NEWS.md

In clam: Classical Age-Depth Modelling of Cores from Deposits

clam 2.5.0

• now points to the renamed rintcal package

clam 2.4.0

• calibrate() and calBP.14C() are now provided by the IntCal package
• replaced .hpd() as now provided as hpd() by the IntCal package
• replaced copyCalibrationCurve() with ccurve() in plots.R
• added vignettes
• some general cleanup of the code
• if depthseq is provided, the depth scale is now plotted correctly

clam 2.3.9

• removed closeAllConnections, as directed by CRAN's maintainers

clam 2.3.8

• repaired a bug where calibrate() couldn't find postbomb curves if required. Reported by David Hein-Griggs, University of Exeter.

clam 2.3.7

• removed links to chrono website, as it has become unstable and could disappear any moment now.
• added an option 'rule' to allow more choice when extrapolating values (see ?approx). This is an internal option and shouldn't normally be important for users.

clam 2.3.6

• now installs and uses the IntCal package to read the radiocarbon calibration curves (this to have less replication of files between packages that use the IntCal curves)
• repaired bug with Est not being the same size as smp (e.g., whenever dates were truncated or removed, either automatically or manually)
• repaired mixed.effect (however, does not use student.t any more)

clam 2.3.5

• updated to the latest IntCal20 calibration curves

clam 2.3.4

• Updated the code to deal with changes in how base-R deals with c() in loops, as suggested by Martin Maechler's e-mail 29 February 2020

clam 2.3.3

• deptime.age and deptime.depth now invisibly return the deposition time values, for future manipulation such as summary(deptime.age(900))
• Updated help functions of clam and calibrate

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, including 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

clam documentation built on Aug. 17, 2022, 5:06 p.m.