NEWS

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clam 2.6.2 (2025-01-11)

• changed the use of tempdir() in documentation examples (to avoid Errors on CRAN package checks)
• linking to updated rice and rintcal
• removed the calib.t function since it is now in rice

clam 2.6.1 (2024-09-25)

• further steps in separating 'rice' from 'rintcal' within 'clam'

clam 2.6.0 (2024-09-04)

• now uses the 'rintcal' package for loading calibration curves, and 'rice' for additional radiocarbon/calibration functions

clam 2.5.0 (2022-08-17)

• now points to the renamed rintcal package

clam 2.4.0 (2021-08-15)

• 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 (2021-05-11)

• removed closeAllConnections, as directed by CRAN's maintainers

clam 2.3.8 (2021-01-23)

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

clam 2.3.7 (2020-11-24)

• 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 (2020-08-10)

• updated to the latest IntCal20 calibration curves

clam 2.3.4 (2020-03-12)

• 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 (2019-01-14)

• 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 (2018-01-08)

• 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