb = FALSE,
  yrsteps = FALSE,
  threshold = 0.001,
  calibt = FALSE,
  BCAD = FALSE,
  rule = 1,
  ccdir = NULL
)

Arguments

age	Uncalibrated radiocarbon age
error	Lab error of the radiocarbon age
cc	Calibration curve to use. Defaults to IntCal20 (cc=1).
postbomb	Whether or not to use a postbomb curve. Required for negative radiocarbon ages.
yrsteps	Steps to use for interpolation. Defaults to the cal BP steps in the calibration curve
threshold	Report only values above a threshold. Defaults to threshold=1e-6.
calibt	Use the student-t distribution as alternative to the normal distribution. Requires 2 parameters, e.g., calibt=c(3,4), defaults to FALSE.
BCAD	Which calendar scale to use. Defaults to cal BP, BCAD=FALSE.
rule	Which extrapolation rule to use. Defaults to rule=1 which returns NAs.
ccdir	Directory of the calibration curves. Defaults to where the package's files are stored (system.file), but can be set to, e.g., ccdir="curves".

Examples

calib <- caldist(130,20)
plot(calib, type="l")
postbomb <- caldist(-3030, 20, "nh1", BCAD=TRUE)

---

Plot individual calibrated dates.

Description

Calibrate individual 14C dates, plot them and report calibrated ranges.

Usage

calibrate(
  age = 2450,
  error = 50,
  cc = 1,
  postbomb = FALSE,
  reservoir = 0,
  prob = 0.95,
  BCAD = FALSE,
  ka = FALSE,
  cal.lab = c(),
  C14.lab = c(),
  cal.lim = c(),
  C14.lim = c(),
  cc.col = rgb(0, 0.5, 0, 0.7),
  cc.fill = rgb(0, 0.5, 0, 0.7),
  date.col = "red",
  dist.col = rgb(0, 0, 0, 0.2),
  dist.fill = rgb(0, 0, 0, 0.2),
  hpd.fill = rgb(0, 0, 0, 0.3),
  dist.height = 0.3,
  cal.rev = FALSE,
  yr.steps = FALSE,
  threshold = 5e-04,
  edge = TRUE,
  calibt = FALSE,
  rounded = 1,
  extend.range = 0.05,
  legend.cex = 0.8,
  legend1.loc = "topleft",
  legend2.loc = "topright",
  mgp = c(2, 1, 0),
  mar = c(3, 3, 1, 1),
  xaxs = "i",
  yaxs = "i",
  bty = "l",
  ccdir = NULL,
  ...
)

Arguments

age	Mean of the uncalibrated C-14 age.
error	Error of the uncalibrated C-14 age.
cc	Calibration curve for C-14 dates (1, 2, 3, or 4, or, e.g., "IntCal20", "Marine20", "SHCal20", "nh1", "sh3", or "mixed").
postbomb	Whether or not this is a postbomb age. Defaults to FALSE.
reservoir	Reservoir age, or reservoir age and age offset.
prob	Probability confidence intervals (between 0 and 1).
BCAD	Use BC/AD or cal BP scale (default cal BP).
ka	Use thousands of years instead of years in the plots and hpd ranges. Defaults to FALSE.
cal.lab	Label of the calendar/horizontal axis. Defaults to the calendar scale, but alternative names can be provided.
C14.lab	Label of the C-14/vertical axis. Defaults to the 14C scale, but alternative names can be provided.
cal.lim	Minimum and maximum of calendar axis (default calculated automatically).
C14.lim	Minimum and maximum of C-14 axis (default calculated automatically).
cc.col	Colour of the lines of the calibration curve. Defaults to semi-transparent dark green; cc.col=rgb(0,.5,0,0.7).
cc.fill	Colour of the inner part of the calibration curve. Defaults to semi-transparent dark green; cc.col=rgb(0,.5,0,0.7).
date.col	Colour of the "dot-bar" plot of the C14 date. Defaults to date.col="red".
dist.col	Colour of the outer lines of the distributions. Defaults to semi-transparent grey, dist.col=rgb(0,0,0,0.2).
dist.fill	Colour of the inner part of the distributions. Defaults to semi-transparent grey, dist.col=rgb(0,0,0,0.2).
hpd.fill	Colour of the highest posterior density. Defaults to semi-transparent grey, dist.col=rgb(0,0,0,0.3).
dist.height	Maximum height of the C14 and calibrated distributions (as proportion of the invisible secondary axes). Defaults to 0.3.
cal.rev	Whether or not to reverse the direction of the calendar axis.
yr.steps	Temporal resolution at which C-14 ages are calibrated (in calendar years). By default follows the spacing in the calibration curve.
threshold	Below which value should probabilities be excluded from calculations.
edge	How to treat dates are at or beyond the edge of the calibration curve. If dates are truncated, a warning is given. If they lie beyond the calibration curve, an error is given.
calibt	Calibration based on the student-t distribution. By default, the Gaussian distribution is used (calibt=FALSE). To use the student-t distribution, provide two parameters such as calibt=c(3,4).
rounded	Rounding of the percentages of the reported hpd ranges. Defaults to 1 decimal.
extend.range	Range by which the axes are extended beyond the data limits. Defaults to 5%.
legend.cex	Size of the font of the legends. Defaults to 0.8.
legend1.loc	Where the first legend (with the calibration curve name and the uncalibrated date) is plotted. Defaults to topleft.
legend2.loc	Where the second legend (with the hpd ranges) is plotted. Defaults to topright.
mgp	Axis text margins (where should titles, labels and tick marks be plotted).
mar	Plot margins (amount of white space along edges of axes 1-4).
xaxs	Whether or not to extend the limits of the horizontal axis. Defaults to xaxs="i" which does not extend the limits.
yaxs	Whether or not to extend the limits of the vertical axis. Defaults to yaxs="i" which does not extend the limits.
bty	Draw a box around the graph ("n" for none, and "l", "7", "c", "u", "]" or "o" for correspondingly shaped boxes).
ccdir	Directory of the calibration curves. Defaults to where the package's files are stored (system.file), but can be set to, e.g., ccdir="curves".
...	Other plotting parameters.

Details

Type calibrate() to see how a date of 2450 +- 50 14C BP gets calibrated (the calibration curve happens to show a plateau around this 14C age). To calibrate a different date, provide its reported mean and error (1 standard deviation error as reported by the radiocarbon laboratory) as follows: calibrate(mean, error), e.g., for a date of 130 +- 20 14C BP, type calibrate(age=130, error=20) or, shorter, calibrate(130,20).

In case the date has a reservoir effect or age offset, e.g. of 100 14C years, provide this as follows: calibrate(130, 20, reservoir=100). If you want to include an uncertainty for this offset, provide this as follows, e.g., for an uncertainty of 50yr, calibrate(130,20,reservoir=c(100, 50)). The uncertainty for the age offset will then be added to the error (by taking the square root of the sum of the squared error and the squared offset uncertainty). If the carbon of your sample has mixed marine/terrestrial sources, instead apply the marine offset using mix.curves and calibrate the date using that custom-built curve (cc="mixed").

If you prefer to work with, e.g., 68 % as opposed to the default 95 % confidence intervals, type: calibrate(130, 20, prob=0.68) or calibrate(130, 20,, 0.68) (the commas between the brackets indicate the position of the option; the standard deviation is the fourth option of the calibrate function). The calibrated distribution can be calculated for every single calendar year (yrsteps=1) within a wide range of the 14C date. Probabilities below a threshold (default threshold=0.0005) will be neglected.

By default the northern hemisphere terrestrial calibration curve is used (cc=1 or cc1="IntCal20"). To use alternative curves, use cc=2 (cc2="Marine20"), cc=3 (cc3="SHCal20C"), cc=4 (cc4="mixed.14C"), or specify a postbomb curve (e.g., cc="nh1").

Calibrate works in cal BP (calendar years before AD 1950) by default, but can work with cal BC/AD through the option BCAD=TRUE.

By default the Gaussian distribution is used to calibrate dates. For use of the student-t distribution instead, provide two sensible values, e.g., calibt=c(3,4).

Calibrated distributions are usually reduced to their 68% or 95% calibrated ranges, taking into account the asymmetric and multi-peaked shape of these distributions. Calibrated ranges at 68% will obviously result in narrower confidence intervals, and a perceived higher precision, than 95% ranges. However, given the often asymmetric and multi-modal nature of calibrated distributions, the probability that the 'true' calendar date lies outside the 1 standard deviation hpd ranges is considerable (c. 32%). Therefore the use of 95% calibrated ranges is preferable, and default.

Negative radiocarbon ages are calibrated with postbomb curves, but the user needs to tell which curve to use. For example, to use the first of the three northern hemisphere curves, provide the option cc="nh1", cc="nh2", cc="nh3", while for southern hemisphere samples, use cc="sh1-2" or cc="sh3".

A graph of the calibration is produced, and it can be adapted in several ways. The limits of the horizontal (calendar scale) and vertical (14C scale) axes are calculated automatically but can be changed by providing alternative values for the options cal.lim, C14.lim. The titles of both axis can be changed by providing alternative titles to cal.lab and/or C14.lab. The heights of the distributions of the 14C and calibrated ages can be set to alternative values using dist.height (default 0.3 which plots the distribution up to 30% of the height of the entire graph). Parameters for white space around the graph can be changed (default mar=c(3.5, 2, 2, 1) for spacing below, to the left, above and to the right respectively), as can the spacing for the axis labels (mgp=c(2,1,0)). By default, the axes are connected at the lower left, bty="l". Check the R documentation of par() for more options.

The colours of the 14C date, the calibration curve, the distributions, and the highest posterior density (hpd) ranges, can be changed by providing an alternative colour in date.col, cc.col, dist.col, and/or hpd.col, respectively. The default colours are transparent grey for the dates probability distributions (dist.col=rgb(0,0,0, 0.3) and sd.col=rgb(0,0,0, 0.5); change the last value of rgb for different greyscale values), red for the uncalibrated mean and error bars (date.col="red"), and transparent green for the calibration curve (cc.col=rgb(0, 0.5, 0, 0.7)). R's rgb() function expects values between 0 and 1 for red, green and blue, respectively, followed by a value for the semi-transparency (also between 0 and 1). Some graphic devices such as postscript are unable to use transparency; in that case provide different colours or leave the fourth value empty.

Value

A graph of the raw and calibrated C-14 date, the calibrated ranges and, invisibly, the calibrated distribution and hpd ranges.

Examples

calibrate()
calibrate(130, 20)
cal <- calibrate(2550, 20, reservoir=100)
cal; plot(cal[[1]])
calibrate(130, 20, prob=0.68)
calibrate(age=130, error=20, BCAD=TRUE)
calibrate(4450, 40, reservoir=c(100, 50))

---

Copy a calibration curve

Description

Copy one of the calibration curves into memory.

Usage

ccurve(cc = 1, postbomb = FALSE, ccdir = NULL)

Arguments

cc	Calibration curve for 14C dates: cc=1 for IntCal20 (northern hemisphere terrestrial), cc=2 for Marine20 (marine), cc=3 for SHCal20 (southern hemisphere terrestrial). Alternatively, one can also write, e.g., "IntCal20", "Marine13".
postbomb	Use postbomb=TRUE to get a postbomb calibration curve (default postbomb=FALSE). For monthly data, type e.g. ccurve("sh1-2_monthly")
ccdir	Directory of the calibration curves. Defaults to where the package's files are stored (system.file), but can be set to, e.g., ccdir="curves".

Details

Copy the radiocarbon calibration curve defined by cc into memory.

Value

The calibration curve (invisible).

References

Hammer and Levin 2017, "Monthly mean atmospheric D14CO2 at Jungfraujoch and Schauinsland from 1986 to 2016", heiDATA: Heidelberg Research Data Repository V2 doi:10.11588/data/10100

Hogg et al. 2013 SHCal13 Southern Hemisphere Calibration, 0–50,000 Years cal BP. Radiocarbon 55, 1889-1903. doi:10.2458/azu_js_rc.55.16783

Hogg et al. 2020 SHCal20 Southern Hemisphere calibration, 0-55,000 years cal BP. Radiocarbon 62. doi:10.1017/RDC.2020.59

Hua et al. 2013 Atmospheric radiocarbon for the period 1950-2010. Radiocarbon 55(4), doi:10.2458/azu_js_rc.v55i2.16177

Hua et al. 2021 Atmospheric radiocarbon for the period 1950-2019. Radiocarbon in press, doi:10.1017/RDC.2021.95

Hughen et al. 2020 Marine20-the marine radiocarbon age calibration curve (0-55,000 cal BP). Radiocarbon 62. doi:10.1017/RDC.2020.68

Levin and Kromer 2004 "The tropospheric 14CO2 level in mid latitudes of the Northern Hemisphere" Radiocarbon 46, 1261-1272

Reimer et al. 2004 IntCal04 terrestrial radiocarbon age calibration, 0–26 cal kyr BP. Radiocarbon 46, 1029–1058. doi:10.1017/S0033822200032999

Reimer et al. 2009 IntCal09 and Marine09 radiocarbon age calibration curves, 0–50,000 years cal BP. Radiocarbon 51, 1111–1150. doi:10.1017/S0033822200034202

Reimer et al. 2013 IntCal13 and Marine13 radiocarbon age calibration curves 0–50,000 years cal BP. Radiocarbon 55, 1869–1887. doi:10.2458/azu_js_rc.55.16947

Reimer et al. 2020 The IntCal20 Northern Hemisphere radiocarbon age calibration curve (0–55 cal kBP). Radiocarbon 62, 725-757. doi:10.1017/RDC.2020.41

Stuiver et al. 1998 INTCAL98 radiocarbon age calibration, 24,000–0 cal BP. Radiocarbon 40, 1041-1083. doi:10.1017/S0033822200019123

Examples

intcal20 <- ccurve(1)
marine20 <- ccurve(2)
shcal20 <- ccurve(3)
marine98 <- ccurve("Marine98")
pb.sh3 <- ccurve("sh3")

---

Copy a calibration curve

Description

Copy one of the calibration curves into memory. Renamed to ccurve, and copyCalibrationCurve will become obsolete

Usage

copyCalibrationCurve(cc = 1, postbomb = FALSE)

Arguments

cc	Calibration curve for 14C dates: cc=1 for IntCal20 (northern hemisphere terrestrial), cc=2 for Marine20 (marine), cc=3 for SHCal20 (southern hemisphere terrestrial). Alternatively, one can also write, e.g., "IntCal20", "Marine13".
postbomb	Use postbomb=TRUE to get a postbomb calibration curve (default postbomb=FALSE).

Details

Copy the radiocarbon calibration curve defined by cc into memory.

Value

The calibration curve (invisible).

---

Draw a calibration curve.

Description

Draw one or two of the calibration curves, or add a calibration curve to an existing plot.

Usage

draw.ccurve(
  cal1 = -50,
  cal2 = 55000,
  cc1 = "IntCal20",
  cc2 = NA,
  cc1.postbomb = FALSE,
  cc2.postbomb = FALSE,
  BCAD = FALSE,
  cal.lab = NA,
  cal.rev = FALSE,
  c14.lab = NA,
  c14.lim = NA,
  c14.rev = FALSE,
  ka = FALSE,
  add.yaxis = FALSE,
  cc1.col = rgb(0, 0, 1, 0.5),
  cc1.fill = rgb(0, 0, 1, 0.2),
  cc2.col = rgb(0, 0.5, 0, 0.5),
  cc2.fill = rgb(0, 0.5, 0, 0.2),
  add = FALSE,
  bty = "l",
  ccdir = NULL,
  ...
)

Arguments

cal1	First calendar year for the plot
cal2	Last calendar year for the plot
cc1	Name of the calibration curve. Can be "IntCal20", "Marine20", "SHCal20", or for the previous curves "IntCal13", "Marine13" or "SHCal13". Can also be "nh1", "nh2", "nh3", "sh1-2", "sh3", "nh1_monthly", "nh1_monthly", "nh2_monthly", "nh3_monthly", "sh1-2_monthly", "sh3_monthly", "Kure", "LevinKromer" or "Santos" for postbomb curves.
cc2	Optional second calibration curve to plot. Can be "IntCal20", "Marine20", "SHCal20", or for the previous curves "IntCal13", "Marine13" or "SHCal13". Defaults to nothing, NA.
cc1.postbomb	Use postbomb=TRUE to get a postbomb calibration curve for cc1 (default cc1.postbomb=FALSE).
cc2.postbomb	Use postbomb=TRUE to get a postbomb calibration curve for cc2 (default cc2.postbomb=FALSE).
BCAD	The calendar scale of graphs and age output-files is in cal BP (calendar or calibrated years before the present, where the present is AD 1950) by default, but can be changed to BC/AD using BCAD=TRUE.
cal.lab	The labels for the calendar axis (default age.lab="cal BP" or "BC/AD" if BCAD=TRUE), or to age.lab="kcal BP" etc. if ka=TRUE.
cal.rev	Reverse the calendar axis.
c14.lab	Label for the C-14 axis. Defaults to 14C BP (or 14C kBP if ka=TRUE).
c14.lim	Axis limits for the C-14 axis. Calculated automatically by default.
c14.rev	Reverse the C-14 axis.
ka	Use kcal BP (and C14 kBP).
add.yaxis	Whether or not to plot the second calibration. Defaults to add.yaxis=FALSE.
cc1.col	Colour of the calibration curve (outline).
cc1.fill	Colour of the calibration curve (fill).
cc2.col	Colour of the calibration curve (outline), if activated (default cc2=NA).
cc2.fill	Colour of the calibration curve (fill), if activated (default cc2=NA).
add	Whether or not to add the curve(s) to an existing plot. Defaults to FALSE, which draws a new plot
bty	Draw a box around a box of a certain shape. Defaults to bty="l".
ccdir	Directory of the calibration curves. Defaults to where the package's files are stored (system.file), but can be set to, e.g., ccdir="curves".
...	Any additional optional plotting parameters.

Value

The calibration curve (invisible).

Examples

draw.ccurve()
draw.ccurve(1000, 3000, cc2="Marine20")
draw.ccurve(1800, 2020, BCAD=TRUE, cc2="nh1", cc2.postbomb=TRUE)
draw.ccurve(1800, 2010, BCAD=TRUE, cc2="nh1", add.yaxis=TRUE)

---

add calibrated distributions to a plot.

Description

Add individual calibrated dates to a plot.

Usage

draw.dates(
  age,
  error,
  depth,
  cc = 1,
  postbomb = FALSE,
  reservoir = c(),
  calibt = c(),
  prob = 0.95,
  threshold = 0.001,
  BCAD = FALSE,
  ex = 0.9,
  normalise = TRUE,
  draw.hpd = TRUE,
  hpd.lwd = 2,
  hpd.col = rgb(0, 0, 1, 0.7),
  mirror = TRUE,
  up = FALSE,
  on.axis = 1,
  col = rgb(0, 0, 1, 0.3),
  border = rgb(0, 0, 1, 0.5),
  add = FALSE,
  cal.lab = c(),
  cal.lim = c(),
  y.lab = c(),
  y.lim = c(),
  y.rev = TRUE,
  labels = c(),
  label.x = 1,
  label.y = c(),
  label.cex = 0.8,
  label.col = border,
  label.offset = c(0, 0),
  label.adj = c(1, 0),
  label.rot = 0,
  ccdir = NULL,
  ...
)

Arguments

age	Mean of the uncalibrated C-14 age (or multiple ages).
error	Error of the uncalibrated C-14 age (or ages).
depth	Depth(s) of the date(s)
cc	Calibration curve for C-14 dates (1, 2, 3, or 4, or, e.g., "IntCal20", "Marine20", "SHCal20", "nh1", "sh3", or "mixed"). If there are multiple dates but all use the same calibration curve, one value can be provided.
postbomb	Whether or not this is a postbomb age. Defaults to FALSE.
reservoir	Reservoir age, or reservoir age and age offset.
calibt	Calibration based on the student-t distribution. By default, the Gaussian distribution is used (calibt=FALSE). To use the student-t distribution, provide two parameters such as calibt=c(3,4).
prob	Probability confidence intervals (between 0 and 1).
threshold	Report only values above a threshold. Defaults to threshold=0.001.
BCAD	Use BC/AD or cal BP scale (default cal BP).
ex	Exaggeration of the height of the distribution
normalise	If TRUE, the date is normalised by setting its peak value to 1 (handy for estimating how high to draw it). If there are multiple dates, it is normalised to the peak of the most precise date. Otherwise the peak of each date is at the same height.
draw.hpd	Whether or not to draw the hpd ranges as a line
hpd.lwd	Width of the line of the hpd ranges
hpd.col	Colour of the hpd rectangle
mirror	Plot distributions mirrored, a bit like a swan. Confuses some people but looks nice to the author so is the default.
up	If mirror is set to FALSE, the distribution can be plotted up or down, depending on the direction of the axis.
on.axis	Which axis to plot on. Defaults to 'x' or 1, but can be set to 'y' or 2.
col	Colour of the inside of the distribution
border	Colour of the border of the distribution
add	Whether or not to add the dates to an existing plot. If set to FALSE (default), a plot will be set up.
cal.lab	Title of the calendar axis (if present)
cal.lim	Limits of the calendar axis (if present)
y.lab	Title of the vertical axis (if present)
y.lim	Limits of the vertical axis (if present)
y.rev	Reverse the y-axis. Defaults to TRUE
labels	Add labels to the dates. Empty by default.
label.x	Horizontal position of the date labels. By default draws them before the youngest age (1), but can also draw them after the oldest age (2), or above its mean (3).
label.y	Vertical positions of the labels. Defaults to 0 (or 1 if label.x is 3 or 4).
label.cex	Size of labels.
label.col	Colour of the labels. Defaults to the colour given to the borders of the dates.
label.offset	Offsets of the positions of the labels, giving the x and y offsets. Defaults to c(0,0).
label.adj	Justification of the labels. Follows R's adj option: A value of ‘0’ produces left-justified text, ‘0.5’ (the default) centered text and ‘1’ right-justified text.
label.rot	Rotation of the label. 0 by default (horizontal).
ccdir	Directory of the calibration curves. Defaults to where the package's files are stored (system.file), but can be set to, e.g., ccdir="curves".
...	Additional plotting options

Examples

plot(0, xlim=c(500,0), ylim=c(0, 2))
  draw.dates(130, 20, depth=1)

---

Glue prebomb and postbomb curves

Description

Produce a custom curve by merging two calibration curves, e.g. a prebomb and a postbomb one for dates which straddle both curves.

Usage

glue.ccurves(prebomb = "IntCal20", postbomb = "NH1")

Arguments

prebomb	The prebomb curve. Defaults to "IntCal20"
postbomb	The postbomb curve. Defaults to "NH1" (Hua et al. 2013)

Value

The custom-made curve (invisibly)

Examples

my.cc <- glue.ccurves()

---

Calculate highest posterior density

Description

Calculate highest posterior density ranges of calibrated distribution

Usage

hpd(calib, prob = 0.95, return.raw = FALSE, rounded = 1)

Arguments

calib	The calibrated distribution, as returned from caldist()
prob	Probability range which should be calculated. Default prob=0.95.
return.raw	The raw data to calculate hpds can be returned, e.g. to draw polygons of the calibrated distributions. Defaults to return.raw=FALSE.
rounded	Rounding for reported probabilities. Defaults to 1 decimal.

Examples

hpd(caldist(130,20))
plot(tmp <- caldist(2450,50), type='l')
abline(v=hpd(tmp)[,1:2], col=4)

---

IntCal

Description

The international IntCal research group publishes ratified radiocarbon calibration curves such as IntCal20, Marine20 and SHCal20 (Reimer et al. 2020). This data package provides the files of these curves, for use by other R package (reducing the need for replication and the size of other packages that use IntCal). It also comes with a limited number of relevant functions, to read in calibration curves, translate pMC ages to 14C ages (et vice versa), etc.

Author(s)

Maarten Blaauw <[email protected]>

---

plot the IntCal20 data

Description

plot the C14 ages underpinning the IntCal20/Marine20/SHCal20 calibration curves

Usage

intcal.data(
  cal1,
  cal2,
  cc1 = "IntCal20",
  cc2 = NA,
  calcurve.data = "IntCal20",
  BCAD = FALSE,
  cal.lab = NA,
  cal.rev = FALSE,
  c14.lab = NA,
  c14.lim = NA,
  c14.rev = FALSE,
  ka = FALSE,
  cc1.col = rgb(0, 0, 1, 0.5),
  cc1.fill = rgb(0, 0, 1, 0.2),
  cc2.col = rgb(0, 0.5, 0, 0.5),
  cc2.fill = rgb(0, 0.5, 0, 0.2),
  data.cols = 1:8,
  data.pch = c(1, 2, 5, 6, 15:19),
  pch.cex = 0.5,
  legend.loc = "topleft",
  legend.ncol = 2,
  legend.cex = 0.7,
  cc.legend = "bottomright",
  bty = "l",
  ...
)

Arguments

cal1	First calendar year for the plot
cal2	Last calendar year for the plot
cc1	Name of the calibration curve. Can be "IntCal20", "Marine20", "SHCal20", or for the previous curves "IntCal13", "Marine13" or "SHCal13".
cc2	Optional second calibration curve to plot. Can be "IntCal20", "Marine20", "SHCal20", or for the previous curves "IntCal13", "Marine13" or "SHCal13". Defaults to nothing, NA.
calcurve.data	Which dataset to use. Defaults to calcurve.data="IntCal20", but can also be calcurve.data="SHCal20". Note that Marine20 is based on IntCal20 and a marine carbon cycle model.
BCAD	The calendar scale of graphs and age output-files is in cal BP (calendar or calibrated years before the present, where the present is AD 1950) by default, but can be changed to BC/AD using BCAD=TRUE.
cal.lab	The labels for the calendar axis (default age.lab="cal BP" or "BC/AD" if BCAD=TRUE), or to age.lab="kcal BP" etc. if ka=TRUE.
cal.rev	Reverse the calendar axis.
c14.lab	Label for the C-14 axis. Defaults to 14C BP (or 14C kBP if ka=TRUE).
c14.lim	Axis limits for the C-14 axis. Calculated automatically by default.
c14.rev	Reverse the C-14 axis.
ka	Use kcal BP (and C14 kBP).
cc1.col	Colour of the calibration curve (outline).
cc1.fill	Colour of the calibration curve (fill).
cc2.col	Colour of the calibration curve (outline), if activated (default cc2=NA).
cc2.fill	Colour of the calibration curve (fill), if activated (default cc2=NA).
data.cols	colours of the data points. Defaults to R's colours 1 to 8 (black, red, green, darkblue, lightblue, purple, orange, and grey)
data.pch	Symbols of the data points. Defaults to R's symbols 1, 2, 5, 6, and 15 to 19 (open circle, open upward triangle, open diamond, open downward triangle, closed square, closed circle, closed upward triangle, closed diamond)
pch.cex	Size of the data symbols. Defaults to 0.5.
legend.loc	Location of the data legend. Defaults to topleft. Set to NA for no plotting.
legend.ncol	Number of columns of the data legend.
legend.cex	Size of the legend. Defaults to 0.7.
cc.legend	Location of the legend for the calibration curve(s).
bty	Box type around the plot. Defaults to "l"-shaped.
...	Any additional optional plotting parameters.

Details

These datasets were downloaded from Intcal.org. All data have both uncertainties in C14 age and on the calendar scale. For trees this is the sample thickness (e.g., 10 years or 1 year). The name of each dataset starts with a lower-case letter which indicates their nature (t = tree-rings, l = lake sediment, c = coral, m = marine sediment, s = speleothem), followed by either the radiocarbon laboratory's placename or the lastname of the main author. Most of the tree-ring datasets are dated at calendar year precision; tSeattle (references 1-2), tBelfast (3-5), tWaikato (4-7), tGroningen (8-10), tHeidelberg (11-14), tPretoria (16), tIrvine (17-20), tGalimberti (21), tMannheim (22-25), tAix (26-27), tAarhus (22, 28-30), tManningKromer (31-32), tVienna (33-34), tTokyo (35-39), tArizona (40), tMiyake (41), tPearson (22, 41-45), and tZurich (22-23, 25, 41, 43, 46-49). Horizontal error bars for these series indicate the numbers of rings in the samples (e.g., 10 tree-rings; 1-yr samples do not have error bars). Additionally, there are some floating tree-ring datasets with imprecisely known calendar ages; tAdolphy (50) and tTurney (51-52). For these and the following datasets, horizontal error bars indicate their 1 sd calendar age uncertainties. Beside trees, other datasets include lake sediment (lSuigestu, 53-54), corals (cBard 55-56, cFairbanks 57, cCutler 58 and cDurand 61, marine sediment (mCariaco 59-60, 62-63, mBard 64-65) and speleothems (sSouthon 66-67, sHoffman 68, sBeck 69). The southern hemisphere calibration curve SHCal20 is mostly modelled on IntCal20, but it contains datasets from the southern hemisphere; tPretoria (70), tWaikato (72-75), tBelfast (76-67), tSydney (78-80), tLivermore (81), tArizona, tIrvineWaikato and tZurich (82-83).

References

[1]Stuiver, M, and Braziunas, TF. 1993. Sun, ocean, climate and atmospheric 14CO2: an evaluation of causal and spectral relationships. Holocene 3: 289-305.

[2] Stuiver, M, Reimer, PJ, Braziunas, TF. 1998. High-precision radiocarbon age calibration for terrestrial and marine samples. Radiocarbon 40:1127-1151.

[3] McCormac FG, Bayliss A, Baillie MGL, Brown DM. 2004. Radiocarbon calibration in the Anglo-Saxon period: AD 495-725. Radiocarbon 46(3):1123-5.

[4] McCormac, FG, Hogg, AG, Higham, TFG, Lynch-Stieglitz, J, Broecker, WS, Baillie, MGL, Palmer, J, Xiong, L, Pilcher, JR, Brown, D, Hoper, ST, 1998. Temporal variation in the interhemispheric C-14 offset. Geophysical Research Letters 25, 1321-1324.

[5] Pearson, G. W., Pilcher, J. R., Baillie, M. G. L., Corbett, D. M., and Qua, F. (1986). High-Precision C-14 Measurement of Irish Oaks to Show the Natural C-14 Variations from AD 1840 to 5210 BC Radiocarbon 28: 911-934.

[6] Hogg, A. G., McCormac, F. G., Higham, T. F. G., Reimer, P. J., Baillie, M. G. L., and Palmer, J. G. (2002). High-precision radiocarbon measurements of contemporaneous tree-ring dated wood from the British Isles and New Zealand: AD 1850-950. Radiocarbon 44: 633-640.

[7] Hogg, A., Palmer, J., Boswijk, G., Reimer, P., and Brown, D. (2009). Investigating the interhemispheric C-14 offset in the 1st millennium AD and assessment of laboratory bias and calibration errors. Radiocarbon 51, 1177-1186.

[8] de Jong, A. F. M., Becker, B., and Mook, W. G. (1986). High-precision calibration of the radiocarbon time scale, 3930-3230 cal BC. Radiocarbon 28: 939-941.

[9] de Jong, AFM, Becker, B, Mook, WG, 1989. Corrected calibration of the radiocarbon time scale. Radiocarbon 31:201-210.

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[12] Kromer, B., and Spurk, M. (1998). Revision and tentative extension of the tree-ring based C-14 calibration, 9200-11,855 cal BP. Radiocarbon 40: 1117-1125.

[13] Kromer, B., Manning, S.W., Kuniholm, P.I., Newton, M.W., Spurk, M. & Levin, I. 2001. Regional 14CO2 offsets in the troposphere: magnitude, mechanisms, and consequences. Science 294: 2529-2532.

[14] Kromer, B., S. W. Manning, M. Friedrich, S. Talamo and N. Trano (2010). 14C Calibration in the 2nd and 1st Millennia BC Eastern Mediterranean Radiocarbon Comparison Project (EMRCP). Radiocarbon 52(3): 875-886.

[15] Hua, Q., Barbetti, M., Fink, D., Kaiser, K. F., Friedrich, M., Kromer, B., Levchenko, V. A., Zoppi, U., Smith, A. M., and Bertuch, F. (2009). Atmospheric 14C variations derived from tree rings during the early Younger Dryas. Quaternary Science Reviews 28, 2982-2990.

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[35] Ozaki, H, Imamura, M, Matsuzaki, H, Mitsutani, T, 2007. Radiocarbon in 9th to 5th century BC tree-ring samples from the Ouban 1 archaeological site, Hiroshima, Japan. Radiocarbon 49, 473-479.

[36] The origin of the farming in the Yayoi Period and East Asia: Establishment of High-Precision Chronology by carbon 14 age analysis. National Museum of Japanese History Edited by Toyohiro Nishimoto, 524p, 2009. (in Japanese, final progress report of JSPS Grant-in-Aids (16GS0118))

[37] Sakamoto, M, Imamura, M, van der Plicht, J, Mitsutani, T, Sahara, M, 2003. Radiocarbon calibration for Japanese wood samples. Radiocarbon 45, 81-89.

[38] Okuno, M, Hakozaki, M, Miyake, F, Kimura, K, Masuda, K, Sakamoto, M, Hong, W, Yatsuzuka, S, Nakamura, T, 2018. Chronological significance of d14C spike and precise age determination of the B-Tm Tephra, China/ North Korea, 23rd International Radiocarbon Conference, Trondheim, Norway.

[39] Sakamoto, M, Hakozaki, M, Nakao, N, Nakatsuka, T, 2017. Fine structure and reproducibility of radiocarbon ages of middle to early modern Japanese tree rings. Radiocarbon 59, 1907-1917.

[40] Jull, AT, Panyushkina, I, Miyake, F, Masuda, K, Nakamura, T, Mitsutani, T, Lange, TE, Cruz, RJ, Baisan, C, Janovics, R, 2018. More Rapid 14 C Excursions in the Tree-Ring Record: A Record of Different Kind of Solar Activity at About 800 BC? Radiocarbon 60, 1237-1248.

[41] Miyake F., Jull A.J.T., Panyushkina I.P., Wacker L., Salzer M., Baisan C., Lange T., Cruz R., Masuda K., Nakamura T. 2017. Large 14C excursion in 5480 BC indicates an abnormal sun in the mid-Holocene. PNAS Physical Sciences - Earth, Atmospheric, and Planetary Sciences 114 (3), doi:10.1073/pnas.161314411

[42] Pearson, C.L., Brewer, P.W., Brown, D., Heaton, T.J., Hodgins, G.W., Jull, A.T., Lange, T. and Salzer, M.W., (2018). Annual radiocarbon record indicates 16th century BCE date for the Thera eruption. Science advances, 4(8), p.eaar8241.

[43] Pearson, CL, Wacker, L, Bayliss, A, Brown, DM, Salzer, M, Brewer, PW, Bollhalder, S, Boswijk, G, Hodgins, GWL, Annual variation in atmospheric 14C between 1700 BC and 1480 BC: Radiocarbon: this issue

[44] Jull A.J.T., Panyushkina I.P., Lange T.E., Kukarskih V.V., Clark K.J., Myglan V.S., Salzer M., Burr G.S., Leavitt S.L. Excursions in the 14C record at AD 774-775 from tree rings from Russia and America.2014. Geophysical Research Letters 41 (8): 3004-3010. 10.1002/2014GL059874

[45] Miyake F., Masuda K., Nakamura T., Kimura K., Hakozaki M., Jull A.T., Lange T., Cruz R., Panyushkina I.P., Baisan C., Salzer M. 2017. Search for annual 14C excursions in the past. Radiocarbon 59 (2): 315-320. DOI: 10.1017/RDC.2016.54

[46] Wacker et al. in prep

[47] Sookdeo, A, Kromer, B, Adolphi, F, Beer, J, Brehm, N, Buntgen, U, Christl, M, Eglinton, TI, Friedrich, M, Guidobaldi, G, Helle, G, Nievergelt, D, Pauly, M, Reinig, F, Tegel, W, Treydte, K, Synal, H-A, Wacker, L, submitted. There Goes the Sun: 14C in trees reveals reduced solar activity during the Younger Dryas. Nature Geoscience.

[48] Buntgen, Ulf, et al, (2018),'Tree rings reveal globally coherent signature of cosmogenic radiocarbon events in 774 and 993 CE'. Nature Communications 9, 3605

[49] Bayliss et al. in prep

[50] Adolphi, F., R. Muscheler, M. Friedrich, D. Guttler, L. Wacker, S. Talamo and B. Kromer (2017). 'Radiocarbon calibration uncertainties during the last deglaciation: Insights from new floating tree-ring chronologies.' Quaternary Science Reviews 170: 98-108.

[51] Turney CS, Palmer J, Ramsey CB, Adolphi F, Muscheler R, Hughen KA, Staff RA, Jones RT, Thomas ZA, Fogwill CJ. 2016. High-precision dating and correlation of ice, marine and terrestrial sequences spanning Heinrich Event 3: Testing mechanisms of interhemispheric change using New Zealand ancient kauri (Agathis australis). Quaternary Science Reviews 137:126-34.

[52] Turney, C.S.M., Fifield, L.K., Hogg, A.G., Palmer, J.G., K., H., Baillie, M.G.L., Galbraith, R., Ogden, J., Lorrey, A., Tims, S.G., Jones, R.T., 2010. Using New Zealand kauri (Agathis australis) to test the synchronicity of abrupt climate change during the Last Glacial Interval (60,000-11,700 years ago). Quaternary Science Reviews 29, 3677-3682.

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[54] Gordon Schlolaut, Richard A Staff, Michael H Marshall, Achim Brauer, Christopher Bronk Ramsey, Henry F Lamb, Takeshi Nakagawa, 2018, An extended and revised Lake Suigetsu varve chronology from ~50 to ~10 ka BP based on detailed sediment micro-facies analyses, Quaternary Science Reviews 200, 351-366

[55] Bard, E, Hamelin, B, Fairbanks, RG, Zindler, A. 1990. Calibration of the 14C timescale over the past 30,000 years using mass spectrometric U-Th ages from Barbados corals. Nature 345: 405-410.

[56] Bard, E, Arnold, M, Hamelin, B, Tisnerat-Laborde, N, Cabioch, G, 1998. Radiocarbon calibration by means of mass spectrometric Th- 230/U-234 and C-14 ages of corals: An updated database including samples from Barbados, Mururoa and Tahiti. Radiocarbon 40, 1085-1092.

[57] Fairbanks, RG, Mortlock, RA, Chiu, TC, Cao, L, Kaplan, A, Guilderson, TP, Fairbanks, TW, Bloom, AL, Grootes, PM & Nadeau, MJ. 2005. Radiocarbon calibration curve spanning 0 to 50,000 years BP based on paired Th-230/U-234/U-238 and C-14 dates on pristine corals. Quaternary Science Reviews 24(16-17): 1781-96.

[58] Cutler, KB, Gray, SC, Burr, GS, Edwards, RL, Taylor, FW, Cabioch, G, Beck, JW, Cheng, H, and Moore, J. 2004. Radiocarbon calibration to 50 kyr BP with paired 14C and 230Th dating of corals from Vanuatu and Papua New Guinea. Radiocarbon 46: 1127-1160.

[59] Hughen, KA, Southon, JR, Lehman, SJ, Overpeck, JT, 2000. Synchronous radiocarbon and climate shifts during the last deglaciation. Science 290, 1951-1954.

[60] Hughen, KA, Southon, JR, Bertrand, CJH, Frantz, B, Zermeno, P. 2004. Cariaco Basin calibration update: revisions to calendar and 14C chronologies for core PL07-58PC. Radiocarbon 46: 1161-1187.

[61] Durand, N, Deschamps, P, Bard, E, Hamelin, B, Camoin, G, Thomas, AL, Henderson, GM, Yokoyama, Y, Matsuzaki, H. 2013. Comparison of 14C and U-Th in corals from IODP #310 cores offshore Tahiti. Radiocarbon 55 (4), 1947-1974.

[62] Hughen, K, Southon, J, Lehman, S, Bertrand, C, Turnbull, J, 2006. Marine-derived 14C calibration and activity record for the past 50,000 years updated from the Cariaco Basin. Quaternary Science Reviews 25, 3216-3227.

[63] Hughen, K, Heaton, TJ. Updated Cariaco Basin 14C Calibration Dataset from 0-60k BP, in prep

[64] Bard, E, Rostek, F, Menot-Combes, G, 2004. Radiocarbon calibration beyond 20,000 14C yr B.P. by means of planktonic foraminifera of the Iberian Margin. Quaternary Research 61, 204-214.

[65] Edouard Bard, Guillemette Menot, Frauke Rostek, Laetitia Licari, Philipp Boening,R Lawrence Edwards, Hai Cheng, Yongjin Wang, Timothy J Heaton, (2013) 'Radiocarbon calibration/comparison records based on marine sediments from the Pakistan and Iberian margins', Radiocarbon, Vol 55, Nr 4, 2013, p 1999-2019

[66] Southon J, Noronha AL, Cheng H, Edwards RL, Wang YJ. (2012). A high-resolution record of atmospheric C-14 based on Hulu Cave speleothem H82. Quaternary Science Reviews 33:32-41

[67] Cheng H, Edwards RL, Southon J, Matsumoto K, Feinberg JM, Sinha A, Zhou W, Li H, Li X, Xu Y. 2018. Atmospheric 14C/12C changes during the last glacial period from Hulu Cave. Science 362(6420):1293-7

[68] Dirk L. Hoffmann, J. Warren Beck, David A. Richards, Peter L. Smart, Joy S. Singarayer, Tricia Ketchmark, Chris J. Hawkesworth. 2010. Towards radiocarbon calibration beyond 28 ka using speleothems from the Bahamas,Earth and Planetary Science Letters,289:1-10.

[69] J. Warren Beck, David A. Richards, R. Lawrence Edwards, Bernard W. Silverman, Peter L. Smart, Douglas J. Donahue, Sofia Hererra-Osterheld, George. S. Burr, Leal Calsoyas, A. J. Timothy Jull, Dana Biddulph. 2001. Extremely Large Variations of Atmospheric 14C Concentration During the Last Glacial Period Science 292:2453

[70] Vogel et al. 1993. Pretoria calibration curve for short-lived samples, 1930-3350 BC. Radiocarbon 35: 73-85.

[71] Stuiver, Braziunas 1998. Anthropogenic and solar components of hemispheric 14C. Geophysical Research Letters 25: 329-332.

[72] Hogg et al. 2002 High-precision radiocarbon measurements of contemporaneous tree-ring dated wood from the British Isles and New Zealand: AD 1850-950. Radiocarbon 44: 633-640.

[73] McCormac et al. 1998. Temporal variation in the interhemispheric C-14 offset. Geophysical Research Letters 25: 1321-1324.

[74] Hogg et al. 2011 High-precision radiocarbon measurements of tree-ring dated wood from New Zealand: 195 BC-AD 995. Radiocarbon 53, 3: 529-542.

[75] Hogg et al. 2013 Is there any evidence for regional 14C offsets in the Southern Hemisphere? doi:10.2458/azu_js_rc.v55i2.16104

[76] Hogg et al. 2002 High-precision radiocarbon measurements of contemporaneous tree-ring dated wood from the British Isles and New Zealand: AD 1850-950. Radiocarbon 44: 633-640.

[77] McCormac et al. 1998. Temporal variation in the interhemispheric C-14 offset. Geophysical Research Letters 25: 1321-1324.

[78] Hua et al. 2009 Atmospheric 14C variations derived from tree rings during the early Younger Dryas. Quaternary Science Reviews, v. 28, 25-26: 2982-2990.

[79] Hua et al. 2004 Radiocarbon in tropical tree rings during the Little Ice Age. Nuclear Instruments and Methods in Physics Research B 223-224:489-94.

[80] Hogg et al. 2013 SHCal13 Southern Hemisphere calibration, 0-50,000 cal yr BP. Radiocarbon 55, 2

[81] Zimmerman et al. 2010 Extension of the Southern Hemisphere atmospheric radiocarbon curve, 2120-850 years BP: results from Tasmanian huon pine. Radiocarbon 52, 203: 887-94.

[82] Boentgen et al. 2018 Tree rings reveal globally coherent signature of cosmogenic radiocarbon events in 774 and 993 CE. Nature Communications, 9: 3605. doi:10.1038/s41467-018-06036-0. [83] Sookdeo et al. 2020 Quality Dating: A well-defined protocol implemented at ETH Zurich for high-precision 14C dates tested on Late Glacial wood. Radiocarbon. doi:10.1017/RDC.2019.132

Examples

intcal.data(100, 200)
  intcal.data(40e3, 55e3, ka=TRUE)

---

List the calibration curves

Description

List the file names of the calibration curves available within the IntCal package.

Usage

list.ccurves()

---

Build a custom-made, mixed calibration curve.

Description

If two curves need to be ‘mixed’ to calibrate, e.g. for dates of mixed terrestrial and marine carbon sources, then this function can be used. The curve will be saved, together with the main calibration curves, in a temporary directory. This temporary directory then has to be specified in further commands, e.g. for rbacon: Bacon(, ccdir=tmpdr) (see examples). It is advisable to make your own curves folder and have ccdir point to that folder.

Usage

mix.ccurves(
  proportion = 0.5,
  cc1 = "IntCal20",
  cc2 = "Marine20",
  name = "mixed.14C",
  dir = c(),
  offset = c(0, 0),
  sep = "\t"
)

Arguments

proportion	Proportion of the first calibration curve required. e.g., change to proportion=0.7 if cc1 should contribute 70% (and cc2 30%) to the mixed curve.
cc1	The first calibration curve to be mixed. Defaults to the northern hemisphere terrestrial curve IntCal20.
cc2	The second calibration curve to be mixed. Defaults to the marine curve IntCal20.
name	Name of the new calibration curve.
dir	Name of the directory where to save the file. Since R does not allow automatic saving of files, this points to a temporary directory by default. Adapt to your own folder, e.g., dir="~/Curves" or in your current working directory, dir=".".
offset	Any offset and error to be applied to cc2 (default 0 +- 0).
sep	Separator between fields (tab by default, "\t")

Details

The proportional contribution of each of both calibration curves has to be set.

Value

A file containing the custom-made calibration curve, based on calibration curves cc1 and cc2.

Examples

mix.ccurves()
tmpdir <- tempdir()
mix.ccurves(dir=tmpdir)
# clean up:
unlink(tmpdir)

---

Make directory and fill with calibration curves

Description

Make an alternative ‘curves’ directory and fill it with the calibration curves.

Usage

new.ccdir(ccdir = "./ccurves")

Arguments

ccdir

Name and location of the new directory. Defaults to ‘ccurves’, a folder within the current working directory, ccdir="./ccurves".

Details

Copies all calibration curves within the ‘IntCal’ package to the new directory.

Examples

new.ccdir(tempdir())

---

Calculate C14 ages from pMC values.

Description

Calculate C14 ages from pMC values of radiocarbon dates.

Usage

pMC.age(mn, sdev, ratio = 100, decimals = 0)

Arguments

mn	Reported mean of the pMC.
sdev	Reported error of the pMC.
ratio	Most modern-date values are reported against 100. If it is against 1 instead, use 1 here.
decimals	Amount of decimals required for the radiocarbon age.

Details

Post-bomb dates are often reported as pMC or percent modern carbon. Since Bacon expects radiocarbon ages, this function can be used to calculate radiocarbon ages from pMC values. The reverse function is age.pMC.

Value

Radiocarbon ages from pMC values. If pMC values are above 100%, the resulting radiocarbon ages will be negative.

See Also

http://www.qub.ac.uk/chrono/blaauw/manualBacon_2.3.pdf

Examples

pMC.age(110, 0.5) # a postbomb date, so with a negative 14C age
  pMC.age(80, 0.5) # prebomb dates can also be calculated
  pMC.age(.8, 0.005, 1) # pMC expressed against 1 (not against 100\%)

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