Package 'rintcal'

Copy a calibration curve

Description

Copy one of the calibration curves into memory.

Usage

ccurve(
  cc = 1,
  postbomb = FALSE,
  cc.dir = NULL,
  resample = 0,
  glue = FALSE,
  as.F = 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". One can also make a custom-built calibration curve, e.g. using mix.ccurves(), and load this using cc=4. In this case, it is recommended to place the custom calibration curve in its own directory, using cc.dir (see below).
postbomb	Use postbomb=TRUE to get a postbomb calibration curve (default postbomb=FALSE). For monthly data, type e.g. ccurve("sh1-2_monthly")
cc.dir	Directory of the calibration curves. Defaults to where the package's files are stored (system.file), but can be set to, e.g., cc.dir="ccurves".
resample	The IntCal curves come at a range of 'bin sizes'; every year from 0 to 5 kcal BP, then every 5 yr until 15 kcal BP, then every 10 yr until 25 kcal BP, and every 20 year thereafter. The curves can be resampled to constant bin sizes, e.g. resample=5. Defaults to FALSE.
glue	If a postbomb curve is requested, it can be 'glued' to the pre-bomb curve. This feature is currently disabled - please use glue.ccurves instead
as.F	If loading a curve that contains 2 additional columns containing the D14C values, then these can be used instead of the curve's C14 ages and errors. Defaults to as.F=FALSE.

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

Heaton et al. 2020 Marine20-the marine radiocarbon age calibration curve (0-55,000 cal BP). Radiocarbon 62, 779-820, doi:10.1017/RDC.2020.68

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, 759-778, 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. 2022 Atmospheric radiocarbon for the period 1950-2019. Radiocarbon 64(4), 723-745, doi:10.1017/RDC.2021.95

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

van der Plicht et al. 2004. NotCal04—Comparison/Calibration 14C Records 26–50 Cal Kyr BP. Radiocarbon 46, 1225-1238, doi:10.1017/S0033822200033117

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).

---

Glue calibration 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",
  thisprebombcurve = c(),
  thispostbombcurve = c(),
  cc.dir = c()
)

Arguments

prebomb	The prebomb curve. Defaults to "IntCal20"
postbomb	The postbomb curve. Defaults to "NH1" (Hua et al. 2013)
thisprebombcurve	As an alternative to using existing curves, a tailor-made curve can be provided for the prebomb curve (as three columns: cal BP, C14 age, error)
thispostbombcurve	As an alternative to using existing curves, a tailor-made curve can be provided for the postbomb curve (as three columns: cal BP, C14 age, error)
cc.dir	Directory of the calibration curves. Defaults to where the package's files are stored (system.file), but can be set to, e.g., cc.dir="ccurves".

Value

The custom-made curve (invisibly)

Examples

my.cc <- glue.ccurves()

---

IntCal20 json file

Description

The IntCal20 calibration curves and their underpinning data. This is based on a json file produced by Prof. Christopher Bronk Ramsey, University of Oxford.

Usage

intcal

Format

## 'intcal' A list with six main entries:

json_application

IntChron project name

records

a list with 139 entries for each IntCal dataset

project_series_list

a list with 5 entries: IntCal20, Marine20, SHCal20, a list of the underlying datasets, and a GICC vs IntCal20 comparison

parameters

an empty list

bibliography

a list with 141 bibliography entries

options

a list of 17 options (not used)

Source

<https://intchron.org/archive/IntCal/IntCal20/index.json>

---

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",
  select.sets = c(),
  realm = "C14",
  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 = c(),
  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.
select.sets	Which datasets to plot. Defaults to all datasets within the selected period.
realm	Which 'realm' of radiocarbon to use. Defaults to realm="C14" but can also be set to realm="F14C", realm="pMC" or realm="D14C". Can be shorted to, respectively, "C", "F", "P" or "D" (or their lower-case equivalents).
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).

Value

A plot of the IntCal curve and the underlying data, as well as (invisibly) the data themselves

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.

[10] Kuitems, M, Plicht, Jvd, Jansma, E, Wood from the Netherlands around the time of the Santorini eruption dated by dendrochronology and Radiocarbon. Radiocarbon this issue.

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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.

[16] Vogel, J. C., and van der Plicht, J. (1993). Calibration Curve for Short-Lived Samples, 1900-3900 BC. Radiocarbon 35: 87-91.

[17] Taylor, R.E. and Southon, J., (2013). Reviewing the Mid-First Millennium BC 14C 'warp' using 14C/bristlecone pine data. NIMB Research Section B: Beam Interactions with Materials and Atoms, 294, pp.440-443

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[20] Simon M. Fahrni, John Southon, Benjamin T. Fuller, Junghun Park, Michael Friedrich, Raimund Muscheler, Lukas Wacker, R. E. Taylor;Single-year German oak and Californian bristlecone pine 14C data at the beginning of the Hallstatt plateau from 856 BC to 626 BC; Radiocarbon

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[26] Capano, M, Miramont, C, Guibal, F, Kromer, B, Tuna, T, Fagault, Y, Bard, E, 2018. Wood 14C Dating with AixMICADAS: Methods and Application to Tree-Ring Sequences from the Younger Dryas Event in the Southern French Alps. Radiocarbon 60, 51-74.

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[32] Manning, S.W., Griggs, C., Lorentzen, B., Bronk Ramsey, C., Chivall, D., Jull, A.J.T., Lange, T.E. 2018. Fluctuating Radiocarbon Offsets Observed in the Southern Levant and Implications for Archaeological Chronology Debates. Proceedings of the National Academy of Sciences of the United States of America 115:6141-6146.

[33] Dellinger, F, Kutschera, W, Nicolussi, K, Schiessling, P, Steier, P, and Wild, E M, 2004 A 14C calibration with AMS from 3500 to 3000 BC, derived from a new high-elevation stone-pine tree-ring chronology, Radiocarbon, 46, 969-83

[34] Steier, P, Dellinger, F, Kutschera, W, Priller, A, Rom, W, and Wild, E M, 2004 Pushing the precision limit of 14C AMS, Radiocarbon, 46, 5-17

[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.

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[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.

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[49] Bayliss et al. in prep

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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

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Examples

intcal.data(100, 200)
  intcal.data(40e3, 55e3, ka=TRUE)
  # plot Suigetsu and Cariaco data only
  dat <- intcal.data(20e3, 25e3)
  unique(dat$set) # ordered against their appearance in the plot's legend
  dat <- intcal.data(20e3, 25e3, select.sets=c(109, 120), data.cols=c(1,2))

---

Extract from the intcal file

Description

Extract items from the intcal json file.

Usage

intcal.data.frames(obj, ...)

Arguments

obj	Name of the object
...	Additional options can be provided, see examples

Examples

intcal <- intcal.read.data()
 # all datasets from the Southern Hemisphere:
 sh.data <- intcal.data.frames(intcal, intcal_set_type='SH') 
 head(sh.data)
 Irish.oaks <- intcal.data.frames(intcal, intcal_set=3) 
 head(Irish.oaks[[2]]$data)

---

Read data underlying the IntCal curves.

Description

Download the json file that contains the IntCal20 radiocarbon calibration curves and the contributing data series.

Usage

intcal.read.data(from.intchron.org = FALSE, from.jsonfile = FALSE)

Arguments

from.intchron.org	Download the IntCal20 json file the inchron.org server. Defaults to FALSE, and then the data will be loaded from within the rintcal package
from.jsonfile	The name and location of the json file (if used). Defaults to FALSE, and then the data will be loaded from within the rintcal package

Details

The intcal curves consist of the IntCal20, SHCal20 and Marine20 calibration curves. The details of these curves can be loaded, as well as the underlying data such as tree-ring records.

Examples

intcal <- intcal.read.data()

---

Write intcal data to a file.

Description

Write the intcal.json file that comes with the rintcal packages to somewhere local. This can be useful if you want to avoid repeatedly downloading the json file from intchron.org.

Usage

intcal.write.data(data, fname)

Arguments

data	intcal variable as obtained from intcal.read.data()
fname	Name of the file to be written

Examples

intcal <- intcal.read.data()
 myintcal <- tempfile()
 intcal.write.data(intcal, myintcal)

---

List the calibration curves

Description

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

Usage

list.ccurves()

Value

A list of the available calibration curves

---

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 returned invisibly, or saved in a temporary directory together with the main calibration curves. This temporary directory then has to be specified in further commands, e.g. for rbacon: Bacon(, cc.dir=tmpdr) (see examples). It is advisable to make your own curves folder and have cc.dir point to that folder.

Usage

mix.ccurves(
  proportion = 0.5,
  cc1 = "IntCal20",
  cc2 = "Marine20",
  postbomb1 = FALSE,
  postbomb2 = FALSE,
  name = "mixed.14C",
  cc.dir = c(),
  thiscurve1 = c(),
  thiscurve2 = c(),
  save = FALSE,
  offset = cbind(0, 0),
  round = c(),
  sep = " "
)

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.
postbomb1	Option to provide a postbomb curve for the first curve (defaults to FALSE).
postbomb2	Option to provide a postbomb curve for the second curve (defaults to FALSE).
name	Name of the new calibration curve.
cc.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., cc.dir="~/ccurves" or in your current working directory, cc.dir=".".
thiscurve1	As an alternative to using curves that come with the package, a tailor-made curve can be provided for the first curve (as three columns: cal BP, C14 age, error).
thiscurve2	As an alternative to using curves that come with the package, a tailor-made curve can be provided for the second curve (as three columns: cal BP, C14 age, error).
save	Save the curve in the folder specified by dir. Defaults to FALSE.
offset	Any offset and error to be applied to cc2 (default 0 +- 0). Entered as two columns (possibly of just one row), e.g. offset=cbind(100,0)
round	The entries can be rounded to a specified amount of decimals. Defaults to no rounding.
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

tmpdir <- tempdir()
new.ccdir(tmpdir)
mix.ccurves(cc.dir=tmpdir)
# now assume the offset is constant but its uncertainty increases over time:
cc <- ccurve()
offset <- cbind(rep(100, nrow(cc)),  seq(0, 1e3, length=nrow(cc)))
# 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(cc.dir)

Arguments

cc.dir

Name and location of the new directory. For example, this could be a folder called 'ccurves', living within the current working directory, cc.dir="./ccurves".

Details

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

Value

A message informing the user the name of the folder into which the calibration curves have been copied.

Examples

new.ccdir(tempdir())

---