Title:	Quantitative Chronology in Archaeology
Version:	0.1.0
Maintainer:	Nicolas Frerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Description:	Simple radiocarbon calibration and chronological analysis. This package allows the calibration of radiocarbon ages and modern carbon fraction values using multiple calibration curves. It allows the calculation of highest density region intervals and credible intervals. The package also provides tools for visualising results and estimating statistical summaries.
License:	GPL (≥ 3)
URL:	https://codeberg.org/tesselle/ananke, https://packages.tesselle.org/ananke/
BugReports:	https://codeberg.org/tesselle/ananke/issues
Depends:	aion (≥ 1.4.0), R (≥ 4.1)
Imports:	arkhe (≥ 1.10.0), graphics, grDevices, methods, utils
Suggests:	folio, knitr, markdown, rsvg, svglite, tinysnapshot, tinytest
Encoding:	UTF-8
LazyData:	true
RoxygenNote:	7.3.2
X-schema.org-applicationCategory:	Archaeological Science
X-schema.org-isPartOf:	https://www.tesselle.org
X-schema.org-keywords:	time-series, archaeology, archaeological-science, chronology, radiocarbon-dates, radiocarbon-calibration, r-package
Collate:	'AllClasses.R' 'AllGenerics.R' 'ananke-internal.R' 'ananke-package.R' 'c14_calibrate.R' 'c14_combine.R' 'c14_curve.R' 'c14_ensemble.R' 'c14_f14c.R' 'c14_sample.R' 'c14_spd.R' 'c14_uncalibrate.R' 'c14_validate.R' 'coerce.R' 'data.R' 'describe.R' 'interval.R' 'mutators.R' 'pb_age.R' 'plot.R' 'proxy.R' 'statistics.R' 'subset.R' 'validate.R' 'zzz.R'
NeedsCompilation:	no
Packaged:	2025-04-16 13:02:12 UTC; nicolas
Author:	Nicolas Frerebeau [aut, cre], Université Bordeaux Montaigne [fnd], CNRS [fnd]
Repository:	CRAN
Date/Publication:	2025-04-18 13:30:05 UTC

ananke: Quantitative Chronology in Archaeology

Description

Simple radiocarbon calibration and chronological analysis. This package allows the calibration of radiocarbon ages and modern carbon fraction values using multiple calibration curves. It allows the calculation of highest density region intervals and credible intervals. The package also provides tools for visualising results and estimating statistical summaries.

Details

Package options

ananke uses the following options() to configure behavior:

• ananke.grid: a numeric value specifying the number of equally spaced points at which densities are to be estimated (defaults to 512). Should be a power of 2 (see stats::density()).

• ananke.round: a character string specifying the rounding convention. It can be one of "none" (the default, no rounding) or "stuiver" (Stuiver & Polach, 1977).

• ananke.progress: a logical scalar. Should progress bars be displayed? Defaults to interactive().

• ananke.verbose: a logical scalar. Should R report extra information on progress? Defaults to interactive().

Author(s)

Full list of authors and contributors (alphabetic order):

Package maintainer

Nicolas Frerebeau
nicolas.frerebeau@u-bordeaux-montaigne.fr

Archéosciences Bordeaux (UMR 6034)
Maison de l'Archéologie
Université Bordeaux Montaigne
F-33607 Pessac cedex
France

See Also

Useful links:

• https://codeberg.org/tesselle/ananke

• https://packages.tesselle.org/ananke/

• Report bugs at https://codeberg.org/tesselle/ananke/issues

Calibrated Radiocarbon Ages

Description

An S4 class to represent calibrated radiocarbon ages.

Arguments

Slots

F14C

A logical scalar: is values F14C instead of radiocarbon ages?

positions

A numeric vector giving the position values (e.g. depths) for each age.

status

An integer vector specifying the calibration status. It must be one of "0" (OK), "1" (out of calibration range) or "2" (may extend out of calibration range).

Note

This class inherits from aion::TimeSeries.

Author(s)

N. Frerebeau

See Also

Other classes: CalibratedIntervals-class, CalibratedSPD-class, ProxyRecord-class, RECE-class

Calibrated Intervals

Description

An S4 class to represent calibrated intervals of radiocarbon ages.

Slots

p

A numeric vector giving the probabilities.

Note

This class inherits from aion::TimeIntervals.

Author(s)

N. Frerebeau

See Also

Other classes: CalibratedAges-class, CalibratedSPD-class, ProxyRecord-class, RECE-class

Calibrated SPD

Description

An S4 class to represent summed probability distributions (SPD) of calibrated radiocarbon ages.

Note

This class inherits from aion::TimeSeries.

Author(s)

N. Frerebeau

See Also

Other classes: CalibratedAges-class, CalibratedIntervals-class, ProxyRecord-class, RECE-class

F14C

Description

Converts F14C values to 14C ages.

Usage

BP14C_to_F14C(values, errors, ...)

F14C_to_BP14C(values, errors, ...)

## S4 method for signature 'numeric,numeric'
BP14C_to_F14C(values, errors, lambda = 8033)

## S4 method for signature 'numeric,numeric'
F14C_to_BP14C(
  values,
  errors,
  lambda = 8033,
  asymmetric = FALSE,
  rounding = getOption("ananke.round")
)

Arguments

Value

A data.frame.

Author(s)

N. Frerebeau

References

Bronk Ramsey, C. (2008). Radiocarbon Dating: Revolutions in Understanding. Archaeometry, 50:249-275. doi:10.1111/j.1475-4754.2008.00394.x.

Stuiver, M., Polach, H. A. (1977). Discussion Reporting of 14C Data. Radiocarbon, 19(3): 355-363. doi:10.1017/S0033822200003672.

van der Plicht, J., Hogg, A. (2006). A Note on Reporting Radiocarbon. Quaternary Geochronology, 1(4): 237-240. doi:10.1016/j.quageo.2006.07.001.

See Also

Other radiocarbon tools: c14_calibrate(), c14_combine(), c14_curve(), c14_ensemble(), c14_plot, c14_sample(), c14_spd(), c14_uncalibrate(), rec_plot

Examples

## Asymmetric 14C errors (van der Plicht and Hogg 2006)
F14C_to_BP14C(0.0052, 0.0006, asym = TRUE)

## Symmetric 14C errors (Bronk Ramsey 2008)
F14C_to_BP14C(0.0052, 0.0006, asym = FALSE)

Proxy Record

Description

An S4 class to store proxy records.

Note

This class inherits from aion::TimeSeries.

Author(s)

N. Frerebeau

See Also

Other classes: CalibratedAges-class, CalibratedIntervals-class, CalibratedSPD-class, RECE-class

Radiocarbon Event Count Ensemble

Description

An S4 class to represent a radiocarbon event count ensemble.

Note

This class inherits from aion::TimeSeries.

Author(s)

N. Frerebeau

See Also

Other classes: CalibratedAges-class, CalibratedIntervals-class, CalibratedSPD-class, ProxyRecord-class

Coerce to a Data Frame

Description

Coerce to a Data Frame

Usage

## S4 method for signature 'CalibratedAges'
as.data.frame(x, ..., calendar = get_calendar())

## S4 method for signature 'CalibratedIntervals'
as.data.frame(x, ..., calendar = get_calendar())

## S4 method for signature 'RECE'
as.data.frame(x, ..., calendar = get_calendar())

## S4 method for signature 'ProxyRecord'
as.data.frame(x, ..., calendar = get_calendar())

Arguments

Value

A data.frame with an extra time column.

Author(s)

N. Frerebeau

See Also

Other mutators: as.list(), labels(), mutators, subset()

Examples

## Calibrate multiple dates
cal <- c14_calibrate(
  values = c(5000, 4500),
  errors = c(45, 35),
  names = c("X", "Y")
)

head(as.data.frame(cal))
head(as.data.frame(cal, calendar = BP()))
head(as.data.frame(cal, calendar = NULL))

Coerce to a list

Description

Coerce to a list

Usage

## S4 method for signature 'CalibratedIntervals'
as.list(x, ..., calendar = get_calendar())

Arguments

Value

A list.

Author(s)

N. Frerebeau

See Also

Other mutators: as.data.frame(), labels(), mutators, subset()

Examples

## Calibrate multiple dates
cal <- c14_calibrate(
  values = c(5000, 4500),
  errors = c(45, 35),
  names = c("X", "Y")
)

head(as.data.frame(cal))
head(as.data.frame(cal, calendar = BP()))
head(as.data.frame(cal, calendar = NULL))

14C Calibration

Description

Calibrates radiocarbon ages.

Usage

c14_calibrate(values, errors, ...)

## S4 method for signature 'numeric,numeric'
c14_calibrate(
  values,
  errors,
  curves = "intcal20",
  names = NULL,
  positions = NULL,
  reservoir_offsets = 0,
  reservoir_errors = 0,
  from = 55000,
  to = 0,
  resolution = 1,
  normalize = TRUE,
  F14C = FALSE,
  method = c("student", "normal"),
  dfs = 100,
  drop = TRUE,
  eps = 1e-06,
  verbose = getOption("ananke.verbose")
)

Arguments

Value

A CalibratedAges object.

Note

Adapted from Bchron BchronCalibrate() by Andrew Parnell and rcarbon calibrate() by Andrew Bevan and Enrico Crema.

Author(s)

N. Frerebeau

References

Bronk Ramsey, C. (2008). Radiocarbon Dating: Revolutions in Understanding. Archaeometry, 50:249-275. doi:10.1111/j.1475-4754.2008.00394.x.

See Also

Other radiocarbon tools: F14C, c14_combine(), c14_curve(), c14_ensemble(), c14_plot, c14_sample(), c14_spd(), c14_uncalibrate(), rec_plot

Examples

## Calibrate a single date
cal <- c14_calibrate(300, 20)
plot(cal, panel.first = graphics::grid())

## Calibrate multiple dates
cal <- c14_calibrate(
  values = c(5000, 4500),
  errors = c(45, 35),
  names = c("X", "Y")
)
plot(cal, panel.first = graphics::grid())


## Out of 14C range?
out <- c14_calibrate(130, 20)
plot(out)

Combine 14C

Description

Combines radiocarbon dates.

Usage

c14_combine(values, errors, ...)

## S4 method for signature 'numeric,numeric'
c14_combine(values, errors, groups = NULL)

Arguments

Value

A data.frame with the following columns:

Author(s)

N. Frerebeau

References

Ward, G. K. and Wilson, S. R. (1978). Procedures for Comparing and Combining Radiocarbon Age Determinations: A Critique. Archaeometry 20(1): 19‑31. doi:10.1111/j.1475-4754.1978.tb00208.x.

See Also

Other radiocarbon tools: F14C, c14_calibrate(), c14_curve(), c14_ensemble(), c14_plot, c14_sample(), c14_spd(), c14_uncalibrate(), rec_plot

Examples

## Replicate Ward and Wilson (1978), p. 28
polach1972 <- data.frame(
  samples = c("ANU-7", "ANU-7", "ANU-7", "W-1571", "ANU-5",
              "C-800", "L-698D", "FSU-3", "Tx-44"),
  ages = c(14550, 15000, 13700, 14650, 11700, 10860, 11840, 11245, 10700),
  errors = c(270, 600, 300, 500, 260, 410, 100, 450, 210)
)

c14_combine(
  values = polach1972$ages,
  errors = polach1972$errors,
  groups = polach1972$samples
)

14C Calibration Curve

Description

14C Calibration Curve

Usage

c14_curve(name, ...)

## S4 method for signature 'character'
c14_curve(name)

## S4 method for signature 'CalibratedAges'
c14_curve(name)

Arguments

Details

The following calibration curves are available:

Value

A list of three-column data.frame:

Author(s)

N. Frerebeau

References

Heaton, Timothy J, Peter Köhler, Martin Butzin, Edouard Bard, Ron W Reimer, William E N Austin, Christopher Bronk Ramsey, et al. (2020). Marine20 The Marine Radiocarbon Age Calibration Curve (0-55,000 Cal BP). Radiocarbon, 62(4): 779-820. doi:10.1017/RDC.2020.68.

Hogg, Alan G, Timothy J Heaton, Quan Hua, Jonathan G Palmer, Chris SM Turney, John Southon, Alex Bayliss, et al. (2020). SHCal20 Southern Hemisphere Calibration, 0-55,000 Years Cal BP. Radiocarbon, 62(4): 759-78. doi:10.1017/RDC.2020.59.

Hogg, Alan G, Quan Hua, Paul G Blackwell, Mu Niu, Caitlin E Buck, Thomas P Guilderson, Timothy J Heaton, et al. (2013). SHCal13 Southern Hemisphere Calibration, 0-50,000 Years Cal BP. Radiocarbon, 55(4): 1889-1903. doi:10.2458/azu_js_rc.55.16783.

Hua, Quan, and Mike Barbetti (2004). Review of Tropospheric Bomb 14C Data for Carbon Cycle Modeling and Age Calibration Purposes. Radiocarbon, 46(3): 1273-1298. doi:10.1017/S0033822200033142.

Hua, Quan, Mike Barbetti, and Andrzej Z Rakowski (2013). Atmospheric Radiocarbon for the Period 1950-2010. Radiocarbon, 55(4): 2059‑2072. doi:10.2458/azu_js_rc.v55i2.16177.

Hua, Quan, Jocelyn C Turnbull, Guaciara M Santos, Andrzej Z Rakowski, Santiago Ancapichún, Ricardo De Pol-Holz, Samuel Hammer, et al. (2022). Atmospheric Radiocarbon for the Period 1950-2019. Radiocarbon, 64(4): 723‑745. doi:10.1017/RDC.2021.95.

Hughen, K., S. Lehman, J. Southon, J. Overpeck, O. Marchal, C. Herring, and J. Turnbull (2004). 14C Activity and Global Carbon Cycle Changes over the Past 50,000 Years. Science, 303(5655): 202‑207. doi:10.1126/science.1090300.

Hughen, Konrad A, Mike G L Baillie, Edouard Bard, J Warren Beck, Chanda J H Bertrand, Paul G Blackwell, Caitlin E Buck, et al. (2004). Marine04 Marine Radiocarbon Age Calibration, 0-26 cal kyr BP. Radiocarbon, 46(3): 1059‑1086. doi:10.1017/S0033822200033002.

Kueppers, Lara M., John Southon, Paul Baer, and John Harte (2004). Dead Wood Biomass and Turnover Time, Measured by Radiocarbon, along a Subalpine Elevation Gradient. Oecologia, 141(4): 641‑651. doi:10.1007/s00442-004-1689-x.

McCormac, F G, A G Hogg, P G Blackwell, C E Buck, T F G Higham, and P J Reimer (2004). Shcal04 Southern Hemisphere Calibration, 0-11.0 cal kyr BP. Radiocarbon, 46(3): 1087‑1092. doi:10.1017/S0033822200033014.

Reimer, P J, M G L Baillie, E Bard, A Bayliss, J W Beck, P G Blackwell, C Bronk Ramsey, et al. (2009). IntCal09 and Marine09 Radiocarbon Age Calibration Curves, 0-50,000 Years cal BP. Radiocarbon, 51(4): 1111‑1150. doi:10.1017/S0033822200034202.

Reimer, Paula J, William E N Austin, Edouard Bard, Alex Bayliss, Paul G Blackwell, Christopher Bronk Ramsey, Martin Butzin, et al. (2020). The IntCal20 Northern Hemisphere Radiocarbon Age Calibration Curve (0-55 cal kBP). Radiocarbon, 62(4): 725‑757. doi:10.1017/RDC.2020.41.

Reimer, Paula J, Mike G L Baillie, Edouard Bard, Alex Bayliss, J Warren Beck, Chanda J H Bertrand, Paul G Blackwell, et al. (2004). Intcal04 Terrestrial Radiocarbon Age Calibration, 0-26 cal kyr BP. Radiocarbon, 46(3): 1029‑1058. doi:10.1017/S0033822200032999.

Reimer, Paula J, Edouard Bard, Alex Bayliss, J Warren Beck, Paul G Blackwell, Christopher Bronk Ramsey, Caitlin E Buck, et al. (2013). IntCal13 and Marine13 Radiocarbon Age Calibration Curves 0-50,000 Years cal BP. Radiocarbon, 55(4): 1869‑1887. doi:10.2458/azu_js_rc.55.16947.

Stuiver, Minze, Paula J. Reimer, Edouard Bard, J. Warren Beck, G. S. Burr, Konrad A. Hughen, Bernd Kromer, Gerry McCormac, Johannes van der Plicht, and Marco Spurk (1998). INTCAL98 Radiocarbon Age Calibration, 24,000-0 cal BP. Radiocarbon, 40(3): 1041‑1083. doi:10.1017/S0033822200019123.

Stuiver, Minze, Paula J. Reimer, and Thomas F. Braziunas. (1998). High-Precision Radiocarbon Age Calibration for Terrestrial and Marine Samples. Radiocarbon, 40(3): 1127‑1151. doi:10.1017/S0033822200019172.

See Also

Other radiocarbon tools: F14C, c14_calibrate(), c14_combine(), c14_ensemble(), c14_plot, c14_sample(), c14_spd(), c14_uncalibrate(), rec_plot

Examples

## IntCal20
intcal20 <- c14_curve("intcal20")
head(intcal20[[1]])

## IntCal
intcal <- c14_curve(c("intcal09", "intcal13", "intcal20"))
lapply(X = intcal, FUN = head)

Radiocarbon Event Count

Description

Radiocarbon Event Count

Usage

c14_ensemble(object, ...)

## S4 method for signature 'CalibratedAges'
c14_ensemble(
  object,
  from = NULL,
  to = NULL,
  by = 10,
  n = 100,
  calendar = BP(),
  progress = getOption("ananke.progress")
)

Arguments

Value

An RECE object.

Note

This function is currently experimental.

Author(s)

N. Frerebeau

References

Carleton, W. C. (2021). Evaluating Bayesian Radiocarbon‐dated Event Count (REC) Models for the Study of Long‐term Human and Environmental Processes. Journal of Quaternary Science, 36(1): 110‑23. doi:10.1002/jqs.3256.

See Also

Other radiocarbon tools: F14C, c14_calibrate(), c14_combine(), c14_curve(), c14_plot, c14_sample(), c14_spd(), c14_uncalibrate(), rec_plot

Plot Calibrated Radiocarbon Ages

Description

Plot Calibrated Radiocarbon Ages

Usage

## S4 method for signature 'CalibratedAges,missing'
plot(
  x,
  calendar = get_calendar(),
  density = TRUE,
  interval = c("hdr", "credible", "none"),
  level = 0.954,
  fixed = TRUE,
  decreasing = TRUE,
  col.density = "grey",
  col.interval = "#77AADD",
  main = NULL,
  sub = NULL,
  axes = TRUE,
  frame.plot = FALSE,
  ann = graphics::par("ann"),
  panel.first = NULL,
  panel.last = NULL,
  ...
)

## S4 method for signature 'CalibratedSPD,missing'
plot(
  x,
  calendar = get_calendar(),
  main = NULL,
  sub = NULL,
  ann = graphics::par("ann"),
  axes = TRUE,
  frame.plot = FALSE,
  panel.first = NULL,
  panel.last = NULL,
  ...
)

Arguments

Value

plot() is called it for its side-effects: it results in a graphic being displayed. Invisibly returns x.

Author(s)

N. Frerebeau

See Also

Other radiocarbon tools: F14C, c14_calibrate(), c14_combine(), c14_curve(), c14_ensemble(), c14_sample(), c14_spd(), c14_uncalibrate(), rec_plot

Examples

## Calibrate multiple dates
cal <- c14_calibrate(
  values = c(5000, 4500),
  errors = c(45, 35),
  names = c("X", "Y")
)

## Specify calendar
plot(cal, calendar = BP())

## HDR intervals (default)
plot(cal, interval = "hdr", level = 0.95)

## Credible intervals
plot(cal, interval = "credible", level = 0.95)

## No intervals
plot(cal, interval = NULL)

## Intervals only
plot(cal, density = FALSE, level = 0.68, lwd = 5)
plot(cal, density = FALSE, level = 0.95, lwd = 5)

## Change colors
plot(cal[, 1, ], col.interval = "red")

Sample Calibrated Ages

Description

Sample Calibrated Ages

Usage

c14_sample(object, ...)

## S4 method for signature 'CalibratedAges'
c14_sample(object, n = 100, calendar = get_calendar())

Arguments

Value

An numeric matrix.

Author(s)

N. Frerebeau

See Also

Other radiocarbon tools: F14C, c14_calibrate(), c14_combine(), c14_curve(), c14_ensemble(), c14_plot, c14_spd(), c14_uncalibrate(), rec_plot

Examples

## Calibrate multiple dates
cal <- c14_calibrate(
  values = c(5000, 4500),
  errors = c(45, 35),
  names = c("X", "Y")
)

## Sample
spl <- c14_sample(cal, n = 100)

Summed Probability Distributions

Description

Computes summed probability distributions (SPD) of radiocarbon dates.

Usage

c14_spd(object, ...)

## S4 method for signature 'CalibratedAges'
c14_spd(object, normalize_date = FALSE, normalize_spd = FALSE)

Arguments

Details

Summed probability distributions (SPD) are not statistically valid estimators of the calendar age of a potential future sample. They should not be used in any dates-as-data approach to provide a population proxy.

Value

A CalibratedSPD object.

Author(s)

N. Frerebeau

See Also

Other radiocarbon tools: F14C, c14_calibrate(), c14_combine(), c14_curve(), c14_ensemble(), c14_plot, c14_sample(), c14_uncalibrate(), rec_plot

Examples

## Radiocarbon data from Bosch et al. 2015
data("ksarakil")

## Calibrate
cal <- c14_calibrate(
  values = ksarakil$date,
  errors = ksarakil$error,
  names = ksarakil$code,
  curves = "marine13",
  reservoir_offsets = 53,
  reservoir_errors = 43,
  from = 50000, to = 0
)
plot(cal, level = 0.68)

## SPD
s <- c14_spd(cal)
plot(s)

Uncalibrate a Radiocarbon Date

Description

Uncalibrate a Radiocarbon Date

Usage

c14_uncalibrate(object, ...)

## S4 method for signature 'numeric'
c14_uncalibrate(object, curves = "intcal20")

## S4 method for signature 'CalibratedAges'
c14_uncalibrate(object, n = 10000, rounding = getOption("ananke.round"), ...)

Arguments

Author(s)

N. Frerebeau

See Also

Other radiocarbon tools: F14C, c14_calibrate(), c14_combine(), c14_curve(), c14_ensemble(), c14_plot, c14_sample(), c14_spd(), rec_plot

Examples

## Calibrate multiple dates
cal <- c14_calibrate(
  values = c(5000, 4500),
  errors = c(45, 35),
  names = c("X", "Y")
)

## Uncalibrate
c14_uncalibrate(cal, rounding = "stuiver")

Check Calibrated Radiocarbon Dates

Description

Check Calibrated Radiocarbon Dates

Usage

c14_validate(object, verbose = getOption("ananke.verbose"))

Arguments

Value

c14_validate() is called it for its side-effects: it prints warning messages if calibrated ages are (partially) out of calibration range. Invisibly returns x.

Author(s)

N. Frerebeau

Examples

## Calibrate a single date
cal <- c14_calibrate(300, 20)
plot(cal, panel.first = graphics::grid())

## Calibrate multiple dates
cal <- c14_calibrate(
  values = c(5000, 4500),
  errors = c(45, 35),
  names = c("X", "Y")
)
plot(cal, panel.first = graphics::grid())


## Out of 14C range?
out <- c14_calibrate(130, 20)
plot(out)

Data Description

Description

Data Description

Usage

## S4 method for signature 'CalibratedAges'
describe(x, calendar = get_calendar(), level = 0.954, ...)

Arguments

Value

describe() is called for its side-effects. Invisibly returns x.

Author(s)

N. Frerebeau

References

Millard, A. R. (2014). Conventions for Reporting Radiocarbon Determinations. Radiocarbon, 56(2): 555-559. doi:10.2458/56.17455.

Examples

## Calibrate multiple dates
cal <- c14_calibrate(
  values = c(5000, 4500),
  errors = c(45, 35),
  names = c("X", "Y")
)

## Full text description
describe(cal)

Bayesian Credible Interval

Description

Bayesian Credible Interval

Usage

## S4 method for signature 'CalibratedAges'
interval_credible(x, level = 0.954, n = 100, ...)

Arguments

Value

A CalibratedIntervals object.

Author(s)

N. Frerebeau

See Also

arkhe::interval_credible()

Other statistics: interval_hdr(), mean(), median(), quantile()

Examples

## Calibrate multiple dates
cal <- c14_calibrate(
  values = c(5000, 4500),
  errors = c(45, 35),
  names = c("X", "Y")
)

## Credible intervals
crd68 <- interval_credible(cal, level = 0.683)
crd95 <- interval_credible(cal, level = 0.954)
crd99 <- interval_credible(cal, level = 0.997)

## Coerce to data.frame
as.data.frame(crd95, calendar = BC())

## Plot
plot(cal, interval = "credible")

Highest Density Regions

Description

Highest Density Regions

Usage

## S4 method for signature 'CalibratedAges,missing'
interval_hdr(x, level = 0.954, ...)

Arguments

Value

A CalibratedIntervals object.

Author(s)

N. Frerebeau

References

Hyndman, R. J. (1996). Computing and graphing highest density regions. American Statistician, 50: 120-126. doi:10.2307/2684423.

See Also

stats::density(), arkhe::interval_hdr()

Other statistics: interval_credible(), mean(), median(), quantile()

Examples

## Calibrate multiple dates
cal <- c14_calibrate(
  values = c(5000, 4500),
  errors = c(45, 35),
  names = c("X", "Y")
)

## HDR
hdr68 <- interval_hdr(cal, level = 0.683)
hdr95 <- interval_hdr(cal, level = 0.954)
hdr99 <- interval_hdr(cal, level = 0.997)

## Coerce to data.frame
as.data.frame(hdr95, calendar = BC())

## Plot
plot(cal, interval = "hdr")

Ksâr 'Akil Radiocarbon Dates

Description

Ksâr 'Akil Radiocarbon Dates

Usage

ksarakil

Format

A data.frame with 16 rows and 5 variables:

code

Laboratory code.

date

Radiocarbon date (year BP).

error

Radiocarbon error (year).

layer

Stratigraphic layer.

phase

Chronological phase.

Source

Bosch, M. D., Mannino, M. A., Prendergast, A. L., O'Connell, T. C., Demarchi, B., Taylor, S. M., Niven, L., van der Plicht, J. and Hublin, J.-J. (2015). New Chronology for Ksâr 'Akil (Lebanon) Supports Levantine Route of Modern Human Dispersal into Europe. Proceedings of the National Academy of Sciences 112(25): 7683-8. doi:10.1073/pnas.1501529112.

Find Labels from Object

Description

Find a suitable set of labels from an object for use in printing or plotting, for example.

Usage

## S4 method for signature 'CalibratedAges'
labels(object, ...)

Arguments

Value

A character vector.

Author(s)

N. Frerebeau

See Also

Other mutators: as.data.frame(), as.list(), mutators, subset()

Mean

Description

Mean

Usage

## S4 method for signature 'CalibratedAges'
mean(x, na.rm = FALSE, ..., calendar = get_calendar())

## S4 method for signature 'ProxyRecord'
mean(x, na.rm = FALSE, ...)

Arguments

Value

A numeric vector.

Author(s)

N. Frerebeau

See Also

Other statistics: interval_credible(), interval_hdr(), median(), quantile()

Examples

## Calibrate multiple dates
cal <- c14_calibrate(
  values = c(5000, 4500),
  errors = c(45, 35),
  names = c("X", "Y")
)

## Statistics
quantile(cal)
median(cal)
mean(cal)

## Plot
plot(cal, calendar = CE())

## Need to set 'calendar'
abline(v = median(cal, calendar = CE()), lty = 2, col = "blue")
abline(v = mean(cal, calendar = CE()), lty = 2, col = "red")

Median

Description

Median

Usage

## S4 method for signature 'CalibratedAges'
median(x, na.rm = FALSE, ..., calendar = get_calendar())

Arguments

Value

A numeric vector.

Author(s)

N. Frerebeau

See Also

Other statistics: interval_credible(), interval_hdr(), mean(), quantile()

Examples

## Calibrate multiple dates
cal <- c14_calibrate(
  values = c(5000, 4500),
  errors = c(45, 35),
  names = c("X", "Y")
)

## Statistics
quantile(cal)
median(cal)
mean(cal)

## Plot
plot(cal, calendar = CE())

## Need to set 'calendar'
abline(v = median(cal, calendar = CE()), lty = 2, col = "blue")
abline(v = mean(cal, calendar = CE()), lty = 2, col = "red")

Get or Set Parts of an Object

Description

Getters and setters to extract or replace parts of an object.

Arguments

Value

An object of the same sort as x with the new values assigned.

Author(s)

N. Frerebeau

See Also

Other mutators: as.data.frame(), as.list(), labels(), subset()

Geological Model Age from Lead Isotope Analysis

Description

Compute geological model age (T) and U/Pb (mu) and Th/U (kappa) ratios from lead isotopic measurements.

Usage

pb_age(x, y, z, ...)

## S4 method for signature 'numeric,numeric,numeric'
pb_age(
  x,
  y,
  z,
  t0 = 3.8,
  x_star = 18.75,
  y_star = 15.63,
  z_star = 38.86,
  mu = 9.66,
  kappa = 3.9,
  th232 = 0.049475,
  u238 = 0.155125,
  u235 = 0.98485,
  u238_235 = 137.79,
  tolerance = sqrt(.Machine$double.eps),
  stop = 100
)

## S4 method for signature 'list,missing,missing'
pb_age(
  x,
  t0 = 3.8,
  x_star = 18.75,
  y_star = 15.63,
  z_star = 38.86,
  mu = 9.66,
  kappa = 3.9,
  th232 = 0.049475,
  u238 = 0.155125,
  u235 = 0.98485,
  u238_235 = 137.79,
  tolerance = sqrt(.Machine$double.eps),
  stop = 100
)

Arguments

Value

A four columns data.frame:

age

Geological model age (in Ma).

mu

238U/204Pb ratio.

kappa

232Th/238U ratio.

residual

Newton loop residual.

Note

Reference values from Albarede & Juteau (1984).

Author(s)

N. Frerebeau, F. Albarede (original Matlab code)

References

Albarède, F., Desaulty, A.-M. & Blichert-Toft, J. (2012). A Geological Perspective on the Use of Pb Isotopes in Archaeometry. Archaeometry, 54: 853-867. doi:10.1111/j.1475-4754.2011.00653.x.

Albarède, F. & Juteau, M. (1984). Unscrambling the Lead Model Ages. Geochimica et Cosmochimica Acta, 48(1): 207-12. doi:10.1016/0016-7037(84)90364-8.

Allègre, C. (2005). Géologie isotopique. Belin sup. Paris: Belin.

Examples

Pb <- data.frame(
  x = c(18.23247, 18.22936, 18.23102), # Pb206/Pb204
  y = c(15.65199, 15.65216, 15.65097), # Pb207/Pb204
  z = c(38.5167, 38.51516, 38.51601)   # Pb208/Pb204
)

## Default reference values from Albarede & Juteau (1984)
pb_age(
  Pb,
  t0 = 3.8,
  x_star = 18.75, y_star = 15.63, z_star = 38.86,
  mu = 9.66, kappa = 3.90, th232 = 0.049475,
  u238 = 0.155125, u235 = 0.98485, u238_235 = 137.79
)

## Reference values from Albarede et al. (2012)
pb_age(
  Pb,
  t0 = 4.43,
  x_star = 18.75, y_star = 15.63, z_star = 38.83,
  mu = 9.66, kappa = 3.90, th232 = 0.049475,
  u238 = 0.155125, u235 = 0.98485, u238_235 = 137.79
)

Layer-Counted Proxy Records Uncertainties

Description

Represents layer-counted proxy records as sequences of probability distributions on absolute, error-free time axes.

Usage

proxy_ensemble(positions, ...)

## S4 method for signature 'numeric'
proxy_ensemble(
  positions,
  proxy_values,
  proxy_errors,
  proxy_step,
  time_values,
  time_errors,
  calendar,
  from = NULL,
  to = NULL,
  by = NULL,
  n = 30,
  progress = getOption("ananke.progress"),
  verbose = getOption("ananke.verbose")
)

Arguments

Value

A ProxyRecord object.

Note

This function is currently experimental.

Author(s)

N. Frerebeau

References

Boers, N., Goswami, B. & Ghil, M. (2017). A Complete Representation of Uncertainties in Layer-Counted Paleoclimatic Archives. Climate of the Past, 13(9): 1169-1180. doi:10.5194/cp-13-1169-2017.

See Also

Other proxy tools: proxy_plot

Examples

## Get NGRIP records
data("ngrip2010", package = "folio")
ngrip2010 <- subset(ngrip2010, !is.na(MCE))
ngrip2010 <- ngrip2010[nrow(ngrip2010):1, ] # Sort in chronological order

## Replicate fig. 3d from Boers et al. (2017)
## /!\ This may take a while... /!\
ngrip_record <- proxy_ensemble(
  positions = ngrip2010$depth,
  proxy_values = ngrip2010$delta,
  proxy_errors = 0.01,
  proxy_step = 0.01,
  time_values = ngrip2010$age,
  time_errors = ngrip2010$MCE,
  calendar = b2k(), # /!\
  by = 20,
  n = 30
)

plot(ngrip_record)

Plot Layer-Counted Proxy Records Uncertainties

Description

Plot Layer-Counted Proxy Records Uncertainties

Usage

## S4 method for signature 'ProxyRecord,missing'
plot(
  x,
  calendar = get_calendar(),
  iqr = TRUE,
  xlab = NULL,
  ylab = NULL,
  col = grDevices::hcl.colors(12, "YlOrRd", rev = TRUE),
  col.mean = "black",
  col.iqr = col.mean,
  lty.mean = 1,
  lty.iqr = 3,
  lwd.mean = 2,
  lwd.iqr = lwd.mean,
  ...
)

Arguments

Value

plot() is called it for its side-effects: it results in a graphic being displayed. Invisibly returns x.

Author(s)

N. Frerebeau

See Also

Other proxy tools: proxy_ensemble()

Examples

## Get NGRIP records
data("ngrip2010", package = "folio")
ngrip2010 <- subset(ngrip2010, !is.na(MCE))
ngrip2010 <- ngrip2010[nrow(ngrip2010):1, ] # Sort in chronological order

## Replicate fig. 3d from Boers et al. (2017)
## /!\ This may take a while... /!\
ngrip_record <- proxy_ensemble(
  positions = ngrip2010$depth,
  proxy_values = ngrip2010$delta,
  proxy_errors = 0.01,
  proxy_step = 0.01,
  time_values = ngrip2010$age,
  time_errors = ngrip2010$MCE,
  calendar = b2k(), # /!\
  by = 20,
  n = 30
)

plot(ngrip_record)

Quantiles of a Density Estimate

Description

Quantiles of a Density Estimate

Usage

## S4 method for signature 'CalibratedAges'
quantile(
  x,
  probs = seq(0, 1, 0.25),
  na.rm = FALSE,
  ...,
  calendar = get_calendar()
)

## S4 method for signature 'ProxyRecord'
quantile(x, probs = seq(0, 1, 0.25), na.rm = FALSE, ...)

Arguments

Value

A numeric matrix containing the quantiles.

Author(s)

N. Frerebeau

See Also

Other statistics: interval_credible(), interval_hdr(), mean(), median()

Examples

## Calibrate multiple dates
cal <- c14_calibrate(
  values = c(5000, 4500),
  errors = c(45, 35),
  names = c("X", "Y")
)

## Statistics
quantile(cal)
median(cal)
mean(cal)

## Plot
plot(cal, calendar = CE())

## Need to set 'calendar'
abline(v = median(cal, calendar = CE()), lty = 2, col = "blue")
abline(v = mean(cal, calendar = CE()), lty = 2, col = "red")

Plot a Radiocarbon Event Count Ensemble

Description

Plot a Radiocarbon Event Count Ensemble

Usage

## S4 method for signature 'RECE,missing'
plot(x, calendar = get_calendar(), ...)

Arguments

Value

image() is called it for its side-effects: it results in a graphic being displayed (invisibly returns x).

Author(s)

N. Frerebeau

References

Carleton, W. C. (2021). Evaluating Bayesian Radiocarbon‐dated Event Count (REC) Models for the Study of Long‐term Human and Environmental Processes. Journal of Quaternary Science, 36(1): 110‑23. doi:10.1002/jqs.3256.

See Also

Other radiocarbon tools: F14C, c14_calibrate(), c14_combine(), c14_curve(), c14_ensemble(), c14_plot, c14_sample(), c14_spd(), c14_uncalibrate()

Extract or Replace Parts of an Object

Description

Operators acting on objects to extract or replace parts.

Usage

## S4 method for signature 'CalibratedAges'
x[i, j, k, drop = FALSE]

Arguments

Value

A subsetted object.

Author(s)

N. Frerebeau

See Also

Other mutators: as.data.frame(), as.list(), labels(), mutators