NEWS.md
In GPawi/clamsy: Classical Age-Depth Modelling of Cores from Deposits
clam 2.3.4
- updated the code to deal with changes in how base-R deals with c() in loops
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, 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
GPawi/clamsy documentation built on July 4, 2020, 12:02 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
clam 2.3.4
- updated the code to deal with changes in how base-R deals with c() in loops
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, 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
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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