Package 'ananke'

Title:	Quantitative Chronology in Archaeology
Description:	A toolbox for quantitative chronology in archaeology. This package provides functions for simple radiocarbon calibration and chronological analysis.
Authors:	Nicolas Frerebeau [aut, cre] (<https://orcid.org/0000-0001-5759-4944>, Université Bordeaux Montaigne), Université Bordeaux Montaigne [fnd], CNRS [fnd]
Maintainer:	Nicolas Frerebeau <[email protected]>
License:	GPL (>= 3)
Version:	0.0.1.9000
Built:	2024-09-03 18:20:05 UTC
Source:	https://github.com/tesselle/ananke

14C Calibration

Description

Calibrates radiocarbon dates.

Usage

c14_calibrate(values, errors, ...)

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

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

Arguments

`values`	A `numeric` vector giving the BP ages or F14C values to be calibrated.
`errors`	A `numeric` vector giving the standard deviation of the values to be calibrated.
`...`	Currently not used.
`names`	A `character` vector specifying the names of the samples (e.g. laboratory codes).
`curves`	A `character` vector specifying the calibration curve to be used. Different curves can be specified per sample.
`reservoir_offsets`	A `numeric` vector giving the offset values for any marine reservoir effect (defaults to 0; i.e. no offset).
`reservoir_errors`	A `numeric` vector giving the offset value errors for any marine reservoir effect (defaults to 0; i.e. no offset).
`from`	length-one `numeric` vector specifying the earliest data to calibrate for, in cal. BP years.
`to`	A length-one `numeric` vector specifying the latest data to calibrate for, in cal. BP years.
`resolution`	A length-one `numeric` vector specifying the temporal resolution (in years) of the calibration.
`normalize`	A `logical` scalar: should the calibration be normalized?
`F14C`	A `logical` scalar: should the calibration be carried out in F14C space? If `TRUE`, `values` must be expressed as F14C.
`drop`	A `logical` scalar: should years with zero probability be discarded? If `TRUE` (the default), results in a narrower time range.
`eps`	A length-one `numeric` value giving the cutoff below which calibration values will be removed.
`verbose`	A `logical` scalar: should extra information be reported (e.g. warning message for dates out of calibration range)?

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.

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, calendar = BP(), panel.first = graphics::grid())
plot(cal, interval = FALSE)
plot(cal[, 1, ], col.interval = "red")

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


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

## 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, calendar = BP(), panel.first = graphics::grid())
plot(cal, interval = FALSE)
plot(cal[, 1, ], col.interval = "red")

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


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

Combine 14C

Description

Combines radiocarbon dates.

Usage

c14_combine(ages, errors, ...)

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

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

Arguments

`ages`	A `numeric` vector giving the BP ages to be calibrated.
`errors`	A `numeric` vector giving the standard deviation of the ages to be calibrated.
`...`	Currently not used.
`groups`	A `factor` in the sense that `as.factor(groups)` defines the the groups to combine with. If `NULL` (the default), all dates are combined. `NA`s will be treated as isolated dates.

Value

A data.frame with the following columns:

`groups`	Group names
`ages`	Combined 14C ages
`errors`	Combined 14C standard deviations
`chi2`	Chi-squared test statistic
`p`	Chi-squared test p-value

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.

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(
  ages = polach1972$ages,
  errors = polach1972$errors,
  groups = polach1972$samples
)
## 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(
  ages = polach1972$ages,
  errors = polach1972$errors,
  groups = polach1972$samples
)

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.

Examples

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

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

`object`	A `CalibratedAges` object.
`...`	Currently not used.
`from`	length-one `numeric` vector specifying the earliest data to calibrate for (in cal BP years).
`to`	A length-one `numeric` vector specifying the latest data to calibrate for (in cal BP years).
`by`	A length-one `numeric` vector specifying the temporal resolution (in years) of the calibration.
`n`	An `integer` specifying the number of item to choose randomly.
`calendar`	An `aion::TimeScale` object specifying the target calendar (see `aion::calendar()`). Defaults to `aion::CE()`. If `NULL`, rata die are returned.
`progress`	A `logical` scalar: should a progress bar be displayed?

Value

An RECE object.

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.

Plot Calibrated Radiocarbon Ages

Description

Plot Calibrated Radiocarbon Ages

Usage

## S4 method for signature 'CalibratedAges,missing'
plot(
  x,
  calendar = getOption("ananke.calendar"),
  density = TRUE,
  interval = TRUE,
  level = 0.954,
  sort = TRUE,
  decreasing = TRUE,
  main = NULL,
  sub = NULL,
  axes = TRUE,
  frame.plot = FALSE,
  ann = graphics::par("ann"),
  panel.first = NULL,
  panel.last = NULL,
  col.density = "grey",
  col.interval = "#77AADD",
  ...
)

## S4 method for signature 'CalibratedSPD,missing'
plot(
  x,
  calendar = getOption("ananke.calendar"),
  main = NULL,
  sub = NULL,
  ann = graphics::par("ann"),
  axes = TRUE,
  frame.plot = FALSE,
  panel.first = NULL,
  panel.last = NULL,
  ...
)
## S4 method for signature 'CalibratedAges,missing'
plot(
  x,
  calendar = getOption("ananke.calendar"),
  density = TRUE,
  interval = TRUE,
  level = 0.954,
  sort = TRUE,
  decreasing = TRUE,
  main = NULL,
  sub = NULL,
  axes = TRUE,
  frame.plot = FALSE,
  ann = graphics::par("ann"),
  panel.first = NULL,
  panel.last = NULL,
  col.density = "grey",
  col.interval = "#77AADD",
  ...
)

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

Arguments

`x`	A `CalibratedAges` or `CalibratedSPD` object.
`calendar`	An `aion::TimeScale` object specifying the target calendar (see `aion::calendar()`). If `NULL`, rata die are returned.
`density`	A `logical` scalar: should density be drawn?
`interval`	A `logical` scalar: should highest density region be drawn?
`level`	A length-one `numeric` vector giving the confidence level. Only used if `interval` is `TRUE`.
`sort`	A `logical` scalar: should the data be sorted?
`decreasing`	A `logical` scalar: should the sort order be decreasing? Only used if `sort` is `TRUE`.
`main`	A `character` string giving a main title for the plot.
`sub`	A `character` string giving a subtitle for the plot.
`axes`	A `logical` scalar: should axes be drawn on the plot?
`frame.plot`	A `logical` scalar: should a box be drawn around the plot?
`ann`	A `logical` scalar: should the default annotation (title and x and y labels) appear on the plot?
`panel.first`	An an `expression` to be evaluated after the plot axes are set up but before any plotting takes place. This can be useful for drawing background grids.
`panel.last`	An `expression` to be evaluated after plotting has taken place but before the axes, title and box are added.
`col.density`, `col.interval`	A specification for the plotting colors.
`...`	Other graphical parameters may also be passed as arguments to this function.

Value

plot() is called it for its side-effects: it results in a graphic being displayed. 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, calendar = BP(), panel.first = graphics::grid())
plot(cal, interval = FALSE)
plot(cal[, 1, ], col.interval = "red")

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


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

## 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, calendar = BP(), panel.first = graphics::grid())
plot(cal, interval = FALSE)
plot(cal[, 1, ], col.interval = "red")

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


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

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)
c14_spd(object, ...)

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

Arguments

`object`	A `CalibratedAges` object.
`...`	Currently not used.
`normalize_date`	A `logical` scalar: should the total probability mass of the calibrated dates be normalised (to sum to unity within the time-span of analysis)?
`normalize_spd`	A `logical` scalar: should the total probability mass of the SPD be normalised (to sum to unity)?

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.

Author(s)

N. Frerebeau

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, flip = TRUE)

## SPD
s <- c14_spd(cal)
plot(s)
## 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, flip = TRUE)

## 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, ...)
c14_uncalibrate(object, ...)

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

## S4 method for signature 'CalibratedAges'
c14_uncalibrate(object, ...)

Arguments

`object`	A `CalibratedAges` object or a `numeric` vector of calibrated ages (BP).
`...`	Currently not used.
`curves`	A `character` vector specifying the calibration curve to be used. Different curves can be specified.

Author(s)

N. Frerebeau

Examples

## Not run: 
## Calibrate multiple dates
cal <- c14_calibrate(
  values = c(5000, 4500),
  errors = c(45, 35),
  names = c("X", "Y")
)

## Uncalibrate
c14_uncalibrate(cal)

## End(Not run)
## Not run: 
## Calibrate multiple dates
cal <- c14_calibrate(
  values = c(5000, 4500),
  errors = c(45, 35),
  names = c("X", "Y")
)

## Uncalibrate
c14_uncalibrate(cal)

## End(Not run)

Check Calibrated Radiocarbon Dates

Description

Check Calibrated Radiocarbon Dates

Usage

c14_validate(object, ...)

## S4 method for signature 'CalibratedAges'
c14_validate(object)
c14_validate(object, ...)

## S4 method for signature 'CalibratedAges'
c14_validate(object)

Arguments

`object`	A `CalibratedAges` object.
`...`	Currently not used.

Value

c14_validate() is called it for its side-effects: it prints warning messages if calibrated agea 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, calendar = BP(), panel.first = graphics::grid())
plot(cal, interval = FALSE)
plot(cal[, 1, ], col.interval = "red")

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


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

## 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, calendar = BP(), panel.first = graphics::grid())
plot(cal, interval = FALSE)
plot(cal[, 1, ], col.interval = "red")

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


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

Coerce to a Data Frame

Description

Coerce to a Data Frame

Usage

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

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

## S4 method for signature 'ProxyRecord'
as.data.frame(x, ..., calendar = getOption("ananke.calendar"))
## S4 method for signature 'CalibratedAges'
as.data.frame(x, ..., calendar = getOption("ananke.calendar"))

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

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

Arguments

`x`	An object.
`...`	Further parameters to be passed to `data.frame()`.
`calendar`	An `aion::TimeScale` object specifying the target calendar (see `aion::calendar()`). If `NULL`, rata die are returned.

Value

A data.frame with an extra time column.

Author(s)

N. Frerebeau

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))
## 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))

Data Description

Description

Data Description

Usage

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

Arguments

`x`	A `CalibratedAges` object.
`calendar`	An `aion::TimeScale` object specifying the target calendar (see `aion::calendar()`).
`level`	A length-one `numeric` vector giving the confidence level.
`...`	Further parameters to be passed to `cat()`.

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

## Full text description
describe(cal)

F14C

Description

Converts F14C values to 14C ages.

Usage

BP14C_to_F14C(ages, errors, ...)

F14C_to_BP14C(values, errors, ...)

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

## S4 method for signature 'numeric,numeric'
F14C_to_BP14C(values, errors, lambda = 8033, asymmetric = FALSE)
BP14C_to_F14C(ages, errors, ...)

F14C_to_BP14C(values, errors, ...)

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

## S4 method for signature 'numeric,numeric'
F14C_to_BP14C(values, errors, lambda = 8033, asymmetric = FALSE)

Arguments

`ages`	A `numeric` vector giving the radiocarbon ages.
`errors`	A `numeric` vector giving the standard deviations.
`...`	Currently not used.
`values`	A `numeric` vector giving the F14C values.
`lambda`	A length-one `numeric` vector specifying the mean-life of radiocarbon (defaults to 14C half-life value as introduced by Libby 1952).
`asymmetric`	A `logical` scalar: should asymmetric 14C errors be returned?

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.

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.

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)
## 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)

Highest Density Regions

Description

Highest Density Regions

Usage

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

Arguments

`x`	A `CalibratedAges` object.
`level`	A length-one `numeric` vector giving the confidence level.
`calendar`	An `aion::TimeScale` object specifying the target calendar (see `aion::calendar()`). If `NULL`, rata die are returned.
`...`	Currently not used.

Value

Returns a list of numeric matrix.

Author(s)

N. Frerebeau

References

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

Examples

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

## HDR
interval_hdr(cal, level = 0.683)
interval_hdr(cal, level = 0.954)
interval_hdr(cal, level = 0.997)
## Calibrate multiple dates
cal <- c14_calibrate(
  values = c(5000, 4500),
  errors = c(45, 35),
  names = c("X", "Y")
)

## HDR
interval_hdr(cal, level = 0.683)
interval_hdr(cal, level = 0.954)
interval_hdr(cal, level = 0.997)

Ksâr 'Akil Radiocarbon Dates

Description

Ksâr 'Akil Radiocarbon Dates

Usage

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

Arguments

`object`	An object from which to find labels.
`...`	Currently not used.

Value

A character vector.

Author(s)

N. Frerebeau

Mean

Description

Mean

Usage

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

## S4 method for signature 'ProxyRecord'
mean(x, na.rm = FALSE, ...)
## S4 method for signature 'CalibratedAges'
mean(x, na.rm = FALSE, ..., calendar = getOption("ananke.calendar"))

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

Arguments

`x`	A `CalibratedAges` object.
`na.rm`	A `logical` scalar: should `NA` values be stripped before the computation proceeds?
`...`	Currently not used.
`calendar`	An `aion::TimeScale` object specifying the target calendar (see `aion::calendar()`). If `NULL`, rata die are returned.

Value

A numeric vector.

Author(s)

N. Frerebeau

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

Arguments

`x`	A `CalibratedAges` object.
`na.rm`	A `logical` scalar: should `NA` values be stripped before the computation proceeds?
`...`	Currently not used.
`calendar`	An `aion::TimeScale` object specifying the target calendar (see `aion::calendar()`). If `NULL`, rata die are returned.

Value

A numeric vector.

Author(s)

N. Frerebeau

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")
## 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

`x`	An object from which to get or set element(s).
`value`	A possible value for the element(s) of `x`.

Value

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

Author(s)

N. Frerebeau

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)
)

## 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)
)
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)
)

## 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)
)

Arguments

`x`	A `numeric` vector of 206Pb/204Pb ratios. If `y` and `z` are missing, must be a `list` (or a `data.frame`) with `numeric` components (columns) `x`, `y` and `z`.
`y`	A `numeric` vector of 207Pb/204Pb ratios. If missing, an attempt is made to interpret `x` in a suitable way.
`z`	A `numeric` vector of 208Pb/204Pb ratios. If missing, an attempt is made to interpret `x` in a suitable way.
`...`	Currently not used.
`t0`	A `numeric` value giving the time of the second stage of the reference model.
`x_star`	A `numeric` value giving the 206Pb/204Pb ratio at $t = 0$ .
`y_star`	A `numeric` value giving the 207Pb/204Pb ratio at $t = 0$ .
`z_star`	A `numeric` value giving the 208Pb/204Pb ratio at $t = 0$ .
`mu`	A `numeric` value giving the 238U/204Pb ratio of the reference model.
`kappa`	A `numeric` value giving the 232Th/238U ratio of the reference model.
`th232`	A `numeric` value giving the decay constants of 232Th.
`u238`	A `numeric` value giving the decay constants of 238U.
`u235`	A `numeric` value giving the decay constants of 235U.
`u238_235`	A `numeric` value giving the actual 238U/235U ratio.
`tolerance`	A `numeric` value specifying the tolerance (stopping criteria for the Newton–Raphson method).

Value

A four columns data.frame:

`age`	Geological model age (in Ma)
`mu`	238U/204Pb ratio
`kappa`	232Th/238U ratio
`f`

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
)

## Reference values from Albarede & Juteau (1984)
pb_age(Pb)

## 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
)
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
)

## Reference values from Albarede & Juteau (1984)
pb_age(Pb)

## 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(depth, ...)

## S4 method for signature 'numeric'
proxy_ensemble(
  depth,
  proxy,
  proxy_error,
  step,
  time,
  time_error,
  calendar,
  from = NULL,
  to = NULL,
  by = NULL,
  n = 30,
  progress = getOption("ananke.progress"),
  verbose = getOption("ananke.verbose")
)
proxy_ensemble(depth, ...)

## S4 method for signature 'numeric'
proxy_ensemble(
  depth,
  proxy,
  proxy_error,
  step,
  time,
  time_error,
  calendar,
  from = NULL,
  to = NULL,
  by = NULL,
  n = 30,
  progress = getOption("ananke.progress"),
  verbose = getOption("ananke.verbose")
)

Arguments

`depth`	A positive `numeric` vector giving the depth at which proxy values and calendar ages were measured. It must be in decreasing order (i.e. in chronological order).
`...`	Currently not used.
`proxy`	A `numeric` vector giving the proxy values.
`proxy_error`	A `numeric` vector giving the proxy uncertainties.
`step`	A length-one `numeric` vector specifying the step size (in units of `proxy`) at which proxy records densities are to be estimated.
`time`	A `numeric` vector giving the calendar ages (in years).
`time_error`	A `numeric` vector giving the calendar age uncertainties (in years).
`calendar`	An `aion::TimeScale` object specifying the target calendar (see `aion::calendar()`). If `NULL`, rata die are returned.
`from`	A length-one `numeric` vector specifying the starting value of the temporal sequence at which densities are to be estimated (in years).
`to`	A length-one `numeric` vector specifying the end value of the temporal sequence at which densities are to be estimated (in cal BP years).
`by`	A length-one `numeric` vector specifying the increment of the temporal sequence at which densities are to be estimated (in years).
`n`	An `integer` specifying the number of item to choose randomly.
`progress`	A `logical` scalar: should a progress bar be displayed?
`verbose`	A `logical` scalar: should extra information be reported?

Value

A ProxyRecord object.

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.

Examples

## Not run: 
## 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(
  depth = ngrip2010$depth,
  proxy = ngrip2010$delta,
  proxy_error = 0.01,
  step = 0.001,
  time = ngrip2010$age,
  time_error = ngrip2010$MCE,
  calendar = b2k(), # /!\
  by = 20,
  n = 30
)

plot(ngrip_record)

## End(Not run)
## Not run: 
## 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(
  depth = ngrip2010$depth,
  proxy = ngrip2010$delta,
  proxy_error = 0.01,
  step = 0.001,
  time = ngrip2010$age,
  time_error = ngrip2010$MCE,
  calendar = b2k(), # /!\
  by = 20,
  n = 30
)

plot(ngrip_record)

## End(Not run)

Plot Layer-Counted Proxy Records Uncertainties

Description

Plot Layer-Counted Proxy Records Uncertainties

Usage

## S4 method for signature 'ProxyRecord,missing'
plot(
  x,
  calendar = getOption("ananke.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,
  ...
)
## S4 method for signature 'ProxyRecord,missing'
plot(
  x,
  calendar = getOption("ananke.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

`x`	A `ProxyRecord` object.
`calendar`	An `aion::TimeScale` object specifying the target calendar (see `aion::calendar()`). If `NULL`, rata die are returned.
`iqr`	A `logical` scalar: should the mean and IQR be displayed?
`xlab`, `ylab`	A `character` string giving a label for the x and y axis.
`col`	A list of colors such as that generated by `grDevices::hcl.colors()`.
`col.mean`, `col.iqr`	A specification for the line colors. Only used if `iqr` is `TRUE`.
`lty.mean`, `lty.iqr`	A specification for the line types. Only used if `iqr` is `TRUE`.
`lwd.mean`, `lwd.iqr`	A specification for the line widths. Only used if `iqr` is `TRUE`.
`...`	Further parameters to be passed to `graphics::image()`.

Value

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

Author(s)

N. Frerebeau

Examples

## Not run: 
## 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(
  depth = ngrip2010$depth,
  proxy = ngrip2010$delta,
  proxy_error = 0.01,
  step = 0.001,
  time = ngrip2010$age,
  time_error = ngrip2010$MCE,
  calendar = b2k(), # /!\
  by = 20,
  n = 30
)

plot(ngrip_record)

## End(Not run)
## Not run: 
## 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(
  depth = ngrip2010$depth,
  proxy = ngrip2010$delta,
  proxy_error = 0.01,
  step = 0.001,
  time = ngrip2010$age,
  time_error = ngrip2010$MCE,
  calendar = b2k(), # /!\
  by = 20,
  n = 30
)

plot(ngrip_record)

## End(Not run)

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 = getOption("ananke.calendar")
)

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

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

Arguments

`x`	A `CalibratedAges` object.
`probs`	A `numeric` vector of probabilities with values in $[0,1]$ .
`na.rm`	A `logical` scalar: should `NA` values be stripped before the computation proceeds?
`...`	Currently not used.
`calendar`	An `aion::TimeScale` object specifying the target calendar (see `aion::calendar()`). If `NULL`, rata die are returned.

Value

A numeric matrix containing the quantiles.

Author(s)

N. Frerebeau

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

Arguments

`x`	An `RECE` object.
`calendar`	An `aion::TimeScale` object specifying the target calendar (see `aion::calendar()`). If `NULL`, rata die are returned.
`...`	Further parameters to be passed to `graphics::image()`.

Value

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

Author(s)

N. Frerebeau

References

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

Arguments

`x`	An object from which to extract element(s) or in which to replace element(s).
`i`, `j`, `k`	Indices specifying elements to extract or replace.
`drop`	A `logical` scalar: should the result be coerced to the lowest possible dimension? This only works for extracting elements, not for the replacement.

Value

A subsetted object.

Author(s)

N. Frerebeau

Curve	Reference
`bomb04nh1`	Hua and Barbetti 2004
`bomb04nh2`	Hua and Barbetti 2004
`bomb04nh3`	Hua and Barbetti 2004
`bomb04sh`	Hua and Barbetti 2004
`bomb13nh1`	Hua, Berbetti and Rakowski 2013
`bomb13nh2`	Hua, Berbetti and Rakowski 2013
`bomb13nh3`	Hua, Berbetti and Rakowski 2013
`bomb13sh12`	Hua, Berbetti and Rakowski 2013
`bomb13sh3`	Hua, Berbetti and Rakowski 2013
`bomb21nh1`	Hua et al. 2022
`bomb21nh2`	Hua et al. 2022
`bomb21nh3`	Hua et al. 2022
`bomb21sh12`	Hua et al. 2022
`bomb21sh3`	Hua et al. 2022
`cariaco04`	Hughen et al. 2004
`intcal98`	Stuiver et al. 1998
`intcal04`	Reimer et al. 2004
`intcal09`	Reimer et al. 2009
`intcal13`	Reimer et al. 2013
`intcal20`	Reimer et al. 2020
`kueppers04`	Kueppers et al. 2004
`marine98`	Stuiver, Reimer and Braziunas 1998
`marine04`	Hughen et al. 2004
`marine09`	Reimer et al. 2009
`marine13`	Reimer et al. 2013
`marine20`	Heaton et al. 2020
`shcal04`	McCormac et al. 2004
`shcal13`	Hogg et al. 2013
`shcal20`	Hogg et al. 2020

`CALBP`	Calibrated age BP
`AGE`	Uncalibrated radiocarbon age
`ERROR`	Standard deviation

`name`	A `character` vector naming calibration curves (see details).
`...`	Currently not used.

Package 'ananke'

Help Index

14C Calibration

Description

Usage

Arguments

Value

Note

Author(s)

References

See Also

Examples

Combine 14C

Description

Usage

Arguments

Value

Author(s)

References

See Also

Examples

14C Calibration Curve

Description

Usage

Arguments

Details

Value

Author(s)

References

See Also

Examples

Radiocarbon Event Count

Description

Usage

Arguments

Value

Author(s)

References

See Also

Plot Calibrated Radiocarbon Ages

Description

Usage

Arguments

Value

Author(s)

See Also

Examples

Summed Probability Distributions

Description

Usage

Arguments

Details

Author(s)

See Also

Examples

Uncalibrate a Radiocarbon Date

Description

Usage

Arguments

Author(s)

See Also

Examples

Check Calibrated Radiocarbon Dates

Description

Usage

Arguments

Value

Author(s)

See Also

Examples

Coerce to a Data Frame

Description

Usage

Arguments

Value

Author(s)

See Also

Examples

Data Description

Description