Classical Age-Depth Modelling of Cores from Deposits

Performs 'classical' age-depth modelling of dated sediment deposits - prior to applying more sophisticated techniques such as Bayesian age-depth modelling. Any radiocarbon dated depths are calibrated. Age-depth models are constructed by sampling repeatedly from the dated levels, each time drawing age-depth curves. Model types include linear interpolation, linear or polynomial regression, and a range of splines. See Blaauw (2010). .


News

clam 2.3.2

  • new function calBP.14C to find the mu (IntCal 14C age) belonging to a single calendar year (suggested by Andres Christen)
  • removed suppression of warnings (suggested by Maris Nartiss)
  • added sep argument to mix.calibrationcurves (suggested by Thomas Dye)
  • calibrate now invisibly returns dat (suggested by Andres Christen) so now can be used as, e.g., cal <- calibrate(130, 30); cal
  • related functions were put into separate .R files
  • unnecessary references to Bacon were removed
  • dummy -5 cal BP lines were removed from the IntCal13 and SHCal13 calibration curves

clam 2.3.1

  • Now a CRAN R package
  • Repaired many sundry bugs
  • updated the help functions

clam 2.2

  • updated calibration curves (IntCal13 for both hemispheres and the ocean, plus postbomb curves)
  • corrected behaviour of est
  • corrected use of alternative separator in .csv files (e.g. ";" instead of ","). Also added option to specify alternative decimal points (e.g. "," instead of ".")
  • repaired bug that caused incorrect depths for plot.proxies
  • repaired bug with slump, causing some dates to be assigned wrong depths
  • corrected bug with drawing sample thickness when extradates applied
  • new option for est, midpoint of entire calibrated distributions (above threshold, est=7). This differs slightly from the midpoint of the calibrated hpd ranges (est=3)
  • minor changes to the manual, incl. more explicit citation suggestions
  • added function student.t to show effect alternative calibration

clam 2.1

  • corrected wrong behaviour when using hiatus and slump, e.g., clam(hiatus=470, slump=c(120,140))
  • polynomial age-modelling now correctly deals with weights (wght)
  • uncertainties for age offsets can be included in calibrate()
  • marine offset can now be specified when producing a mixed terrestrial/marine curve (mix.curves())
  • new function glue.curves that can be used to extend SHCal04 to 50 kcal BP using IntCal09 and a specified SH offset (obsolete since release of SHCal13)
  • corrected references in the manual

clam 2.0

  • Depth segments of abrupt sedimentation can now be excised with the option slump

  • different colours for C14 and calendar dates

  • accumulation rates are calculated and added as a fifth column to the _ages.txt file

  • future ages can be avoided in the dates and the age-depth model

  • option to rotate the axes, or reverse the order for the age or depth axes

  • optional calibt calibration (Christen and Perez 2009)

  • option to provide .txt files with ages and probs for depths

  • single instead of mirrored calibrated histograms can be drawn in age-depth graphs

  • New function mix.curves

  • New functions pMC.age, age.pMC to convert between 14C ages and percent modern carbon

  • New function proxy plot

  • histograms and confidence ranges for accumulation rates can be calculated for specific depths or ages

  • probability distributions are now normalised, so that precise ages have higher heights than imprecise ages. This can be turned off

  • more consistent naming of dmax, dmin, etc.

  • Warnings are provided in case of clearly wrong settings (e.g. type > 5)

  • Internal calculations for C14 dates are now done in F14C (as in OxCal)

  • core name added to age-plots

  • can now leave thickness column out of .csv file (so, need 6 columns only)

  • instead of standard deviation, the statistically more correct probability is used (e.g., what was formerly sdev=2 is now prob=0.95)

  • use of file _depths.txt now needs to be activated explicitly

  • corrected a bug with calibrating single dates on old or young extremes of the calibration curve

  • corrected wrong behaviour when outliers and mixed.effect are used together

  • corrected a reservoir effect bug in mixed.effect

  • corrected a bug in hpds around 0 BC/AD when BCAD=TRUE

  • corrected a wrong reaction to clam(BCAD=TRUE)

  • corrected wrong yr.axis titles in png and pdf

  • corrected a bug in title option calibrate()

  • better error message when type=5 & hiatus

  • enhanced treatment of plotting parameters (par)

  • better rounding for ages.txt

  • squashed many more small to invisible bugs

Reference manual

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install.packages("clam")

2.3.2 by Maarten Blaauw, a year ago


Browse source code at https://github.com/cran/clam


Authors: Maarten Blaauw [aut, cre] , J. Andres Christen [ctb] , Judith Esquivel Vazquez [ctb] , Simon Goring [ctb]


Documentation:   PDF Manual  


GPL (>= 2) license


Imports grDevices, graphics, stats, utils


See at CRAN