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: | 2024-10-03 05:59:55 UTC |
Source: | https://github.com/tesselle/ananke |
Calibrates radiocarbon dates.
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") )
values |
A |
errors |
A |
... |
Currently not used. |
names |
A |
curves |
A |
reservoir_offsets |
A |
reservoir_errors |
A |
from |
length-one |
to |
A length-one |
resolution |
A length-one |
normalize |
A |
F14C |
A |
drop |
A |
eps |
A length-one |
verbose |
A |
A CalibratedAges
object.
Adapted from Bchron::BchronCalibrate()
by Andrew Parnell and
rcarbon::calibrate()
by Andrew Bevan and Enrico Crema.
N. Frerebeau
Bronk Ramsey, C. (2008). Radiocarbon Dating: Revolutions in Understanding. Archaeometry, 50:249-275. doi:10.1111/j.1475-4754.2008.00394.x.
Other radiocarbon tools:
F14C
,
c14_combine()
,
c14_curve()
,
c14_ensemble()
,
c14_plot
,
c14_spd()
,
c14_uncalibrate()
,
c14_validate()
,
rec_plot
## 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)
Combines radiocarbon dates.
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)
ages |
A |
errors |
A |
... |
Currently not used. |
groups |
A |
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 |
N. Frerebeau
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.
Other radiocarbon tools:
F14C
,
c14_calibrate()
,
c14_curve()
,
c14_ensemble()
,
c14_plot
,
c14_spd()
,
c14_uncalibrate()
,
c14_validate()
,
rec_plot
## 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 )
14C Calibration Curve
c14_curve(name, ...) ## S4 method for signature 'character' c14_curve(name) ## S4 method for signature 'CalibratedAges' c14_curve(name)
c14_curve(name, ...) ## S4 method for signature 'character' c14_curve(name) ## S4 method for signature 'CalibratedAges' c14_curve(name)
name |
A |
... |
Currently not used. |
The following calibration curves are available:
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 |
A list
of three-column data.frame
:
CALBP |
Calibrated age BP |
AGE |
Uncalibrated radiocarbon age |
ERROR |
Standard deviation |
N. Frerebeau
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.
Other radiocarbon tools:
F14C
,
c14_calibrate()
,
c14_combine()
,
c14_ensemble()
,
c14_plot
,
c14_spd()
,
c14_uncalibrate()
,
c14_validate()
,
rec_plot
## 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
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") )
object |
A |
... |
Currently not used. |
from |
length-one |
to |
A length-one |
by |
A length-one |
n |
An |
calendar |
An |
progress |
A |
An RECE
object.
N. Frerebeau
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.
Other radiocarbon tools:
F14C
,
c14_calibrate()
,
c14_combine()
,
c14_curve()
,
c14_plot
,
c14_spd()
,
c14_uncalibrate()
,
c14_validate()
,
rec_plot
Plot Calibrated Radiocarbon Ages
## 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, ... )
x |
A |
calendar |
An |
density |
A |
interval |
A |
level |
A length-one |
sort |
A |
decreasing |
A |
main |
A |
sub |
A |
axes |
A |
frame.plot |
A |
ann |
A |
panel.first |
An an |
panel.last |
An |
col.density , col.interval
|
A specification for the plotting colors. |
... |
Other graphical parameters may also be passed as arguments to this function. |
plot()
is called it for its side-effects: it results in a graphic
being displayed. Invisibly returns x
.
N. Frerebeau
Other radiocarbon tools:
F14C
,
c14_calibrate()
,
c14_combine()
,
c14_curve()
,
c14_ensemble()
,
c14_spd()
,
c14_uncalibrate()
,
c14_validate()
,
rec_plot
## 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)
Computes summed probability distributions (SPD) of radiocarbon dates.
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)
object |
A |
... |
Currently not used. |
normalize_date |
A |
normalize_spd |
A |
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.
N. Frerebeau
Other radiocarbon tools:
F14C
,
c14_calibrate()
,
c14_combine()
,
c14_curve()
,
c14_ensemble()
,
c14_plot
,
c14_uncalibrate()
,
c14_validate()
,
rec_plot
## 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
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, ...)
object |
A |
... |
Currently not used. |
curves |
A |
N. Frerebeau
Other radiocarbon tools:
F14C
,
c14_calibrate()
,
c14_combine()
,
c14_curve()
,
c14_ensemble()
,
c14_plot
,
c14_spd()
,
c14_validate()
,
rec_plot
## 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
c14_validate(object, ...) ## S4 method for signature 'CalibratedAges' c14_validate(object)
c14_validate(object, ...) ## S4 method for signature 'CalibratedAges' c14_validate(object)
object |
A |
... |
Currently not used. |
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
.
N. Frerebeau
Other radiocarbon tools:
F14C
,
c14_calibrate()
,
c14_combine()
,
c14_curve()
,
c14_ensemble()
,
c14_plot
,
c14_spd()
,
c14_uncalibrate()
,
rec_plot
## 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
## 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"))
x |
An object. |
... |
Further parameters to be passed to |
calendar |
An |
A data.frame
with an extra time
column.
N. Frerebeau
Other mutators:
labels()
,
mutators
,
subset()
## 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
## 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, ...)
x |
A |
calendar |
An |
level |
A length-one |
... |
Further parameters to be passed to |
describe()
is called for its side-effects. Invisibly returns x
.
N. Frerebeau
Millard, A. R. (2014). Conventions for Reporting Radiocarbon Determinations. Radiocarbon, 56(2): 555-559. doi:10.2458/56.17455.
## 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)
Converts F14C values to 14C ages.
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)
ages |
A |
errors |
A |
... |
Currently not used. |
values |
A |
lambda |
A length-one |
asymmetric |
A |
A data.frame
.
N. Frerebeau
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.
Other radiocarbon tools:
c14_calibrate()
,
c14_combine()
,
c14_curve()
,
c14_ensemble()
,
c14_plot
,
c14_spd()
,
c14_uncalibrate()
,
c14_validate()
,
rec_plot
## 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
## 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"), ...)
x |
A |
level |
A length-one |
calendar |
An |
... |
Currently not used. |
Returns a list
of numeric
matrix
.
N. Frerebeau
Hyndman, R. J. (1996). Computing and graphing highest density regions. American Statistician, 50: 120-126. doi:10.2307/2684423.
stats::density()
, arkhe::interval_hdr()
Other statistics:
mean()
,
median()
,
quantile()
## 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
ksarakil
ksarakil
A data.frame
with 16 rows and 5 variables:
Laboratory code.
Radiocarbon date (year BP).
Radiocarbon error (year).
Stratigraphic layer.
Chronological phase.
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 a suitable set of labels from an object for use in printing or plotting, for example.
## S4 method for signature 'CalibratedAges' labels(object, ...)
## S4 method for signature 'CalibratedAges' labels(object, ...)
object |
An object from which to find labels. |
... |
Currently not used. |
A character
vector.
N. Frerebeau
Other mutators:
data.frame
,
mutators
,
subset()
Mean
## 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, ...)
x |
A |
na.rm |
A |
... |
Currently not used. |
calendar |
An |
A numeric
vector.
N. Frerebeau
Other statistics:
hdr
,
median()
,
quantile()
## 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
## 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"))
x |
A |
na.rm |
A |
... |
Currently not used. |
calendar |
An |
A numeric
vector.
N. Frerebeau
Other statistics:
hdr
,
mean()
,
quantile()
## 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")
Getters and setters to extract or replace parts of an object.
x |
An object from which to get or set element(s). |
value |
A possible value for the element(s) of |
An object of the same sort as x
with the new values assigned.
N. Frerebeau
Other mutators:
data.frame
,
labels()
,
subset()
Compute geological model age (T) and U/Pb (mu) and Th/U (kappa) ratios from lead isotopic measurements.
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) )
x |
A |
y |
A |
z |
A |
... |
Currently not used. |
t0 |
A |
x_star |
A |
y_star |
A |
z_star |
A |
mu |
A |
kappa |
A |
th232 |
A |
u238 |
A |
u235 |
A |
u238_235 |
A |
tolerance |
A |
A four columns data.frame
:
age |
Geological model age (in Ma) |
mu |
238U/204Pb ratio |
kappa |
232Th/238U ratio |
f |
|
Reference values from Albarede & Juteau (1984).
N. Frerebeau, F. Albarede (original Matlab code)
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.
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 )
Represents layer-counted proxy records as sequences of probability distributions on absolute, error-free time axes.
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") )
depth |
A positive |
... |
Currently not used. |
proxy |
A |
proxy_error |
A |
step |
A length-one |
time |
A |
time_error |
A |
calendar |
An |
from |
A length-one |
to |
A length-one |
by |
A length-one |
n |
An |
progress |
A |
verbose |
A |
A ProxyRecord
object.
N. Frerebeau
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.
Other proxy tools:
proxy_plot
## 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
## 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, ... )
x |
A |
calendar |
An |
iqr |
A |
xlab , ylab
|
A |
col |
A list of colors such as that generated by |
col.mean , col.iqr
|
A specification for the line colors. Only used if
|
lty.mean , lty.iqr
|
A specification for the line types. Only used if
|
lwd.mean , lwd.iqr
|
A specification for the line widths. Only used if
|
... |
Further parameters to be passed to |
plot()
is called it for its side-effects: it results in a graphic
being displayed. Invisibly returns x
.
N. Frerebeau
Other proxy tools:
proxy_ensemble()
## 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
## 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, ...)
x |
A |
probs |
A |
na.rm |
A |
... |
Currently not used. |
calendar |
An |
A numeric
matrix
containing the quantiles.
N. Frerebeau
Other statistics:
hdr
,
mean()
,
median()
## 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
## S4 method for signature 'RECE,missing' plot(x, calendar = getOption("ananke.calendar"), ...)
## S4 method for signature 'RECE,missing' plot(x, calendar = getOption("ananke.calendar"), ...)
x |
An |
calendar |
An |
... |
Further parameters to be passed to |
image()
is called it for its side-effects: it results in a graphic being
displayed (invisibly returns x
).
N. Frerebeau
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.
Other radiocarbon tools:
F14C
,
c14_calibrate()
,
c14_combine()
,
c14_curve()
,
c14_ensemble()
,
c14_plot
,
c14_spd()
,
c14_uncalibrate()
,
c14_validate()
Operators acting on objects to extract or replace parts.
## S4 method for signature 'CalibratedAges' x[i, j, k, drop = FALSE]
## S4 method for signature 'CalibratedAges' x[i, j, k, drop = FALSE]
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 |
A subsetted object.
N. Frerebeau
Other mutators:
data.frame
,
labels()
,
mutators