- further steps in separating ‘rice’ from ‘rintcal’ within ‘clam’

- now uses the ‘rintcal’ package for loading calibration curves, and ‘rice’ for additional radiocarbon/calibration functions

- now points to the renamed rintcal package

- 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

- removed closeAllConnections, as directed by CRAN’s maintainers

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

- 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.

- 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)

- updated to the latest IntCal20 calibration curves

- 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

- 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

- 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

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

- 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

- 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