diff --git a/ananke/articles/bibliography.html b/ananke/articles/bibliography.html
index f69f2143f..1107bb959 100644
--- a/ananke/articles/bibliography.html
+++ b/ananke/articles/bibliography.html
@@ -102,9 +102,9 @@ <h4 data-toc-skip class="date">2023-11-29</h4>
 Archives.”</span> <em>Climate of the Past</em> 13 (9): 1169–80. <a href="https://doi.org/10.5194/cp-13-1169-2017" class="external-link">https://doi.org/10.5194/cp-13-1169-2017</a>.
 </div>
 <div id="ref-bronkramsey2008" class="csl-entry">
-Bronk Ramsey, C. 2008. <span>“<span>RADIOCARBON DATING</span>:
-<span>REVOLUTIONS IN UNDERSTANDING</span>.”</span> <em>Archaeometry</em>
-50 (2): 249–75. <a href="https://doi.org/10.1111/j.1475-4754.2008.00394.x" class="external-link">https://doi.org/10.1111/j.1475-4754.2008.00394.x</a>.
+Bronk Ramsey, C. 2008. <span>“Radiocarbon <span>Dating</span>:
+<span>Revolutions</span> in <span>Understanding</span>.”</span>
+<em>Archaeometry</em> 50 (2): 249–75. <a href="https://doi.org/10.1111/j.1475-4754.2008.00394.x" class="external-link">https://doi.org/10.1111/j.1475-4754.2008.00394.x</a>.
 </div>
 <div id="ref-carleton2021" class="csl-entry">
 Carleton, W. Christopher. 2021. <span>“Evaluating <span>Bayesian
diff --git a/ananke/pkgdown.yml b/ananke/pkgdown.yml
index 865c80b50..1e61775e4 100644
--- a/ananke/pkgdown.yml
+++ b/ananke/pkgdown.yml
@@ -3,7 +3,7 @@ pkgdown: 2.0.7
 pkgdown_sha: ~
 articles:
   bibliography: bibliography.html
-last_built: 2023-11-29T16:29Z
+last_built: 2023-11-29T16:41Z
 urls:
   reference: https://packages.tesselle.org/ananke/reference
   article: https://packages.tesselle.org/ananke/articles
diff --git a/ananke/reference/F14C.html b/ananke/reference/F14C.html
index 3a4c4cc4c..cbfdea73b 100644
--- a/ananke/reference/F14C.html
+++ b/ananke/reference/F14C.html
@@ -44,7 +44,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="" class="logo" alt=""><h1>F14C</h1>
-      <small class="dont-index">Source: <a href="https://github.com/tesselle/ananke/blob/HEAD/R/AllGenerics.R" class="external-link"><code>R/AllGenerics.R</code></a>, <a href="https://github.com/tesselle/ananke/blob/HEAD/R/f14c.R" class="external-link"><code>R/f14c.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/tesselle/ananke/blob/HEAD/R/AllGenerics.R" class="external-link"><code>R/AllGenerics.R</code></a>, <a href="https://github.com/tesselle/ananke/blob/HEAD/R/c14_f14c.R" class="external-link"><code>R/c14_f14c.R</code></a></small>
       <div class="d-none name"><code>F14C.Rd</code></div>
     </div>
 
@@ -101,7 +101,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
     </div>
     <div class="section level2">
     <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2>
-    <p>Bronk Ramsey, C. (2008). RADIOCARBON DATING: REVOLUTIONS IN UNDERSTANDING.
+    <p>Bronk Ramsey, C. (2008). Radiocarbon Dating: Revolutions in Understanding.
 <em>Archaeometry</em>, 50:249-275. <a href="https://doi.org/10.1111/j.1475-4754.2008.00394.x" class="external-link">doi:10.1111/j.1475-4754.2008.00394.x</a>
 .</p>
 <p>van der Plicht, J., Hogg, A. (2006). A Note on Reporting Radiocarbon.
diff --git a/ananke/reference/c14_calibrate.html b/ananke/reference/c14_calibrate.html
index 2ee80f939..59ae7e45c 100644
--- a/ananke/reference/c14_calibrate.html
+++ b/ananke/reference/c14_calibrate.html
@@ -157,7 +157,7 @@ <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2>
     </div>
     <div class="section level2">
     <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2>
-    <p>Bronk Ramsey, C. (2008). RADIOCARBON DATING: REVOLUTIONS IN UNDERSTANDING.
+    <p>Bronk Ramsey, C. (2008). Radiocarbon Dating: Revolutions in Understanding.
 <em>Archaeometry</em>, 50:249-275. <a href="https://doi.org/10.1111/j.1475-4754.2008.00394.x" class="external-link">doi:10.1111/j.1475-4754.2008.00394.x</a>
 .</p>
     </div>
diff --git a/ananke/search.json b/ananke/search.json
index 1e6dc29ba..8e2943cf8 100644
--- a/ananke/search.json
+++ b/ananke/search.json
@@ -1 +1 @@
-[{"path":[]},{"path":"https://packages.tesselle.org/ananke/index.html","id":"overview","dir":"","previous_headings":"","what":"Overview","title":"Quantitative Chronology in Archaeology","text":"ananke provides functions radiocarbon calibration chronological analysis.","code":""},{"path":"https://packages.tesselle.org/ananke/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Quantitative Chronology in Archaeology","text":"can install released version ananke CRAN : development version GitHub :","code":"install.packages(\"ananke\") # install.packages(\"remotes\") remotes::install_github(\"tesselle/ananke\")"},{"path":"https://packages.tesselle.org/ananke/index.html","id":"usage","dir":"","previous_headings":"","what":"Usage","title":"Quantitative Chronology in Archaeology","text":"","code":"## Load packages library(ananke) ## Data from Bosch et al. 2015 data(\"ksarakil\")  ## Calibrate multiple dates 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 plot(cal) plot(cal, density = FALSE, level = 0.95, lwd = 5)"},{"path":"https://packages.tesselle.org/ananke/index.html","id":"contributing","dir":"","previous_headings":"","what":"Contributing","title":"Quantitative Chronology in Archaeology","text":"Please note ananke project released Contributor Code Conduct. contributing project, agree abide terms.","code":""},{"path":[]},{"path":[]},{"path":[]},{"path":"https://packages.tesselle.org/ananke/reference/CalibratedAges-class.html","id":null,"dir":"Reference","previous_headings":"","what":"Calibrated Radiocarbon Ages — CalibratedAges-class","title":"Calibrated Radiocarbon Ages — CalibratedAges-class","text":"S4 class represent calibrated radiocarbon ages.","code":""},{"path":"https://packages.tesselle.org/ananke/reference/CalibratedAges-class.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calibrated Radiocarbon Ages — CalibratedAges-class","text":"values numeric vector giving BP ages F14C values calibrated. errors numeric vector giving standard deviation values calibrated. curves character vector specifying calibration curves used.","code":""},{"path":"https://packages.tesselle.org/ananke/reference/CalibratedAges-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"Calibrated Radiocarbon Ages — CalibratedAges-class","text":"F14C logical scalar: values F14C instead radiocarbon ages? status integer vector specifying calibration status. must one \"0\" (OK), \"1\" (calibration range) \"2\" (may extend calibration range).","code":""},{"path":"https://packages.tesselle.org/ananke/reference/CalibratedAges-class.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Calibrated Radiocarbon Ages — CalibratedAges-class","text":"class inherits TimeSeries.","code":""},{"path":[]},{"path":"https://packages.tesselle.org/ananke/reference/CalibratedAges-class.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calibrated Radiocarbon Ages — CalibratedAges-class","text":"N. Frerebeau","code":""},{"path":"https://packages.tesselle.org/ananke/reference/CalibratedSPD-class.html","id":null,"dir":"Reference","previous_headings":"","what":"Calibrated SPD — CalibratedSPD-class","title":"Calibrated SPD — CalibratedSPD-class","text":"S4 class represent summed probability distributions (SPD) radiocarbon dates.","code":""},{"path":"https://packages.tesselle.org/ananke/reference/CalibratedSPD-class.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Calibrated SPD — CalibratedSPD-class","text":"class inherits TimeSeries.","code":""},{"path":[]},{"path":"https://packages.tesselle.org/ananke/reference/CalibratedSPD-class.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calibrated SPD — CalibratedSPD-class","text":"N. Frerebeau","code":""},{"path":"https://packages.tesselle.org/ananke/reference/F14C.html","id":null,"dir":"Reference","previous_headings":"","what":"F14C — F14C","title":"F14C — F14C","text":"Converts F14C values 14C ages.","code":""},{"path":"https://packages.tesselle.org/ananke/reference/F14C.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"F14C — F14C","text":"","code":"BP14C_to_F14C(ages, errors, ...)  F14C_to_BP14C(values, errors, ...)  # S4 method for numeric,numeric BP14C_to_F14C(ages, errors, lambda = 8033)  # S4 method for numeric,numeric F14C_to_BP14C(values, errors, lambda = 8033, asymmetric = FALSE)"},{"path":"https://packages.tesselle.org/ananke/reference/F14C.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"F14C — F14C","text":"ages numeric vector giving radiocarbon ages. errors numeric vector giving standard deviations. ... Currently used. values numeric vector giving F14C values. lambda length-one numeric vector specifying mean-life radiocarbon (defaults 14C half-life value introduced Libby 1952). asymmetric logical scalar: asymmetric 14C errors returned?","code":""},{"path":"https://packages.tesselle.org/ananke/reference/F14C.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"F14C — F14C","text":"data.frame.","code":""},{"path":"https://packages.tesselle.org/ananke/reference/F14C.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"F14C — F14C","text":"Bronk Ramsey, C. (2008). RADIOCARBON DATING: REVOLUTIONS UNDERSTANDING. Archaeometry, 50:249-275. doi:10.1111/j.1475-4754.2008.00394.x . van der Plicht, J., Hogg, . (2006). Note Reporting Radiocarbon. Quaternary Geochronology, 1(4): 237-240. doi:10.1016/j.quageo.2006.07.001 .","code":""},{"path":[]},{"path":"https://packages.tesselle.org/ananke/reference/F14C.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"F14C — F14C","text":"N. Frerebeau","code":""},{"path":"https://packages.tesselle.org/ananke/reference/F14C.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"F14C — F14C","text":"","code":"## Asymmetric 14C errors (van der Plicht and Hogg 2006) F14C_to_BP14C(0.0052, 0.0006, asym = TRUE) #>        age     plus    minus #> 1 42246.32 984.8645 877.1979  ## Symmetric 14C errors (Bronk Ramsey 2008) F14C_to_BP14C(0.0052, 0.0006, asym = FALSE) #>        age     plus    minus #> 1 42246.32 926.8846 926.8846"},{"path":"https://packages.tesselle.org/ananke/reference/ProxyRecord-class.html","id":null,"dir":"Reference","previous_headings":"","what":"Proxy Record — ProxyRecord-class","title":"Proxy Record — ProxyRecord-class","text":"S4 class store proxy records.","code":""},{"path":"https://packages.tesselle.org/ananke/reference/ProxyRecord-class.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Proxy Record — ProxyRecord-class","text":"class inherits TimeSeries.","code":""},{"path":[]},{"path":"https://packages.tesselle.org/ananke/reference/ProxyRecord-class.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Proxy Record — ProxyRecord-class","text":"N. Frerebeau","code":""},{"path":"https://packages.tesselle.org/ananke/reference/RECE-class.html","id":null,"dir":"Reference","previous_headings":"","what":"Radiocarbon Event Count Ensemble — RECE-class","title":"Radiocarbon Event Count Ensemble — RECE-class","text":"S4 class represent radiocarbon event count ensemble.","code":""},{"path":"https://packages.tesselle.org/ananke/reference/RECE-class.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Radiocarbon Event Count Ensemble — RECE-class","text":"class inherits TimeSeries.","code":""},{"path":[]},{"path":"https://packages.tesselle.org/ananke/reference/RECE-class.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Radiocarbon Event Count Ensemble — RECE-class","text":"N. Frerebeau","code":""},{"path":"https://packages.tesselle.org/ananke/reference/ananke-package.html","id":null,"dir":"Reference","previous_headings":"","what":"ananke: Quantitative Chronology in Archaeology — ananke-package","title":"ananke: Quantitative Chronology in Archaeology — ananke-package","text":"package (one paragraph).","code":""},{"path":[]},{"path":"https://packages.tesselle.org/ananke/reference/ananke-package.html","id":"package-options","dir":"Reference","previous_headings":"","what":"Package options","title":"ananke: Quantitative Chronology in Archaeology — ananke-package","text":"ananke uses following options() configure behavior: ananke.calendar: TimeScale object (default calendar printing). ananke.grid: numeric value specifying number equally spaced points densities estimated (defaults \\(512\\)). power \\(2\\). ananke.progress: logical scalar. progress bars displayed? ananke.verbose: logical scalar. R report extra information progress? Defaults TRUE.","code":""},{"path":[]},{"path":"https://packages.tesselle.org/ananke/reference/ananke-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"ananke: Quantitative Chronology in Archaeology — ananke-package","text":"Full list authors contributors (alphabetic order): Package maintainer Nicolas Frerebeaunicolas.frerebeau@u-bordeaux-montaigne.fr Archéosciences Bordeaux (UMR 6034) Maison de l'Archéologie Université Bordeaux Montaigne F-33607 Pessac cedex France","code":""},{"path":"https://packages.tesselle.org/ananke/reference/c14_calibrate.html","id":null,"dir":"Reference","previous_headings":"","what":"14C Calibration — c14_calibrate","title":"14C Calibration — c14_calibrate","text":"Calibrates radiocarbon dates.","code":""},{"path":"https://packages.tesselle.org/ananke/reference/c14_calibrate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"14C Calibration — c14_calibrate","text":"","code":"c14_calibrate(values, errors, ...)  # S4 method for 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 )"},{"path":"https://packages.tesselle.org/ananke/reference/c14_calibrate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"14C Calibration — c14_calibrate","text":"values numeric vector giving BP ages F14C values calibrated. errors numeric vector giving standard deviation values calibrated. ... Currently used. names character vector specifying names samples (e.g. laboratory codes). curves character vector specifying calibration curve used. Different curves can specified per sample. reservoir_offsets numeric vector giving offset values marine reservoir effect (defaults 0; .e. offset). reservoir_errors numeric vector giving offset value errors marine reservoir effect (defaults 0; .e. offset). length-one numeric vector specifying earliest data calibrate , cal. BP years. length-one numeric vector specifying latest data calibrate , cal. BP years. resolution length-one numeric vector specifying temporal resolution (years) calibration. normalize logical scalar: calibration normalized? F14C logical scalar: calibration carried F14C space? TRUE, values must expressed F14C. drop logical scalar: years zero probability discarded? TRUE (default), results narrower time range. eps length-one numeric value giving cutoff calibration values removed.","code":""},{"path":"https://packages.tesselle.org/ananke/reference/c14_calibrate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"14C Calibration — c14_calibrate","text":"CalibratedAges object.","code":""},{"path":"https://packages.tesselle.org/ananke/reference/c14_calibrate.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"14C Calibration — c14_calibrate","text":"Adapted Bchron::BchronCalibrate() Andrew Parnell rcarbon::calibrate() Andrew Bevan Enrico Crema.","code":""},{"path":"https://packages.tesselle.org/ananke/reference/c14_calibrate.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"14C Calibration — c14_calibrate","text":"Bronk Ramsey, C. (2008). RADIOCARBON DATING: REVOLUTIONS UNDERSTANDING. Archaeometry, 50:249-275. doi:10.1111/j.1475-4754.2008.00394.x .","code":""},{"path":[]},{"path":"https://packages.tesselle.org/ananke/reference/c14_calibrate.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"14C Calibration — c14_calibrate","text":"N. Frerebeau","code":""},{"path":"https://packages.tesselle.org/ananke/reference/c14_calibrate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"14C Calibration — c14_calibrate","text":"","code":"## 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)   # \\donttest{ ## Out of 14C range? out <- c14_calibrate(130, 20) #> Warning: Date “X1” may extent out of range. plot(out) #> Warning: Date “X1” may extent out of range.  # }"},{"path":"https://packages.tesselle.org/ananke/reference/c14_combine.html","id":null,"dir":"Reference","previous_headings":"","what":"Combine 14C — c14_combine","title":"Combine 14C — c14_combine","text":"Combines radiocarbon dates.","code":""},{"path":"https://packages.tesselle.org/ananke/reference/c14_combine.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Combine 14C — c14_combine","text":"","code":"c14_combine(ages, errors, ...)  # S4 method for numeric,numeric c14_combine(ages, errors, groups = NULL)"},{"path":"https://packages.tesselle.org/ananke/reference/c14_combine.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Combine 14C — c14_combine","text":"ages numeric vector giving BP ages calibrated. errors numeric vector giving standard deviation ages calibrated. ... Currently used. groups factor sense .factor(groups) defines groups combine . NULL (default), dates combined. NAs treated isolated dates.","code":""},{"path":"https://packages.tesselle.org/ananke/reference/c14_combine.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Combine 14C — c14_combine","text":"data.frame following columns:","code":""},{"path":"https://packages.tesselle.org/ananke/reference/c14_combine.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Combine 14C — c14_combine","text":"Ward, G. K. Wilson, S. R. (1978). Procedures Comparing Combining Radiocarbon Age Determinations: Critique. Archaeometry 20(1): 19‑31. doi:10.1111/j.1475-4754.1978.tb00208.x .","code":""},{"path":[]},{"path":"https://packages.tesselle.org/ananke/reference/c14_combine.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Combine 14C — c14_combine","text":"N. Frerebeau","code":""},{"path":"https://packages.tesselle.org/ananke/reference/c14_combine.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Combine 14C — c14_combine","text":"","code":"## 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 ) #>   groups     ages  errors     chi2         p #> 1 W-1571 14650.00 500.000       NA        NA #> 2  ANU-5 11700.00 260.000       NA        NA #> 3  C-800 10860.00 410.000       NA        NA #> 4 L-698D 11840.00 100.000       NA        NA #> 5  FSU-3 11245.00 450.000       NA        NA #> 6  Tx-44 10700.00 210.000       NA        NA #> 7  ANU-7 14253.17 190.325 6.157902 0.1041756"},{"path":"https://packages.tesselle.org/ananke/reference/c14_curve.html","id":null,"dir":"Reference","previous_headings":"","what":"14C Calibration Curve — c14_curve","title":"14C Calibration Curve — c14_curve","text":"14C Calibration Curve","code":""},{"path":"https://packages.tesselle.org/ananke/reference/c14_curve.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"14C Calibration Curve — c14_curve","text":"","code":"c14_curve(name, ...)  # S4 method for character c14_curve(name)  # S4 method for CalibratedAges c14_curve(name)"},{"path":"https://packages.tesselle.org/ananke/reference/c14_curve.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"14C Calibration Curve — c14_curve","text":"name character vector naming calibration curves (see details). ... Currently used.","code":""},{"path":"https://packages.tesselle.org/ananke/reference/c14_curve.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"14C Calibration Curve — c14_curve","text":"list three-column data.frame:","code":""},{"path":"https://packages.tesselle.org/ananke/reference/c14_curve.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"14C Calibration Curve — c14_curve","text":"following calibration curves available:","code":""},{"path":"https://packages.tesselle.org/ananke/reference/c14_curve.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"14C Calibration Curve — c14_curve","text":"Heaton, Timothy J, Peter Köhler, Martin Butzin, Edouard Bard, Ron W Reimer, William E N Austin, Christopher Bronk Ramsey, et al. (2020). Marine20 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, Mike Barbetti (2004). Review Tropospheric Bomb 14C Data Carbon Cycle Modeling Age Calibration Purposes. Radiocarbon, 46(3): 1273-1298. doi:10.1017/S0033822200033142 . Hua, Quan, Mike Barbetti, Andrzej Z Rakowski (2013). Atmospheric Radiocarbon 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 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, J. Turnbull (2004). 14C Activity Global Carbon Cycle Changes Past 50,000 Years. Science, 303(5655): 202‑207. doi:10.1126/science.1090300 . Hughen, Konrad , 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, John Harte (2004). Dead Wood Biomass Turnover Time, Measured Radiocarbon, along Subalpine Elevation Gradient. Oecologia, 141(4): 641‑651. doi:10.1007/s00442-004-1689-x . McCormac, F G, G Hogg, P G Blackwell, C E Buck, T F G Higham, 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, Bayliss, J W Beck, P G Blackwell, C Bronk Ramsey, et al. (2009). IntCal09 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). 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 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 . Hughen, Bernd Kromer, Gerry McCormac, Johannes van der Plicht, 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, Thomas F. Braziunas. (1998). High-Precision Radiocarbon Age Calibration Terrestrial Marine Samples. Radiocarbon, 40(3): 1127‑1151. doi:10.1017/S0033822200019172 .","code":""},{"path":[]},{"path":"https://packages.tesselle.org/ananke/reference/c14_curve.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"14C Calibration Curve — c14_curve","text":"N. Frerebeau","code":""},{"path":"https://packages.tesselle.org/ananke/reference/c14_curve.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"14C Calibration Curve — c14_curve","text":"","code":"## IntCal20 intcal20 <- c14_curve(\"intcal20\") head(intcal20[[1]]) #>   CALBP   AGE ERROR #> 1 55000 50100  1024 #> 2 54980 50081  1018 #> 3 54960 50063  1013 #> 4 54940 50043  1007 #> 5 54920 50027  1003 #> 6 54900 50009   997  ## IntCal intcal <- c14_curve(c(\"intcal09\", \"intcal13\", \"intcal20\")) lapply(X = intcal, FUN = head) #> $intcal09 #>   CALBP   AGE ERROR #> 1 50000 46400   415 #> 2 49900 46316   410 #> 3 49800 46229   403 #> 4 49700 46135   396 #> 5 49600 46036   389 #> 6 49500 45933   380 #>  #> $intcal13 #>   CALBP   AGE ERROR #> 1 50000 46401   274 #> 2 49980 46381   273 #> 3 49960 46362   271 #> 4 49940 46343   270 #> 5 49920 46324   269 #> 6 49900 46305   268 #>  #> $intcal20 #>   CALBP   AGE ERROR #> 1 55000 50100  1024 #> 2 54980 50081  1018 #> 3 54960 50063  1013 #> 4 54940 50043  1007 #> 5 54920 50027  1003 #> 6 54900 50009   997 #>"},{"path":"https://packages.tesselle.org/ananke/reference/c14_ensemble.html","id":null,"dir":"Reference","previous_headings":"","what":"Radiocarbon Event Count — c14_ensemble","title":"Radiocarbon Event Count — c14_ensemble","text":"Radiocarbon Event Count","code":""},{"path":"https://packages.tesselle.org/ananke/reference/c14_ensemble.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Radiocarbon Event Count — c14_ensemble","text":"","code":"c14_ensemble(object, ...)  # S4 method for CalibratedAges c14_ensemble(   object,   from = NULL,   to = NULL,   by = 10,   n = 100,   calendar = BP(),   progress = getOption(\"ananke.progress\") )"},{"path":"https://packages.tesselle.org/ananke/reference/c14_ensemble.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Radiocarbon Event Count — c14_ensemble","text":"object CalibratedAges object. ... Currently used. length-one numeric vector specifying earliest data calibrate (cal BP years). length-one numeric vector specifying latest data calibrate (cal BP years). length-one numeric vector specifying temporal resolution (years) calibration. n integer specifying number item choose randomly. calendar TimeScale object specifying calendar (see calendar()). Defaults CE(). progress logical scalar: progress bar displayed?","code":""},{"path":"https://packages.tesselle.org/ananke/reference/c14_ensemble.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Radiocarbon Event Count — c14_ensemble","text":"RECE object.","code":""},{"path":"https://packages.tesselle.org/ananke/reference/c14_ensemble.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Radiocarbon Event Count — c14_ensemble","text":"Carleton, W. C. (2021). Evaluating Bayesian Radiocarbon‐dated Event Count (REC) Models Study Long‐term Human Environmental Processes. Journal Quaternary Science, 36(1): 110‑23. doi:10.1002/jqs.3256 .","code":""},{"path":[]},{"path":"https://packages.tesselle.org/ananke/reference/c14_ensemble.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Radiocarbon Event Count — c14_ensemble","text":"N. Frerebeau","code":""},{"path":"https://packages.tesselle.org/ananke/reference/c14_plot.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot Calibrated Radiocarbon Ages — c14_plot","title":"Plot Calibrated Radiocarbon Ages — c14_plot","text":"Plot Calibrated Radiocarbon Ages","code":""},{"path":"https://packages.tesselle.org/ananke/reference/c14_plot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot Calibrated Radiocarbon Ages — c14_plot","text":"","code":"# S4 method for 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 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,   ... )"},{"path":"https://packages.tesselle.org/ananke/reference/c14_plot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot Calibrated Radiocarbon Ages — c14_plot","text":"x CalibratedAges CalibratedSPD object. calendar TimeScale object specifying target calendar (see calendar()). density logical scalar: density drawn? interval logical scalar: highest density region drawn? level length-one numeric vector giving confidence level. used interval TRUE. sort logical scalar: data sorted? decreasing logical scalar: sort order decreasing? used sort TRUE. main character string giving main title plot. sub character string giving subtitle plot. axes logical scalar: axes drawn plot? frame.plot logical scalar: box drawn around plot? ann logical scalar: default annotation (title x y labels) appear plot? panel.first expression evaluated plot axes set plotting takes place. can useful drawing background grids. panel.last expression evaluated plotting taken place axes, title box added. col.density, col.interval specification plotting colors. ... graphical parameters may also passed arguments function.","code":""},{"path":"https://packages.tesselle.org/ananke/reference/c14_plot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot Calibrated Radiocarbon Ages — c14_plot","text":"plot() called side-effects: results graphic displayed. Invisibly returns x.","code":""},{"path":[]},{"path":"https://packages.tesselle.org/ananke/reference/c14_plot.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Plot Calibrated Radiocarbon Ages — c14_plot","text":"N. Frerebeau","code":""},{"path":"https://packages.tesselle.org/ananke/reference/c14_plot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot Calibrated Radiocarbon Ages — c14_plot","text":"","code":"## 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)   # \\donttest{ ## Out of 14C range? out <- c14_calibrate(130, 20) #> Warning: Date “X1” may extent out of range. plot(out) #> Warning: Date “X1” may extent out of range.  # }"},{"path":"https://packages.tesselle.org/ananke/reference/c14_spd.html","id":null,"dir":"Reference","previous_headings":"","what":"Summed Probability Distributions — c14_spd","title":"Summed Probability Distributions — c14_spd","text":"Computes summed probability distributions (SPD) radiocarbon dates.","code":""},{"path":"https://packages.tesselle.org/ananke/reference/c14_spd.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Summed Probability Distributions — c14_spd","text":"","code":"c14_spd(object, ...)  # S4 method for CalibratedAges c14_spd(object, normalize_date = FALSE, normalize_spd = FALSE)"},{"path":"https://packages.tesselle.org/ananke/reference/c14_spd.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Summed Probability Distributions — c14_spd","text":"object CalibratedAges object. ... Currently used. normalize_date logical scalar: total probability mass calibrated dates normalised (sum unity within time-span analysis)? normalize_spd logical scalar: total probability mass SPD normalised (sum unity)?","code":""},{"path":[]},{"path":"https://packages.tesselle.org/ananke/reference/c14_spd.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Summed Probability Distributions — c14_spd","text":"N. Frerebeau","code":""},{"path":"https://packages.tesselle.org/ananke/reference/c14_spd.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Summed Probability Distributions — c14_spd","text":"","code":"## 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) #> Warning: \"flip\" is not a graphical parameter #> Warning: \"flip\" is not a graphical parameter #> Warning: \"flip\" is not a graphical parameter #> Warning: \"flip\" is not a graphical parameter #> Warning: \"flip\" is not a graphical parameter #> Warning: \"flip\" is not a graphical parameter #> Warning: \"flip\" is not a graphical parameter #> Warning: \"flip\" is not a graphical parameter #> Warning: \"flip\" is not a graphical parameter #> Warning: \"flip\" is not a graphical parameter #> Warning: \"flip\" is not a graphical parameter #> Warning: \"flip\" is not a graphical parameter #> Warning: \"flip\" is not a graphical parameter #> Warning: \"flip\" is not a graphical parameter #> Warning: \"flip\" is not a graphical parameter #> Warning: \"flip\" is not a graphical parameter #> Warning: \"flip\" is not a graphical parameter #> Warning: \"flip\" is not a graphical parameter #> Warning: \"flip\" is not a graphical parameter #> Warning: \"flip\" is not a graphical parameter #> Warning: \"flip\" is not a graphical parameter #> Warning: \"flip\" is not a graphical parameter #> Warning: \"flip\" is not a graphical parameter #> Warning: \"flip\" is not a graphical parameter #> Warning: \"flip\" is not a graphical parameter #> Warning: \"flip\" is not a graphical parameter #> Warning: \"flip\" is not a graphical parameter #> Warning: \"flip\" is not a graphical parameter #> Warning: \"flip\" is not a graphical parameter #> Warning: \"flip\" is not a graphical parameter #> Warning: \"flip\" is not a graphical parameter #> Warning: \"flip\" is not a graphical parameter   ## SPD s <- c14_spd(cal) plot(s)"},{"path":"https://packages.tesselle.org/ananke/reference/c14_uncalibrate.html","id":null,"dir":"Reference","previous_headings":"","what":"Uncalibrate a Radiocarbon Date — c14_uncalibrate","title":"Uncalibrate a Radiocarbon Date — c14_uncalibrate","text":"Uncalibrate Radiocarbon Date","code":""},{"path":"https://packages.tesselle.org/ananke/reference/c14_uncalibrate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Uncalibrate a Radiocarbon Date — c14_uncalibrate","text":"","code":"c14_uncalibrate(object, ...)  # S4 method for numeric c14_uncalibrate(object, curves = \"intcal20\")  # S4 method for CalibratedAges c14_uncalibrate(object, ...)"},{"path":"https://packages.tesselle.org/ananke/reference/c14_uncalibrate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Uncalibrate a Radiocarbon Date — c14_uncalibrate","text":"object CalibratedAges object numeric vector calibrated ages (BP). ... Currently used. curves character vector specifying calibration curve used. Different curves can specified.","code":""},{"path":[]},{"path":"https://packages.tesselle.org/ananke/reference/c14_uncalibrate.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Uncalibrate a Radiocarbon Date — c14_uncalibrate","text":"N. Frerebeau","code":""},{"path":"https://packages.tesselle.org/ananke/reference/c14_uncalibrate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Uncalibrate a Radiocarbon Date — c14_uncalibrate","text":"","code":"if (FALSE) { ## Calibrate multiple dates cal <- c14_calibrate(   values = c(5000, 4500),   errors = c(45, 35),   names = c(\"X\", \"Y\") )  ## Uncalibrate c14_uncalibrate(cal) }"},{"path":"https://packages.tesselle.org/ananke/reference/data.frame.html","id":null,"dir":"Reference","previous_headings":"","what":"Coerce to a Data Frame — data.frame","title":"Coerce to a Data Frame — data.frame","text":"Coerce Data Frame","code":""},{"path":"https://packages.tesselle.org/ananke/reference/data.frame.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Coerce to a Data Frame — data.frame","text":"","code":"# S4 method for CalibratedAges as.data.frame(x, ..., calendar = getOption(\"ananke.calendar\"))  # S4 method for RECE as.data.frame(x, ..., calendar = getOption(\"ananke.calendar\"))  # S4 method for ProxyRecord as.data.frame(x, ..., calendar = getOption(\"ananke.calendar\"))"},{"path":"https://packages.tesselle.org/ananke/reference/data.frame.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Coerce to a Data Frame — data.frame","text":"x object. ... parameters passed data.frame(). calendar TimeScale object specifying target calendar (see calendar()). NULL, rata die returned.","code":""},{"path":"https://packages.tesselle.org/ananke/reference/data.frame.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Coerce to a Data Frame — data.frame","text":"data.frame extra time column.","code":""},{"path":[]},{"path":"https://packages.tesselle.org/ananke/reference/data.frame.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Coerce to a Data Frame — data.frame","text":"N. Frerebeau","code":""},{"path":"https://packages.tesselle.org/ananke/reference/data.frame.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Coerce to a Data Frame — data.frame","text":"","code":"## Calibrate multiple dates cal <- c14_calibrate(   values = c(5000, 4500),   errors = c(45, 35),   names = c(\"X\", \"Y\") )  head(as.data.frame(cal)) #>    time            X Y #> 1 -3984 1.110191e-06 0 #> 2 -3983 1.434164e-06 0 #> 3 -3982 1.845486e-06 0 #> 4 -3981 2.365558e-06 0 #> 5 -3980 3.020421e-06 0 #> 6 -3979 3.589420e-06 0 head(as.data.frame(cal, calendar = BP())) #>   time            X Y #> 1 5934 1.110191e-06 0 #> 2 5933 1.434164e-06 0 #> 3 5932 1.845486e-06 0 #> 4 5931 2.365558e-06 0 #> 5 5930 3.020421e-06 0 #> 6 5929 3.589420e-06 0 head(as.data.frame(cal, calendar = NULL)) #>       time            X Y #> 1 -1455491 1.110191e-06 0 #> 2 -1455125 1.434164e-06 0 #> 3 -1454760 1.845486e-06 0 #> 4 -1454395 2.365558e-06 0 #> 5 -1454030 3.020421e-06 0 #> 6 -1453664 3.589420e-06 0"},{"path":"https://packages.tesselle.org/ananke/reference/interval_hdr.html","id":null,"dir":"Reference","previous_headings":"","what":"Highest Density Regions — hdr","title":"Highest Density Regions — hdr","text":"Highest Density Regions","code":""},{"path":"https://packages.tesselle.org/ananke/reference/interval_hdr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Highest Density Regions — hdr","text":"","code":"# S4 method for CalibratedAges,missing interval_hdr(x, level = 0.954, calendar = getOption(\"ananke.calendar\"), ...)"},{"path":"https://packages.tesselle.org/ananke/reference/interval_hdr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Highest Density Regions — hdr","text":"x CalibratedAges object. level length-one numeric vector giving confidence level. calendar TimeScale object specifying target calendar (see calendar()). ... Currently used.","code":""},{"path":"https://packages.tesselle.org/ananke/reference/interval_hdr.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Highest Density Regions — hdr","text":"Returns list numeric  matrix.","code":""},{"path":"https://packages.tesselle.org/ananke/reference/interval_hdr.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Highest Density Regions — hdr","text":"Hyndman, R. J. (1996). Computing graphing highest density regions. American Statistician, 50: 120-126. doi:10.2307/2684423 .","code":""},{"path":[]},{"path":"https://packages.tesselle.org/ananke/reference/interval_hdr.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Highest Density Regions — hdr","text":"N. Frerebeau","code":""},{"path":"https://packages.tesselle.org/ananke/reference/interval_hdr.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Highest Density Regions — hdr","text":"","code":"## 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) #> $X #>      start   end    p #> [1,] -3911 -3876 0.15 #> [2,] -3802 -3706 0.50 #> [3,] -3669 -3659 0.04 #>  #> $Y #>      start   end    p #> [1,] -3336 -3310 0.11 #> [2,] -3297 -3283 0.06 #> [3,] -3272 -3267 0.02 #> [4,] -3240 -3207 0.14 #> [5,] -3194 -3103 0.37 #>  interval_hdr(cal, level = 0.954) #> $X #>      start   end    p #> [1,] -3944 -3855 0.29 #> [2,] -3844 -3833 0.02 #> [3,] -3818 -3653 0.65 #>  #> $Y #>      start   end    p #> [1,] -3355 -3091 0.94 #> [2,] -3050 -3040 0.01 #>  interval_hdr(cal, level = 0.997) #> $X #>      start   end p #> [1,] -3953 -3647 1 #>  #> $Y #>      start   end p #> [1,] -3366 -3014 1 #>"},{"path":"https://packages.tesselle.org/ananke/reference/ksarakil.html","id":null,"dir":"Reference","previous_headings":"","what":"Ksâr 'Akil Radiocarbon Dates — ksarakil","title":"Ksâr 'Akil Radiocarbon Dates — ksarakil","text":"Ksâr 'Akil Radiocarbon Dates","code":""},{"path":"https://packages.tesselle.org/ananke/reference/ksarakil.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Ksâr 'Akil Radiocarbon Dates — ksarakil","text":"","code":"ksarakil"},{"path":"https://packages.tesselle.org/ananke/reference/ksarakil.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Ksâr 'Akil Radiocarbon Dates — ksarakil","text":"data.frame 16 rows 5 variables: code Laboratory code. date Radiocarbon date (year BP). error Radiocarbon error (year). layer Stratigraphic layer. phase Chronological phase.","code":""},{"path":"https://packages.tesselle.org/ananke/reference/ksarakil.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Ksâr 'Akil Radiocarbon Dates — ksarakil","text":"Bosch, M. D., Mannino, M. ., Prendergast, . L., O'Connell, T. C., Demarchi, B., Taylor, S. M., Niven, L., van der Plicht, J. Hublin, J.-J. (2015). New Chronology Ksâr 'Akil (Lebanon) Supports Levantine Route Modern Human Dispersal Europe. Proceedings National Academy Sciences 112(25): 7683-8. doi:10.1073/pnas.1501529112 .","code":""},{"path":"https://packages.tesselle.org/ananke/reference/labels.html","id":null,"dir":"Reference","previous_headings":"","what":"Find Labels from Object — labels","title":"Find Labels from Object — labels","text":"Find suitable set labels object use printing plotting, example.","code":""},{"path":"https://packages.tesselle.org/ananke/reference/labels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Find Labels from Object — labels","text":"","code":"# S4 method for CalibratedAges labels(object, ...)"},{"path":"https://packages.tesselle.org/ananke/reference/labels.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Find Labels from Object — labels","text":"object object find labels. ... Currently used.","code":""},{"path":"https://packages.tesselle.org/ananke/reference/labels.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Find Labels from Object — labels","text":"character vector.","code":""},{"path":[]},{"path":"https://packages.tesselle.org/ananke/reference/labels.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Find Labels from Object — labels","text":"N. Frerebeau","code":""},{"path":"https://packages.tesselle.org/ananke/reference/mean.html","id":null,"dir":"Reference","previous_headings":"","what":"Mean — mean","title":"Mean — mean","text":"Mean","code":""},{"path":"https://packages.tesselle.org/ananke/reference/mean.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Mean — mean","text":"","code":"# S4 method for CalibratedAges mean(x, na.rm = FALSE, ..., calendar = getOption(\"ananke.calendar\"))  # S4 method for ProxyRecord mean(x, na.rm = FALSE, ...)"},{"path":"https://packages.tesselle.org/ananke/reference/mean.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Mean — mean","text":"x CalibratedAges object. na.rm logical scalar: NA values stripped computation proceeds? ... Currently used. calendar TimeScale object specifying target calendar (see calendar()).","code":""},{"path":"https://packages.tesselle.org/ananke/reference/mean.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Mean — mean","text":"numeric vector.","code":""},{"path":[]},{"path":"https://packages.tesselle.org/ananke/reference/mean.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Mean — mean","text":"N. Frerebeau","code":""},{"path":"https://packages.tesselle.org/ananke/reference/mean.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Mean — mean","text":"","code":"## Calibrate multiple dates cal <- c14_calibrate(   values = c(5000, 4500),   errors = c(45, 35),   names = c(\"X\", \"Y\") )  ## Statistics quantile(cal) #>      0%   25%   50%   75%  100% #> X -3984 -3876 -3778 -3729 -3545 #> Y -3984 -3283 -3211 -3145 -2917 median(cal) #>     X     Y  #> -3778 -3211  mean(cal) #>         X         Y  #> -3792.679 -3211.160   ## 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\")"},{"path":"https://packages.tesselle.org/ananke/reference/median.html","id":null,"dir":"Reference","previous_headings":"","what":"Median — median","title":"Median — median","text":"Median","code":""},{"path":"https://packages.tesselle.org/ananke/reference/median.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Median — median","text":"","code":"# S4 method for CalibratedAges median(x, na.rm = FALSE, ..., calendar = getOption(\"ananke.calendar\"))"},{"path":"https://packages.tesselle.org/ananke/reference/median.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Median — median","text":"x CalibratedAges object. na.rm logical scalar: NA values stripped computation proceeds? ... Currently used. calendar TimeScale object specifying target calendar (see calendar()).","code":""},{"path":"https://packages.tesselle.org/ananke/reference/median.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Median — median","text":"numeric vector.","code":""},{"path":[]},{"path":"https://packages.tesselle.org/ananke/reference/median.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Median — median","text":"N. Frerebeau","code":""},{"path":"https://packages.tesselle.org/ananke/reference/median.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Median — median","text":"","code":"## Calibrate multiple dates cal <- c14_calibrate(   values = c(5000, 4500),   errors = c(45, 35),   names = c(\"X\", \"Y\") )  ## Statistics quantile(cal) #>      0%   25%   50%   75%  100% #> X -3984 -3876 -3778 -3729 -3545 #> Y -3984 -3283 -3211 -3145 -2917 median(cal) #>     X     Y  #> -3778 -3211  mean(cal) #>         X         Y  #> -3792.679 -3211.160   ## 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\")"},{"path":"https://packages.tesselle.org/ananke/reference/mutators.html","id":null,"dir":"Reference","previous_headings":"","what":"Get or Set Parts of an Object — mutators","title":"Get or Set Parts of an Object — mutators","text":"Getters setters extract replace parts object.","code":""},{"path":"https://packages.tesselle.org/ananke/reference/mutators.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get or Set Parts of an Object — mutators","text":"x object get set element(s). value possible value element(s) x.","code":""},{"path":"https://packages.tesselle.org/ananke/reference/mutators.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get or Set Parts of an Object — mutators","text":"object sort x new values assigned.","code":""},{"path":[]},{"path":"https://packages.tesselle.org/ananke/reference/mutators.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Get or Set Parts of an Object — mutators","text":"N. Frerebeau","code":""},{"path":"https://packages.tesselle.org/ananke/reference/pb_age.html","id":null,"dir":"Reference","previous_headings":"","what":"Geological Model Age from Lead Isotope Analysis — pb_age","title":"Geological Model Age from Lead Isotope Analysis — pb_age","text":"Compute geological model age (T) U/Pb (mu) Th/U (kappa) ratios lead isotopic measurements.","code":""},{"path":"https://packages.tesselle.org/ananke/reference/pb_age.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Geological Model Age from Lead Isotope Analysis — pb_age","text":"","code":"pb_age(x, y, z, ...)  # S4 method for 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 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) )"},{"path":"https://packages.tesselle.org/ananke/reference/pb_age.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Geological Model Age from Lead Isotope Analysis — pb_age","text":"x numeric vector 206Pb/204Pb ratios. y z missing, must list (data.frame) numeric components (columns) x, y z. y numeric vector 207Pb/204Pb ratios.  missing, attempt made interpret x suitable way. z numeric vector 208Pb/204Pb ratios.  missing, attempt made interpret x suitable way. ... Currently used. t0 numeric value giving time second stage reference model. x_star numeric value giving 206Pb/204Pb ratio \\(t = 0\\). y_star numeric value giving 207Pb/204Pb ratio \\(t = 0\\). z_star numeric value giving 208Pb/204Pb ratio \\(t = 0\\). mu numeric value giving 238U/204Pb ratio reference model. kappa numeric value giving 232Th/238U ratio reference model. th232 numeric value giving decay constants 232Th. u238 numeric value giving decay constants 238U. u235 numeric value giving decay constants 235U. u238_235 numeric value giving 238U/235U ratio. tolerance numeric value specifying tolerance (stopping criteria Newton–Raphson method).","code":""},{"path":"https://packages.tesselle.org/ananke/reference/pb_age.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Geological Model Age from Lead Isotope Analysis — pb_age","text":"four columns data.frame:","code":""},{"path":"https://packages.tesselle.org/ananke/reference/pb_age.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Geological Model Age from Lead Isotope Analysis — pb_age","text":"Reference values Albarede & Juteau (1984).","code":""},{"path":"https://packages.tesselle.org/ananke/reference/pb_age.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Geological Model Age from Lead Isotope Analysis — pb_age","text":"Albarède, F., Desaulty, .-M. & Blichert-Toft, J. (2012). Geological Perspective Use Pb Isotopes Archaeometry. Archaeometry, 54: 853-867. doi:10.1111/j.1475-4754.2011.00653.x . Albarède, F. & Juteau, M. (1984). Unscrambling Lead Model Ages. Geochimica et Cosmochimica Acta, 48(1): 207-12. doi:10.1016/0016-7037(84)90364-8 .","code":""},{"path":"https://packages.tesselle.org/ananke/reference/pb_age.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Geological Model Age from Lead Isotope Analysis — pb_age","text":"N. Frerebeau, F. Albarede (original Matlab code)","code":""},{"path":"https://packages.tesselle.org/ananke/reference/pb_age.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Geological Model Age from Lead Isotope Analysis — pb_age","text":"","code":"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 )  pb_age(Pb) #>        age       mu    kappa            f #> 1 428.3959 9.859142 4.074891 1.004859e-14 #> 2 430.9796 9.860659 4.076292 1.004859e-14 #> 3 427.6003 9.855397 4.075178 1.004859e-14"},{"path":"https://packages.tesselle.org/ananke/reference/proxy_ensemble.html","id":null,"dir":"Reference","previous_headings":"","what":"Layer-Counted Proxy Records Uncertainties — proxy_ensemble","title":"Layer-Counted Proxy Records Uncertainties — proxy_ensemble","text":"Represents layer-counted proxy records sequences probability distributions absolute, error-free time axes.","code":""},{"path":"https://packages.tesselle.org/ananke/reference/proxy_ensemble.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Layer-Counted Proxy Records Uncertainties — proxy_ensemble","text":"","code":"proxy_ensemble(depth, ...)  # S4 method for 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\") )"},{"path":"https://packages.tesselle.org/ananke/reference/proxy_ensemble.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Layer-Counted Proxy Records Uncertainties — proxy_ensemble","text":"depth positive numeric vector giving depth proxy values calendar ages measured. must decreasing order (.e. chronological order). ... Currently used. proxy numeric vector giving proxy values. proxy_error numeric vector giving proxy uncertainties. step length-one numeric vector specifying step size (units proxy) proxy records densities estimated. time numeric vector giving calendar ages (years). time_error numeric vector giving calendar age uncertainties (years). calendar TimeScale object specifying calendar time (see calendar()). length-one numeric vector specifying starting value temporal sequence densities estimated (years). length-one numeric vector specifying end value temporal sequence densities estimated (cal BP years). length-one numeric vector specifying increment temporal sequence densities estimated (years). n integer specifying number item choose randomly. progress logical scalar: progress bar displayed? verbose logical scalar: extra information reported?","code":""},{"path":"https://packages.tesselle.org/ananke/reference/proxy_ensemble.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Layer-Counted Proxy Records Uncertainties — proxy_ensemble","text":"ProxyRecord object.","code":""},{"path":"https://packages.tesselle.org/ananke/reference/proxy_ensemble.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Layer-Counted Proxy Records Uncertainties — proxy_ensemble","text":"Boers, N., Goswami, B. & Ghil, M. (2017). Complete Representation Uncertainties Layer-Counted Paleoclimatic Archives. Climate Past, 13(9): 1169-1180. doi:10.5194/cp-13-1169-2017 .","code":""},{"path":[]},{"path":"https://packages.tesselle.org/ananke/reference/proxy_ensemble.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Layer-Counted Proxy Records Uncertainties — proxy_ensemble","text":"N. Frerebeau","code":""},{"path":"https://packages.tesselle.org/ananke/reference/proxy_ensemble.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Layer-Counted Proxy Records Uncertainties — proxy_ensemble","text":"","code":"if (FALSE) { ## 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) }"},{"path":"https://packages.tesselle.org/ananke/reference/proxy_plot.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot Layer-Counted Proxy Records Uncertainties — proxy_plot","title":"Plot Layer-Counted Proxy Records Uncertainties — proxy_plot","text":"Plot Layer-Counted Proxy Records Uncertainties","code":""},{"path":"https://packages.tesselle.org/ananke/reference/proxy_plot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot Layer-Counted Proxy Records Uncertainties — proxy_plot","text":"","code":"# S4 method for 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,   ... )"},{"path":"https://packages.tesselle.org/ananke/reference/proxy_plot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot Layer-Counted Proxy Records Uncertainties — proxy_plot","text":"x ProxyRecord object. calendar TimeScale object specifying target calendar (see calendar()). iqr logical scalar: mean IQR displayed? xlab, ylab character string giving label x y axis. col list colors generated grDevices::hcl.colors(). col.mean, col.iqr specification line colors. used iqr TRUE. lty.mean, lty.iqr specification line types. used iqr TRUE. lwd.mean, lwd.iqr specification line widths. used iqr TRUE. ... parameters passed graphics::image().","code":""},{"path":"https://packages.tesselle.org/ananke/reference/proxy_plot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot Layer-Counted Proxy Records Uncertainties — proxy_plot","text":"plot() called side-effects: results graphic displayed. Invisibly returns x.","code":""},{"path":[]},{"path":"https://packages.tesselle.org/ananke/reference/proxy_plot.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Plot Layer-Counted Proxy Records Uncertainties — proxy_plot","text":"N. Frerebeau","code":""},{"path":"https://packages.tesselle.org/ananke/reference/proxy_plot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot Layer-Counted Proxy Records Uncertainties — proxy_plot","text":"","code":"if (FALSE) { ## 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) }"},{"path":"https://packages.tesselle.org/ananke/reference/quantile.html","id":null,"dir":"Reference","previous_headings":"","what":"Quantiles of a Density Estimate — quantile","title":"Quantiles of a Density Estimate — quantile","text":"Quantiles Density Estimate","code":""},{"path":"https://packages.tesselle.org/ananke/reference/quantile.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Quantiles of a Density Estimate — quantile","text":"","code":"# S4 method for CalibratedAges quantile(   x,   probs = seq(0, 1, 0.25),   na.rm = FALSE,   ...,   calendar = getOption(\"ananke.calendar\") )  # S4 method for ProxyRecord quantile(x, probs = seq(0, 1, 0.25), na.rm = FALSE, ...)"},{"path":"https://packages.tesselle.org/ananke/reference/quantile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Quantiles of a Density Estimate — quantile","text":"x CalibratedAges object. probs numeric vector probabilities values \\([0,1]\\). na.rm logical scalar: NA values stripped computation proceeds? ... Currently used. calendar TimeScale object specifying target calendar (see calendar()).","code":""},{"path":"https://packages.tesselle.org/ananke/reference/quantile.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Quantiles of a Density Estimate — quantile","text":"numeric  matrix containing quantiles.","code":""},{"path":[]},{"path":"https://packages.tesselle.org/ananke/reference/quantile.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Quantiles of a Density Estimate — quantile","text":"N. Frerebeau","code":""},{"path":"https://packages.tesselle.org/ananke/reference/quantile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Quantiles of a Density Estimate — quantile","text":"","code":"## Calibrate multiple dates cal <- c14_calibrate(   values = c(5000, 4500),   errors = c(45, 35),   names = c(\"X\", \"Y\") )  ## Statistics quantile(cal) #>      0%   25%   50%   75%  100% #> X -3984 -3876 -3778 -3729 -3545 #> Y -3984 -3283 -3211 -3145 -2917 median(cal) #>     X     Y  #> -3778 -3211  mean(cal) #>         X         Y  #> -3792.679 -3211.160   ## 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\")"},{"path":"https://packages.tesselle.org/ananke/reference/rec_plot.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot a Radiocarbon Event Count Ensemble — rec_plot","title":"Plot a Radiocarbon Event Count Ensemble — rec_plot","text":"Plot Radiocarbon Event Count Ensemble","code":""},{"path":"https://packages.tesselle.org/ananke/reference/rec_plot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot a Radiocarbon Event Count Ensemble — rec_plot","text":"","code":"# S4 method for RECE,missing plot(x, calendar = getOption(\"ananke.calendar\"), ...)"},{"path":"https://packages.tesselle.org/ananke/reference/rec_plot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot a Radiocarbon Event Count Ensemble — rec_plot","text":"x RECE object. calendar TimeScale object specifying target calendar (see calendar()). ... parameters passed graphics::image().","code":""},{"path":"https://packages.tesselle.org/ananke/reference/rec_plot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot a Radiocarbon Event Count Ensemble — rec_plot","text":"image() called side-effects: results graphic displayed (invisibly returns x).","code":""},{"path":"https://packages.tesselle.org/ananke/reference/rec_plot.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Plot a Radiocarbon Event Count Ensemble — rec_plot","text":"Carleton, W. C. (2021). Evaluating Bayesian Radiocarbon‐dated Event Count (REC) Models Study Long‐term Human Environmental Processes. Journal Quaternary Science, 36(1): 110‑23. doi:10.1002/jqs.3256 .","code":""},{"path":[]},{"path":"https://packages.tesselle.org/ananke/reference/rec_plot.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Plot a Radiocarbon Event Count Ensemble — rec_plot","text":"N. Frerebeau","code":""},{"path":"https://packages.tesselle.org/ananke/reference/reexports.html","id":null,"dir":"Reference","previous_headings":"","what":"Objects exported from other packages — reexports","title":"Objects exported from other packages — reexports","text":"objects imported packages. Follow links see documentation. aion AD, BC, BCE, BP, CE, b2k, calendar, image, plot, start, start, time, year_axis arkhe interval_hdr","code":""},{"path":"https://packages.tesselle.org/ananke/reference/subset.html","id":null,"dir":"Reference","previous_headings":"","what":"Extract or Replace Parts of an Object — subset","title":"Extract or Replace Parts of an Object — subset","text":"Operators acting objects extract replace parts.","code":""},{"path":"https://packages.tesselle.org/ananke/reference/subset.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extract or Replace Parts of an Object — subset","text":"","code":"# S4 method for CalibratedAges [(x, i, j, k, drop = FALSE)"},{"path":"https://packages.tesselle.org/ananke/reference/subset.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extract or Replace Parts of an Object — subset","text":"x object extract element(s) replace element(s). , j, k Indices specifying elements extract replace. drop logical scalar: result coerced lowest possible dimension? works extracting elements, replacement.","code":""},{"path":"https://packages.tesselle.org/ananke/reference/subset.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extract or Replace Parts of an Object — subset","text":"subsetted object.","code":""},{"path":[]},{"path":"https://packages.tesselle.org/ananke/reference/subset.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Extract or Replace Parts of an Object — subset","text":"N. Frerebeau","code":""}]
+[{"path":[]},{"path":"https://packages.tesselle.org/ananke/index.html","id":"overview","dir":"","previous_headings":"","what":"Overview","title":"Quantitative Chronology in Archaeology","text":"ananke provides functions radiocarbon calibration chronological analysis.","code":""},{"path":"https://packages.tesselle.org/ananke/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Quantitative Chronology in Archaeology","text":"can install released version ananke CRAN : development version GitHub :","code":"install.packages(\"ananke\") # install.packages(\"remotes\") remotes::install_github(\"tesselle/ananke\")"},{"path":"https://packages.tesselle.org/ananke/index.html","id":"usage","dir":"","previous_headings":"","what":"Usage","title":"Quantitative Chronology in Archaeology","text":"","code":"## Load packages library(ananke) ## Data from Bosch et al. 2015 data(\"ksarakil\")  ## Calibrate multiple dates 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 plot(cal) plot(cal, density = FALSE, level = 0.95, lwd = 5)"},{"path":"https://packages.tesselle.org/ananke/index.html","id":"contributing","dir":"","previous_headings":"","what":"Contributing","title":"Quantitative Chronology in Archaeology","text":"Please note ananke project released Contributor Code Conduct. contributing project, agree abide terms.","code":""},{"path":[]},{"path":[]},{"path":[]},{"path":"https://packages.tesselle.org/ananke/reference/CalibratedAges-class.html","id":null,"dir":"Reference","previous_headings":"","what":"Calibrated Radiocarbon Ages — CalibratedAges-class","title":"Calibrated Radiocarbon Ages — CalibratedAges-class","text":"S4 class represent calibrated radiocarbon ages.","code":""},{"path":"https://packages.tesselle.org/ananke/reference/CalibratedAges-class.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calibrated Radiocarbon Ages — CalibratedAges-class","text":"values numeric vector giving BP ages F14C values calibrated. errors numeric vector giving standard deviation values calibrated. curves character vector specifying calibration curves used.","code":""},{"path":"https://packages.tesselle.org/ananke/reference/CalibratedAges-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"Calibrated Radiocarbon Ages — CalibratedAges-class","text":"F14C logical scalar: values F14C instead radiocarbon ages? status integer vector specifying calibration status. must one \"0\" (OK), \"1\" (calibration range) \"2\" (may extend calibration range).","code":""},{"path":"https://packages.tesselle.org/ananke/reference/CalibratedAges-class.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Calibrated Radiocarbon Ages — CalibratedAges-class","text":"class inherits TimeSeries.","code":""},{"path":[]},{"path":"https://packages.tesselle.org/ananke/reference/CalibratedAges-class.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calibrated Radiocarbon Ages — CalibratedAges-class","text":"N. Frerebeau","code":""},{"path":"https://packages.tesselle.org/ananke/reference/CalibratedSPD-class.html","id":null,"dir":"Reference","previous_headings":"","what":"Calibrated SPD — CalibratedSPD-class","title":"Calibrated SPD — CalibratedSPD-class","text":"S4 class represent summed probability distributions (SPD) radiocarbon dates.","code":""},{"path":"https://packages.tesselle.org/ananke/reference/CalibratedSPD-class.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Calibrated SPD — CalibratedSPD-class","text":"class inherits TimeSeries.","code":""},{"path":[]},{"path":"https://packages.tesselle.org/ananke/reference/CalibratedSPD-class.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calibrated SPD — CalibratedSPD-class","text":"N. Frerebeau","code":""},{"path":"https://packages.tesselle.org/ananke/reference/F14C.html","id":null,"dir":"Reference","previous_headings":"","what":"F14C — F14C","title":"F14C — F14C","text":"Converts F14C values 14C ages.","code":""},{"path":"https://packages.tesselle.org/ananke/reference/F14C.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"F14C — F14C","text":"","code":"BP14C_to_F14C(ages, errors, ...)  F14C_to_BP14C(values, errors, ...)  # S4 method for numeric,numeric BP14C_to_F14C(ages, errors, lambda = 8033)  # S4 method for numeric,numeric F14C_to_BP14C(values, errors, lambda = 8033, asymmetric = FALSE)"},{"path":"https://packages.tesselle.org/ananke/reference/F14C.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"F14C — F14C","text":"ages numeric vector giving radiocarbon ages. errors numeric vector giving standard deviations. ... Currently used. values numeric vector giving F14C values. lambda length-one numeric vector specifying mean-life radiocarbon (defaults 14C half-life value introduced Libby 1952). asymmetric logical scalar: asymmetric 14C errors returned?","code":""},{"path":"https://packages.tesselle.org/ananke/reference/F14C.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"F14C — F14C","text":"data.frame.","code":""},{"path":"https://packages.tesselle.org/ananke/reference/F14C.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"F14C — F14C","text":"Bronk Ramsey, C. (2008). Radiocarbon Dating: Revolutions Understanding. Archaeometry, 50:249-275. doi:10.1111/j.1475-4754.2008.00394.x . van der Plicht, J., Hogg, . (2006). Note Reporting Radiocarbon. Quaternary Geochronology, 1(4): 237-240. doi:10.1016/j.quageo.2006.07.001 .","code":""},{"path":[]},{"path":"https://packages.tesselle.org/ananke/reference/F14C.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"F14C — F14C","text":"N. Frerebeau","code":""},{"path":"https://packages.tesselle.org/ananke/reference/F14C.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"F14C — F14C","text":"","code":"## Asymmetric 14C errors (van der Plicht and Hogg 2006) F14C_to_BP14C(0.0052, 0.0006, asym = TRUE) #>        age     plus    minus #> 1 42246.32 984.8645 877.1979  ## Symmetric 14C errors (Bronk Ramsey 2008) F14C_to_BP14C(0.0052, 0.0006, asym = FALSE) #>        age     plus    minus #> 1 42246.32 926.8846 926.8846"},{"path":"https://packages.tesselle.org/ananke/reference/ProxyRecord-class.html","id":null,"dir":"Reference","previous_headings":"","what":"Proxy Record — ProxyRecord-class","title":"Proxy Record — ProxyRecord-class","text":"S4 class store proxy records.","code":""},{"path":"https://packages.tesselle.org/ananke/reference/ProxyRecord-class.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Proxy Record — ProxyRecord-class","text":"class inherits TimeSeries.","code":""},{"path":[]},{"path":"https://packages.tesselle.org/ananke/reference/ProxyRecord-class.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Proxy Record — ProxyRecord-class","text":"N. Frerebeau","code":""},{"path":"https://packages.tesselle.org/ananke/reference/RECE-class.html","id":null,"dir":"Reference","previous_headings":"","what":"Radiocarbon Event Count Ensemble — RECE-class","title":"Radiocarbon Event Count Ensemble — RECE-class","text":"S4 class represent radiocarbon event count ensemble.","code":""},{"path":"https://packages.tesselle.org/ananke/reference/RECE-class.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Radiocarbon Event Count Ensemble — RECE-class","text":"class inherits TimeSeries.","code":""},{"path":[]},{"path":"https://packages.tesselle.org/ananke/reference/RECE-class.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Radiocarbon Event Count Ensemble — RECE-class","text":"N. Frerebeau","code":""},{"path":"https://packages.tesselle.org/ananke/reference/ananke-package.html","id":null,"dir":"Reference","previous_headings":"","what":"ananke: Quantitative Chronology in Archaeology — ananke-package","title":"ananke: Quantitative Chronology in Archaeology — ananke-package","text":"package (one paragraph).","code":""},{"path":[]},{"path":"https://packages.tesselle.org/ananke/reference/ananke-package.html","id":"package-options","dir":"Reference","previous_headings":"","what":"Package options","title":"ananke: Quantitative Chronology in Archaeology — ananke-package","text":"ananke uses following options() configure behavior: ananke.calendar: TimeScale object (default calendar printing). ananke.grid: numeric value specifying number equally spaced points densities estimated (defaults \\(512\\)). power \\(2\\). ananke.progress: logical scalar. progress bars displayed? ananke.verbose: logical scalar. R report extra information progress? Defaults TRUE.","code":""},{"path":[]},{"path":"https://packages.tesselle.org/ananke/reference/ananke-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"ananke: Quantitative Chronology in Archaeology — ananke-package","text":"Full list authors contributors (alphabetic order): Package maintainer Nicolas Frerebeaunicolas.frerebeau@u-bordeaux-montaigne.fr Archéosciences Bordeaux (UMR 6034) Maison de l'Archéologie Université Bordeaux Montaigne F-33607 Pessac cedex France","code":""},{"path":"https://packages.tesselle.org/ananke/reference/c14_calibrate.html","id":null,"dir":"Reference","previous_headings":"","what":"14C Calibration — c14_calibrate","title":"14C Calibration — c14_calibrate","text":"Calibrates radiocarbon dates.","code":""},{"path":"https://packages.tesselle.org/ananke/reference/c14_calibrate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"14C Calibration — c14_calibrate","text":"","code":"c14_calibrate(values, errors, ...)  # S4 method for 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 )"},{"path":"https://packages.tesselle.org/ananke/reference/c14_calibrate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"14C Calibration — c14_calibrate","text":"values numeric vector giving BP ages F14C values calibrated. errors numeric vector giving standard deviation values calibrated. ... Currently used. names character vector specifying names samples (e.g. laboratory codes). curves character vector specifying calibration curve used. Different curves can specified per sample. reservoir_offsets numeric vector giving offset values marine reservoir effect (defaults 0; .e. offset). reservoir_errors numeric vector giving offset value errors marine reservoir effect (defaults 0; .e. offset). length-one numeric vector specifying earliest data calibrate , cal. BP years. length-one numeric vector specifying latest data calibrate , cal. BP years. resolution length-one numeric vector specifying temporal resolution (years) calibration. normalize logical scalar: calibration normalized? F14C logical scalar: calibration carried F14C space? TRUE, values must expressed F14C. drop logical scalar: years zero probability discarded? TRUE (default), results narrower time range. eps length-one numeric value giving cutoff calibration values removed.","code":""},{"path":"https://packages.tesselle.org/ananke/reference/c14_calibrate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"14C Calibration — c14_calibrate","text":"CalibratedAges object.","code":""},{"path":"https://packages.tesselle.org/ananke/reference/c14_calibrate.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"14C Calibration — c14_calibrate","text":"Adapted Bchron::BchronCalibrate() Andrew Parnell rcarbon::calibrate() Andrew Bevan Enrico Crema.","code":""},{"path":"https://packages.tesselle.org/ananke/reference/c14_calibrate.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"14C Calibration — c14_calibrate","text":"Bronk Ramsey, C. (2008). Radiocarbon Dating: Revolutions Understanding. Archaeometry, 50:249-275. doi:10.1111/j.1475-4754.2008.00394.x .","code":""},{"path":[]},{"path":"https://packages.tesselle.org/ananke/reference/c14_calibrate.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"14C Calibration — c14_calibrate","text":"N. Frerebeau","code":""},{"path":"https://packages.tesselle.org/ananke/reference/c14_calibrate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"14C Calibration — c14_calibrate","text":"","code":"## 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)   # \\donttest{ ## Out of 14C range? out <- c14_calibrate(130, 20) #> Warning: Date “X1” may extent out of range. plot(out) #> Warning: Date “X1” may extent out of range.  # }"},{"path":"https://packages.tesselle.org/ananke/reference/c14_combine.html","id":null,"dir":"Reference","previous_headings":"","what":"Combine 14C — c14_combine","title":"Combine 14C — c14_combine","text":"Combines radiocarbon dates.","code":""},{"path":"https://packages.tesselle.org/ananke/reference/c14_combine.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Combine 14C — c14_combine","text":"","code":"c14_combine(ages, errors, ...)  # S4 method for numeric,numeric c14_combine(ages, errors, groups = NULL)"},{"path":"https://packages.tesselle.org/ananke/reference/c14_combine.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Combine 14C — c14_combine","text":"ages numeric vector giving BP ages calibrated. errors numeric vector giving standard deviation ages calibrated. ... Currently used. groups factor sense .factor(groups) defines groups combine . NULL (default), dates combined. NAs treated isolated dates.","code":""},{"path":"https://packages.tesselle.org/ananke/reference/c14_combine.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Combine 14C — c14_combine","text":"data.frame following columns:","code":""},{"path":"https://packages.tesselle.org/ananke/reference/c14_combine.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Combine 14C — c14_combine","text":"Ward, G. K. Wilson, S. R. (1978). Procedures Comparing Combining Radiocarbon Age Determinations: Critique. Archaeometry 20(1): 19‑31. doi:10.1111/j.1475-4754.1978.tb00208.x .","code":""},{"path":[]},{"path":"https://packages.tesselle.org/ananke/reference/c14_combine.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Combine 14C — c14_combine","text":"N. Frerebeau","code":""},{"path":"https://packages.tesselle.org/ananke/reference/c14_combine.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Combine 14C — c14_combine","text":"","code":"## 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 ) #>   groups     ages  errors     chi2         p #> 1 W-1571 14650.00 500.000       NA        NA #> 2  ANU-5 11700.00 260.000       NA        NA #> 3  C-800 10860.00 410.000       NA        NA #> 4 L-698D 11840.00 100.000       NA        NA #> 5  FSU-3 11245.00 450.000       NA        NA #> 6  Tx-44 10700.00 210.000       NA        NA #> 7  ANU-7 14253.17 190.325 6.157902 0.1041756"},{"path":"https://packages.tesselle.org/ananke/reference/c14_curve.html","id":null,"dir":"Reference","previous_headings":"","what":"14C Calibration Curve — c14_curve","title":"14C Calibration Curve — c14_curve","text":"14C Calibration Curve","code":""},{"path":"https://packages.tesselle.org/ananke/reference/c14_curve.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"14C Calibration Curve — c14_curve","text":"","code":"c14_curve(name, ...)  # S4 method for character c14_curve(name)  # S4 method for CalibratedAges c14_curve(name)"},{"path":"https://packages.tesselle.org/ananke/reference/c14_curve.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"14C Calibration Curve — c14_curve","text":"name character vector naming calibration curves (see details). ... Currently used.","code":""},{"path":"https://packages.tesselle.org/ananke/reference/c14_curve.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"14C Calibration Curve — c14_curve","text":"list three-column data.frame:","code":""},{"path":"https://packages.tesselle.org/ananke/reference/c14_curve.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"14C Calibration Curve — c14_curve","text":"following calibration curves available:","code":""},{"path":"https://packages.tesselle.org/ananke/reference/c14_curve.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"14C Calibration Curve — c14_curve","text":"Heaton, Timothy J, Peter Köhler, Martin Butzin, Edouard Bard, Ron W Reimer, William E N Austin, Christopher Bronk Ramsey, et al. (2020). Marine20 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, Mike Barbetti (2004). Review Tropospheric Bomb 14C Data Carbon Cycle Modeling Age Calibration Purposes. Radiocarbon, 46(3): 1273-1298. doi:10.1017/S0033822200033142 . Hua, Quan, Mike Barbetti, Andrzej Z Rakowski (2013). Atmospheric Radiocarbon 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 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, J. Turnbull (2004). 14C Activity Global Carbon Cycle Changes Past 50,000 Years. Science, 303(5655): 202‑207. doi:10.1126/science.1090300 . Hughen, Konrad , 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, John Harte (2004). Dead Wood Biomass Turnover Time, Measured Radiocarbon, along Subalpine Elevation Gradient. Oecologia, 141(4): 641‑651. doi:10.1007/s00442-004-1689-x . McCormac, F G, G Hogg, P G Blackwell, C E Buck, T F G Higham, 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, Bayliss, J W Beck, P G Blackwell, C Bronk Ramsey, et al. (2009). IntCal09 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). 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 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 . Hughen, Bernd Kromer, Gerry McCormac, Johannes van der Plicht, 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, Thomas F. Braziunas. (1998). High-Precision Radiocarbon Age Calibration Terrestrial Marine Samples. Radiocarbon, 40(3): 1127‑1151. doi:10.1017/S0033822200019172 .","code":""},{"path":[]},{"path":"https://packages.tesselle.org/ananke/reference/c14_curve.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"14C Calibration Curve — c14_curve","text":"N. Frerebeau","code":""},{"path":"https://packages.tesselle.org/ananke/reference/c14_curve.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"14C Calibration Curve — c14_curve","text":"","code":"## IntCal20 intcal20 <- c14_curve(\"intcal20\") head(intcal20[[1]]) #>   CALBP   AGE ERROR #> 1 55000 50100  1024 #> 2 54980 50081  1018 #> 3 54960 50063  1013 #> 4 54940 50043  1007 #> 5 54920 50027  1003 #> 6 54900 50009   997  ## IntCal intcal <- c14_curve(c(\"intcal09\", \"intcal13\", \"intcal20\")) lapply(X = intcal, FUN = head) #> $intcal09 #>   CALBP   AGE ERROR #> 1 50000 46400   415 #> 2 49900 46316   410 #> 3 49800 46229   403 #> 4 49700 46135   396 #> 5 49600 46036   389 #> 6 49500 45933   380 #>  #> $intcal13 #>   CALBP   AGE ERROR #> 1 50000 46401   274 #> 2 49980 46381   273 #> 3 49960 46362   271 #> 4 49940 46343   270 #> 5 49920 46324   269 #> 6 49900 46305   268 #>  #> $intcal20 #>   CALBP   AGE ERROR #> 1 55000 50100  1024 #> 2 54980 50081  1018 #> 3 54960 50063  1013 #> 4 54940 50043  1007 #> 5 54920 50027  1003 #> 6 54900 50009   997 #>"},{"path":"https://packages.tesselle.org/ananke/reference/c14_ensemble.html","id":null,"dir":"Reference","previous_headings":"","what":"Radiocarbon Event Count — c14_ensemble","title":"Radiocarbon Event Count — c14_ensemble","text":"Radiocarbon Event Count","code":""},{"path":"https://packages.tesselle.org/ananke/reference/c14_ensemble.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Radiocarbon Event Count — c14_ensemble","text":"","code":"c14_ensemble(object, ...)  # S4 method for CalibratedAges c14_ensemble(   object,   from = NULL,   to = NULL,   by = 10,   n = 100,   calendar = BP(),   progress = getOption(\"ananke.progress\") )"},{"path":"https://packages.tesselle.org/ananke/reference/c14_ensemble.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Radiocarbon Event Count — c14_ensemble","text":"object CalibratedAges object. ... Currently used. length-one numeric vector specifying earliest data calibrate (cal BP years). length-one numeric vector specifying latest data calibrate (cal BP years). length-one numeric vector specifying temporal resolution (years) calibration. n integer specifying number item choose randomly. calendar TimeScale object specifying calendar (see calendar()). Defaults CE(). progress logical scalar: progress bar displayed?","code":""},{"path":"https://packages.tesselle.org/ananke/reference/c14_ensemble.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Radiocarbon Event Count — c14_ensemble","text":"RECE object.","code":""},{"path":"https://packages.tesselle.org/ananke/reference/c14_ensemble.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Radiocarbon Event Count — c14_ensemble","text":"Carleton, W. C. (2021). Evaluating Bayesian Radiocarbon‐dated Event Count (REC) Models Study Long‐term Human Environmental Processes. Journal Quaternary Science, 36(1): 110‑23. doi:10.1002/jqs.3256 .","code":""},{"path":[]},{"path":"https://packages.tesselle.org/ananke/reference/c14_ensemble.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Radiocarbon Event Count — c14_ensemble","text":"N. Frerebeau","code":""},{"path":"https://packages.tesselle.org/ananke/reference/c14_plot.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot Calibrated Radiocarbon Ages — c14_plot","title":"Plot Calibrated Radiocarbon Ages — c14_plot","text":"Plot Calibrated Radiocarbon Ages","code":""},{"path":"https://packages.tesselle.org/ananke/reference/c14_plot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot Calibrated Radiocarbon Ages — c14_plot","text":"","code":"# S4 method for 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 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,   ... )"},{"path":"https://packages.tesselle.org/ananke/reference/c14_plot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot Calibrated Radiocarbon Ages — c14_plot","text":"x CalibratedAges CalibratedSPD object. calendar TimeScale object specifying target calendar (see calendar()). density logical scalar: density drawn? interval logical scalar: highest density region drawn? level length-one numeric vector giving confidence level. used interval TRUE. sort logical scalar: data sorted? decreasing logical scalar: sort order decreasing? used sort TRUE. main character string giving main title plot. sub character string giving subtitle plot. axes logical scalar: axes drawn plot? frame.plot logical scalar: box drawn around plot? ann logical scalar: default annotation (title x y labels) appear plot? panel.first expression evaluated plot axes set plotting takes place. can useful drawing background grids. panel.last expression evaluated plotting taken place axes, title box added. col.density, col.interval specification plotting colors. ... graphical parameters may also passed arguments function.","code":""},{"path":"https://packages.tesselle.org/ananke/reference/c14_plot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot Calibrated Radiocarbon Ages — c14_plot","text":"plot() called side-effects: results graphic displayed. Invisibly returns x.","code":""},{"path":[]},{"path":"https://packages.tesselle.org/ananke/reference/c14_plot.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Plot Calibrated Radiocarbon Ages — c14_plot","text":"N. Frerebeau","code":""},{"path":"https://packages.tesselle.org/ananke/reference/c14_plot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot Calibrated Radiocarbon Ages — c14_plot","text":"","code":"## 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)   # \\donttest{ ## Out of 14C range? out <- c14_calibrate(130, 20) #> Warning: Date “X1” may extent out of range. plot(out) #> Warning: Date “X1” may extent out of range.  # }"},{"path":"https://packages.tesselle.org/ananke/reference/c14_spd.html","id":null,"dir":"Reference","previous_headings":"","what":"Summed Probability Distributions — c14_spd","title":"Summed Probability Distributions — c14_spd","text":"Computes summed probability distributions (SPD) radiocarbon dates.","code":""},{"path":"https://packages.tesselle.org/ananke/reference/c14_spd.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Summed Probability Distributions — c14_spd","text":"","code":"c14_spd(object, ...)  # S4 method for CalibratedAges c14_spd(object, normalize_date = FALSE, normalize_spd = FALSE)"},{"path":"https://packages.tesselle.org/ananke/reference/c14_spd.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Summed Probability Distributions — c14_spd","text":"object CalibratedAges object. ... Currently used. normalize_date logical scalar: total probability mass calibrated dates normalised (sum unity within time-span analysis)? normalize_spd logical scalar: total probability mass SPD normalised (sum unity)?","code":""},{"path":[]},{"path":"https://packages.tesselle.org/ananke/reference/c14_spd.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Summed Probability Distributions — c14_spd","text":"N. Frerebeau","code":""},{"path":"https://packages.tesselle.org/ananke/reference/c14_spd.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Summed Probability Distributions — c14_spd","text":"","code":"## 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) #> Warning: \"flip\" is not a graphical parameter #> Warning: \"flip\" is not a graphical parameter #> Warning: \"flip\" is not a graphical parameter #> Warning: \"flip\" is not a graphical parameter #> Warning: \"flip\" is not a graphical parameter #> Warning: \"flip\" is not a graphical parameter #> Warning: \"flip\" is not a graphical parameter #> Warning: \"flip\" is not a graphical parameter #> Warning: \"flip\" is not a graphical parameter #> Warning: \"flip\" is not a graphical parameter #> Warning: \"flip\" is not a graphical parameter #> Warning: \"flip\" is not a graphical parameter #> Warning: \"flip\" is not a graphical parameter #> Warning: \"flip\" is not a graphical parameter #> Warning: \"flip\" is not a graphical parameter #> Warning: \"flip\" is not a graphical parameter #> Warning: \"flip\" is not a graphical parameter #> Warning: \"flip\" is not a graphical parameter #> Warning: \"flip\" is not a graphical parameter #> Warning: \"flip\" is not a graphical parameter #> Warning: \"flip\" is not a graphical parameter #> Warning: \"flip\" is not a graphical parameter #> Warning: \"flip\" is not a graphical parameter #> Warning: \"flip\" is not a graphical parameter #> Warning: \"flip\" is not a graphical parameter #> Warning: \"flip\" is not a graphical parameter #> Warning: \"flip\" is not a graphical parameter #> Warning: \"flip\" is not a graphical parameter #> Warning: \"flip\" is not a graphical parameter #> Warning: \"flip\" is not a graphical parameter #> Warning: \"flip\" is not a graphical parameter #> Warning: \"flip\" is not a graphical parameter   ## SPD s <- c14_spd(cal) plot(s)"},{"path":"https://packages.tesselle.org/ananke/reference/c14_uncalibrate.html","id":null,"dir":"Reference","previous_headings":"","what":"Uncalibrate a Radiocarbon Date — c14_uncalibrate","title":"Uncalibrate a Radiocarbon Date — c14_uncalibrate","text":"Uncalibrate Radiocarbon Date","code":""},{"path":"https://packages.tesselle.org/ananke/reference/c14_uncalibrate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Uncalibrate a Radiocarbon Date — c14_uncalibrate","text":"","code":"c14_uncalibrate(object, ...)  # S4 method for numeric c14_uncalibrate(object, curves = \"intcal20\")  # S4 method for CalibratedAges c14_uncalibrate(object, ...)"},{"path":"https://packages.tesselle.org/ananke/reference/c14_uncalibrate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Uncalibrate a Radiocarbon Date — c14_uncalibrate","text":"object CalibratedAges object numeric vector calibrated ages (BP). ... Currently used. curves character vector specifying calibration curve used. Different curves can specified.","code":""},{"path":[]},{"path":"https://packages.tesselle.org/ananke/reference/c14_uncalibrate.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Uncalibrate a Radiocarbon Date — c14_uncalibrate","text":"N. Frerebeau","code":""},{"path":"https://packages.tesselle.org/ananke/reference/c14_uncalibrate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Uncalibrate a Radiocarbon Date — c14_uncalibrate","text":"","code":"if (FALSE) { ## Calibrate multiple dates cal <- c14_calibrate(   values = c(5000, 4500),   errors = c(45, 35),   names = c(\"X\", \"Y\") )  ## Uncalibrate c14_uncalibrate(cal) }"},{"path":"https://packages.tesselle.org/ananke/reference/data.frame.html","id":null,"dir":"Reference","previous_headings":"","what":"Coerce to a Data Frame — data.frame","title":"Coerce to a Data Frame — data.frame","text":"Coerce Data Frame","code":""},{"path":"https://packages.tesselle.org/ananke/reference/data.frame.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Coerce to a Data Frame — data.frame","text":"","code":"# S4 method for CalibratedAges as.data.frame(x, ..., calendar = getOption(\"ananke.calendar\"))  # S4 method for RECE as.data.frame(x, ..., calendar = getOption(\"ananke.calendar\"))  # S4 method for ProxyRecord as.data.frame(x, ..., calendar = getOption(\"ananke.calendar\"))"},{"path":"https://packages.tesselle.org/ananke/reference/data.frame.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Coerce to a Data Frame — data.frame","text":"x object. ... parameters passed data.frame(). calendar TimeScale object specifying target calendar (see calendar()). NULL, rata die returned.","code":""},{"path":"https://packages.tesselle.org/ananke/reference/data.frame.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Coerce to a Data Frame — data.frame","text":"data.frame extra time column.","code":""},{"path":[]},{"path":"https://packages.tesselle.org/ananke/reference/data.frame.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Coerce to a Data Frame — data.frame","text":"N. Frerebeau","code":""},{"path":"https://packages.tesselle.org/ananke/reference/data.frame.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Coerce to a Data Frame — data.frame","text":"","code":"## Calibrate multiple dates cal <- c14_calibrate(   values = c(5000, 4500),   errors = c(45, 35),   names = c(\"X\", \"Y\") )  head(as.data.frame(cal)) #>    time            X Y #> 1 -3984 1.110191e-06 0 #> 2 -3983 1.434164e-06 0 #> 3 -3982 1.845486e-06 0 #> 4 -3981 2.365558e-06 0 #> 5 -3980 3.020421e-06 0 #> 6 -3979 3.589420e-06 0 head(as.data.frame(cal, calendar = BP())) #>   time            X Y #> 1 5934 1.110191e-06 0 #> 2 5933 1.434164e-06 0 #> 3 5932 1.845486e-06 0 #> 4 5931 2.365558e-06 0 #> 5 5930 3.020421e-06 0 #> 6 5929 3.589420e-06 0 head(as.data.frame(cal, calendar = NULL)) #>       time            X Y #> 1 -1455491 1.110191e-06 0 #> 2 -1455125 1.434164e-06 0 #> 3 -1454760 1.845486e-06 0 #> 4 -1454395 2.365558e-06 0 #> 5 -1454030 3.020421e-06 0 #> 6 -1453664 3.589420e-06 0"},{"path":"https://packages.tesselle.org/ananke/reference/interval_hdr.html","id":null,"dir":"Reference","previous_headings":"","what":"Highest Density Regions — hdr","title":"Highest Density Regions — hdr","text":"Highest Density Regions","code":""},{"path":"https://packages.tesselle.org/ananke/reference/interval_hdr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Highest Density Regions — hdr","text":"","code":"# S4 method for CalibratedAges,missing interval_hdr(x, level = 0.954, calendar = getOption(\"ananke.calendar\"), ...)"},{"path":"https://packages.tesselle.org/ananke/reference/interval_hdr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Highest Density Regions — hdr","text":"x CalibratedAges object. level length-one numeric vector giving confidence level. calendar TimeScale object specifying target calendar (see calendar()). ... Currently used.","code":""},{"path":"https://packages.tesselle.org/ananke/reference/interval_hdr.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Highest Density Regions — hdr","text":"Returns list numeric  matrix.","code":""},{"path":"https://packages.tesselle.org/ananke/reference/interval_hdr.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Highest Density Regions — hdr","text":"Hyndman, R. J. (1996). Computing graphing highest density regions. American Statistician, 50: 120-126. doi:10.2307/2684423 .","code":""},{"path":[]},{"path":"https://packages.tesselle.org/ananke/reference/interval_hdr.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Highest Density Regions — hdr","text":"N. Frerebeau","code":""},{"path":"https://packages.tesselle.org/ananke/reference/interval_hdr.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Highest Density Regions — hdr","text":"","code":"## 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) #> $X #>      start   end    p #> [1,] -3911 -3876 0.15 #> [2,] -3802 -3706 0.50 #> [3,] -3669 -3659 0.04 #>  #> $Y #>      start   end    p #> [1,] -3336 -3310 0.11 #> [2,] -3297 -3283 0.06 #> [3,] -3272 -3267 0.02 #> [4,] -3240 -3207 0.14 #> [5,] -3194 -3103 0.37 #>  interval_hdr(cal, level = 0.954) #> $X #>      start   end    p #> [1,] -3944 -3855 0.29 #> [2,] -3844 -3833 0.02 #> [3,] -3818 -3653 0.65 #>  #> $Y #>      start   end    p #> [1,] -3355 -3091 0.94 #> [2,] -3050 -3040 0.01 #>  interval_hdr(cal, level = 0.997) #> $X #>      start   end p #> [1,] -3953 -3647 1 #>  #> $Y #>      start   end p #> [1,] -3366 -3014 1 #>"},{"path":"https://packages.tesselle.org/ananke/reference/ksarakil.html","id":null,"dir":"Reference","previous_headings":"","what":"Ksâr 'Akil Radiocarbon Dates — ksarakil","title":"Ksâr 'Akil Radiocarbon Dates — ksarakil","text":"Ksâr 'Akil Radiocarbon Dates","code":""},{"path":"https://packages.tesselle.org/ananke/reference/ksarakil.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Ksâr 'Akil Radiocarbon Dates — ksarakil","text":"","code":"ksarakil"},{"path":"https://packages.tesselle.org/ananke/reference/ksarakil.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Ksâr 'Akil Radiocarbon Dates — ksarakil","text":"data.frame 16 rows 5 variables: code Laboratory code. date Radiocarbon date (year BP). error Radiocarbon error (year). layer Stratigraphic layer. phase Chronological phase.","code":""},{"path":"https://packages.tesselle.org/ananke/reference/ksarakil.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Ksâr 'Akil Radiocarbon Dates — ksarakil","text":"Bosch, M. D., Mannino, M. ., Prendergast, . L., O'Connell, T. C., Demarchi, B., Taylor, S. M., Niven, L., van der Plicht, J. Hublin, J.-J. (2015). New Chronology Ksâr 'Akil (Lebanon) Supports Levantine Route Modern Human Dispersal Europe. Proceedings National Academy Sciences 112(25): 7683-8. doi:10.1073/pnas.1501529112 .","code":""},{"path":"https://packages.tesselle.org/ananke/reference/labels.html","id":null,"dir":"Reference","previous_headings":"","what":"Find Labels from Object — labels","title":"Find Labels from Object — labels","text":"Find suitable set labels object use printing plotting, example.","code":""},{"path":"https://packages.tesselle.org/ananke/reference/labels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Find Labels from Object — labels","text":"","code":"# S4 method for CalibratedAges labels(object, ...)"},{"path":"https://packages.tesselle.org/ananke/reference/labels.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Find Labels from Object — labels","text":"object object find labels. ... Currently used.","code":""},{"path":"https://packages.tesselle.org/ananke/reference/labels.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Find Labels from Object — labels","text":"character vector.","code":""},{"path":[]},{"path":"https://packages.tesselle.org/ananke/reference/labels.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Find Labels from Object — labels","text":"N. Frerebeau","code":""},{"path":"https://packages.tesselle.org/ananke/reference/mean.html","id":null,"dir":"Reference","previous_headings":"","what":"Mean — mean","title":"Mean — mean","text":"Mean","code":""},{"path":"https://packages.tesselle.org/ananke/reference/mean.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Mean — mean","text":"","code":"# S4 method for CalibratedAges mean(x, na.rm = FALSE, ..., calendar = getOption(\"ananke.calendar\"))  # S4 method for ProxyRecord mean(x, na.rm = FALSE, ...)"},{"path":"https://packages.tesselle.org/ananke/reference/mean.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Mean — mean","text":"x CalibratedAges object. na.rm logical scalar: NA values stripped computation proceeds? ... Currently used. calendar TimeScale object specifying target calendar (see calendar()).","code":""},{"path":"https://packages.tesselle.org/ananke/reference/mean.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Mean — mean","text":"numeric vector.","code":""},{"path":[]},{"path":"https://packages.tesselle.org/ananke/reference/mean.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Mean — mean","text":"N. Frerebeau","code":""},{"path":"https://packages.tesselle.org/ananke/reference/mean.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Mean — mean","text":"","code":"## Calibrate multiple dates cal <- c14_calibrate(   values = c(5000, 4500),   errors = c(45, 35),   names = c(\"X\", \"Y\") )  ## Statistics quantile(cal) #>      0%   25%   50%   75%  100% #> X -3984 -3876 -3778 -3729 -3545 #> Y -3984 -3283 -3211 -3145 -2917 median(cal) #>     X     Y  #> -3778 -3211  mean(cal) #>         X         Y  #> -3792.679 -3211.160   ## 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\")"},{"path":"https://packages.tesselle.org/ananke/reference/median.html","id":null,"dir":"Reference","previous_headings":"","what":"Median — median","title":"Median — median","text":"Median","code":""},{"path":"https://packages.tesselle.org/ananke/reference/median.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Median — median","text":"","code":"# S4 method for CalibratedAges median(x, na.rm = FALSE, ..., calendar = getOption(\"ananke.calendar\"))"},{"path":"https://packages.tesselle.org/ananke/reference/median.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Median — median","text":"x CalibratedAges object. na.rm logical scalar: NA values stripped computation proceeds? ... Currently used. calendar TimeScale object specifying target calendar (see calendar()).","code":""},{"path":"https://packages.tesselle.org/ananke/reference/median.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Median — median","text":"numeric vector.","code":""},{"path":[]},{"path":"https://packages.tesselle.org/ananke/reference/median.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Median — median","text":"N. Frerebeau","code":""},{"path":"https://packages.tesselle.org/ananke/reference/median.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Median — median","text":"","code":"## Calibrate multiple dates cal <- c14_calibrate(   values = c(5000, 4500),   errors = c(45, 35),   names = c(\"X\", \"Y\") )  ## Statistics quantile(cal) #>      0%   25%   50%   75%  100% #> X -3984 -3876 -3778 -3729 -3545 #> Y -3984 -3283 -3211 -3145 -2917 median(cal) #>     X     Y  #> -3778 -3211  mean(cal) #>         X         Y  #> -3792.679 -3211.160   ## 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\")"},{"path":"https://packages.tesselle.org/ananke/reference/mutators.html","id":null,"dir":"Reference","previous_headings":"","what":"Get or Set Parts of an Object — mutators","title":"Get or Set Parts of an Object — mutators","text":"Getters setters extract replace parts object.","code":""},{"path":"https://packages.tesselle.org/ananke/reference/mutators.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get or Set Parts of an Object — mutators","text":"x object get set element(s). value possible value element(s) x.","code":""},{"path":"https://packages.tesselle.org/ananke/reference/mutators.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get or Set Parts of an Object — mutators","text":"object sort x new values assigned.","code":""},{"path":[]},{"path":"https://packages.tesselle.org/ananke/reference/mutators.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Get or Set Parts of an Object — mutators","text":"N. Frerebeau","code":""},{"path":"https://packages.tesselle.org/ananke/reference/pb_age.html","id":null,"dir":"Reference","previous_headings":"","what":"Geological Model Age from Lead Isotope Analysis — pb_age","title":"Geological Model Age from Lead Isotope Analysis — pb_age","text":"Compute geological model age (T) U/Pb (mu) Th/U (kappa) ratios lead isotopic measurements.","code":""},{"path":"https://packages.tesselle.org/ananke/reference/pb_age.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Geological Model Age from Lead Isotope Analysis — pb_age","text":"","code":"pb_age(x, y, z, ...)  # S4 method for 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 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) )"},{"path":"https://packages.tesselle.org/ananke/reference/pb_age.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Geological Model Age from Lead Isotope Analysis — pb_age","text":"x numeric vector 206Pb/204Pb ratios. y z missing, must list (data.frame) numeric components (columns) x, y z. y numeric vector 207Pb/204Pb ratios.  missing, attempt made interpret x suitable way. z numeric vector 208Pb/204Pb ratios.  missing, attempt made interpret x suitable way. ... Currently used. t0 numeric value giving time second stage reference model. x_star numeric value giving 206Pb/204Pb ratio \\(t = 0\\). y_star numeric value giving 207Pb/204Pb ratio \\(t = 0\\). z_star numeric value giving 208Pb/204Pb ratio \\(t = 0\\). mu numeric value giving 238U/204Pb ratio reference model. kappa numeric value giving 232Th/238U ratio reference model. th232 numeric value giving decay constants 232Th. u238 numeric value giving decay constants 238U. u235 numeric value giving decay constants 235U. u238_235 numeric value giving 238U/235U ratio. tolerance numeric value specifying tolerance (stopping criteria Newton–Raphson method).","code":""},{"path":"https://packages.tesselle.org/ananke/reference/pb_age.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Geological Model Age from Lead Isotope Analysis — pb_age","text":"four columns data.frame:","code":""},{"path":"https://packages.tesselle.org/ananke/reference/pb_age.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Geological Model Age from Lead Isotope Analysis — pb_age","text":"Reference values Albarede & Juteau (1984).","code":""},{"path":"https://packages.tesselle.org/ananke/reference/pb_age.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Geological Model Age from Lead Isotope Analysis — pb_age","text":"Albarède, F., Desaulty, .-M. & Blichert-Toft, J. (2012). Geological Perspective Use Pb Isotopes Archaeometry. Archaeometry, 54: 853-867. doi:10.1111/j.1475-4754.2011.00653.x . Albarède, F. & Juteau, M. (1984). Unscrambling Lead Model Ages. Geochimica et Cosmochimica Acta, 48(1): 207-12. doi:10.1016/0016-7037(84)90364-8 .","code":""},{"path":"https://packages.tesselle.org/ananke/reference/pb_age.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Geological Model Age from Lead Isotope Analysis — pb_age","text":"N. Frerebeau, F. Albarede (original Matlab code)","code":""},{"path":"https://packages.tesselle.org/ananke/reference/pb_age.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Geological Model Age from Lead Isotope Analysis — pb_age","text":"","code":"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 )  pb_age(Pb) #>        age       mu    kappa            f #> 1 428.3959 9.859142 4.074891 1.004859e-14 #> 2 430.9796 9.860659 4.076292 1.004859e-14 #> 3 427.6003 9.855397 4.075178 1.004859e-14"},{"path":"https://packages.tesselle.org/ananke/reference/proxy_ensemble.html","id":null,"dir":"Reference","previous_headings":"","what":"Layer-Counted Proxy Records Uncertainties — proxy_ensemble","title":"Layer-Counted Proxy Records Uncertainties — proxy_ensemble","text":"Represents layer-counted proxy records sequences probability distributions absolute, error-free time axes.","code":""},{"path":"https://packages.tesselle.org/ananke/reference/proxy_ensemble.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Layer-Counted Proxy Records Uncertainties — proxy_ensemble","text":"","code":"proxy_ensemble(depth, ...)  # S4 method for 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\") )"},{"path":"https://packages.tesselle.org/ananke/reference/proxy_ensemble.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Layer-Counted Proxy Records Uncertainties — proxy_ensemble","text":"depth positive numeric vector giving depth proxy values calendar ages measured. must decreasing order (.e. chronological order). ... Currently used. proxy numeric vector giving proxy values. proxy_error numeric vector giving proxy uncertainties. step length-one numeric vector specifying step size (units proxy) proxy records densities estimated. time numeric vector giving calendar ages (years). time_error numeric vector giving calendar age uncertainties (years). calendar TimeScale object specifying calendar time (see calendar()). length-one numeric vector specifying starting value temporal sequence densities estimated (years). length-one numeric vector specifying end value temporal sequence densities estimated (cal BP years). length-one numeric vector specifying increment temporal sequence densities estimated (years). n integer specifying number item choose randomly. progress logical scalar: progress bar displayed? verbose logical scalar: extra information reported?","code":""},{"path":"https://packages.tesselle.org/ananke/reference/proxy_ensemble.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Layer-Counted Proxy Records Uncertainties — proxy_ensemble","text":"ProxyRecord object.","code":""},{"path":"https://packages.tesselle.org/ananke/reference/proxy_ensemble.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Layer-Counted Proxy Records Uncertainties — proxy_ensemble","text":"Boers, N., Goswami, B. & Ghil, M. (2017). Complete Representation Uncertainties Layer-Counted Paleoclimatic Archives. Climate Past, 13(9): 1169-1180. doi:10.5194/cp-13-1169-2017 .","code":""},{"path":[]},{"path":"https://packages.tesselle.org/ananke/reference/proxy_ensemble.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Layer-Counted Proxy Records Uncertainties — proxy_ensemble","text":"N. Frerebeau","code":""},{"path":"https://packages.tesselle.org/ananke/reference/proxy_ensemble.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Layer-Counted Proxy Records Uncertainties — proxy_ensemble","text":"","code":"if (FALSE) { ## 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) }"},{"path":"https://packages.tesselle.org/ananke/reference/proxy_plot.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot Layer-Counted Proxy Records Uncertainties — proxy_plot","title":"Plot Layer-Counted Proxy Records Uncertainties — proxy_plot","text":"Plot Layer-Counted Proxy Records Uncertainties","code":""},{"path":"https://packages.tesselle.org/ananke/reference/proxy_plot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot Layer-Counted Proxy Records Uncertainties — proxy_plot","text":"","code":"# S4 method for 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,   ... )"},{"path":"https://packages.tesselle.org/ananke/reference/proxy_plot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot Layer-Counted Proxy Records Uncertainties — proxy_plot","text":"x ProxyRecord object. calendar TimeScale object specifying target calendar (see calendar()). iqr logical scalar: mean IQR displayed? xlab, ylab character string giving label x y axis. col list colors generated grDevices::hcl.colors(). col.mean, col.iqr specification line colors. used iqr TRUE. lty.mean, lty.iqr specification line types. used iqr TRUE. lwd.mean, lwd.iqr specification line widths. used iqr TRUE. ... parameters passed graphics::image().","code":""},{"path":"https://packages.tesselle.org/ananke/reference/proxy_plot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot Layer-Counted Proxy Records Uncertainties — proxy_plot","text":"plot() called side-effects: results graphic displayed. Invisibly returns x.","code":""},{"path":[]},{"path":"https://packages.tesselle.org/ananke/reference/proxy_plot.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Plot Layer-Counted Proxy Records Uncertainties — proxy_plot","text":"N. Frerebeau","code":""},{"path":"https://packages.tesselle.org/ananke/reference/proxy_plot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot Layer-Counted Proxy Records Uncertainties — proxy_plot","text":"","code":"if (FALSE) { ## 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) }"},{"path":"https://packages.tesselle.org/ananke/reference/quantile.html","id":null,"dir":"Reference","previous_headings":"","what":"Quantiles of a Density Estimate — quantile","title":"Quantiles of a Density Estimate — quantile","text":"Quantiles Density Estimate","code":""},{"path":"https://packages.tesselle.org/ananke/reference/quantile.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Quantiles of a Density Estimate — quantile","text":"","code":"# S4 method for CalibratedAges quantile(   x,   probs = seq(0, 1, 0.25),   na.rm = FALSE,   ...,   calendar = getOption(\"ananke.calendar\") )  # S4 method for ProxyRecord quantile(x, probs = seq(0, 1, 0.25), na.rm = FALSE, ...)"},{"path":"https://packages.tesselle.org/ananke/reference/quantile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Quantiles of a Density Estimate — quantile","text":"x CalibratedAges object. probs numeric vector probabilities values \\([0,1]\\). na.rm logical scalar: NA values stripped computation proceeds? ... Currently used. calendar TimeScale object specifying target calendar (see calendar()).","code":""},{"path":"https://packages.tesselle.org/ananke/reference/quantile.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Quantiles of a Density Estimate — quantile","text":"numeric  matrix containing quantiles.","code":""},{"path":[]},{"path":"https://packages.tesselle.org/ananke/reference/quantile.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Quantiles of a Density Estimate — quantile","text":"N. Frerebeau","code":""},{"path":"https://packages.tesselle.org/ananke/reference/quantile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Quantiles of a Density Estimate — quantile","text":"","code":"## Calibrate multiple dates cal <- c14_calibrate(   values = c(5000, 4500),   errors = c(45, 35),   names = c(\"X\", \"Y\") )  ## Statistics quantile(cal) #>      0%   25%   50%   75%  100% #> X -3984 -3876 -3778 -3729 -3545 #> Y -3984 -3283 -3211 -3145 -2917 median(cal) #>     X     Y  #> -3778 -3211  mean(cal) #>         X         Y  #> -3792.679 -3211.160   ## 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\")"},{"path":"https://packages.tesselle.org/ananke/reference/rec_plot.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot a Radiocarbon Event Count Ensemble — rec_plot","title":"Plot a Radiocarbon Event Count Ensemble — rec_plot","text":"Plot Radiocarbon Event Count Ensemble","code":""},{"path":"https://packages.tesselle.org/ananke/reference/rec_plot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot a Radiocarbon Event Count Ensemble — rec_plot","text":"","code":"# S4 method for RECE,missing plot(x, calendar = getOption(\"ananke.calendar\"), ...)"},{"path":"https://packages.tesselle.org/ananke/reference/rec_plot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot a Radiocarbon Event Count Ensemble — rec_plot","text":"x RECE object. calendar TimeScale object specifying target calendar (see calendar()). ... parameters passed graphics::image().","code":""},{"path":"https://packages.tesselle.org/ananke/reference/rec_plot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot a Radiocarbon Event Count Ensemble — rec_plot","text":"image() called side-effects: results graphic displayed (invisibly returns x).","code":""},{"path":"https://packages.tesselle.org/ananke/reference/rec_plot.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Plot a Radiocarbon Event Count Ensemble — rec_plot","text":"Carleton, W. C. (2021). Evaluating Bayesian Radiocarbon‐dated Event Count (REC) Models Study Long‐term Human Environmental Processes. Journal Quaternary Science, 36(1): 110‑23. doi:10.1002/jqs.3256 .","code":""},{"path":[]},{"path":"https://packages.tesselle.org/ananke/reference/rec_plot.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Plot a Radiocarbon Event Count Ensemble — rec_plot","text":"N. Frerebeau","code":""},{"path":"https://packages.tesselle.org/ananke/reference/reexports.html","id":null,"dir":"Reference","previous_headings":"","what":"Objects exported from other packages — reexports","title":"Objects exported from other packages — reexports","text":"objects imported packages. Follow links see documentation. aion AD, BC, BCE, BP, CE, b2k, calendar, image, plot, start, start, time, year_axis arkhe interval_hdr","code":""},{"path":"https://packages.tesselle.org/ananke/reference/subset.html","id":null,"dir":"Reference","previous_headings":"","what":"Extract or Replace Parts of an Object — subset","title":"Extract or Replace Parts of an Object — subset","text":"Operators acting objects extract replace parts.","code":""},{"path":"https://packages.tesselle.org/ananke/reference/subset.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extract or Replace Parts of an Object — subset","text":"","code":"# S4 method for CalibratedAges [(x, i, j, k, drop = FALSE)"},{"path":"https://packages.tesselle.org/ananke/reference/subset.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extract or Replace Parts of an Object — subset","text":"x object extract element(s) replace element(s). , j, k Indices specifying elements extract replace. drop logical scalar: result coerced lowest possible dimension? works extracting elements, replacement.","code":""},{"path":"https://packages.tesselle.org/ananke/reference/subset.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extract or Replace Parts of an Object — subset","text":"subsetted object.","code":""},{"path":[]},{"path":"https://packages.tesselle.org/ananke/reference/subset.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Extract or Replace Parts of an Object — subset","text":"N. Frerebeau","code":""}]