Package: rbacon 3.3.1

rbacon: Age-Depth Modelling using Bayesian Statistics

An approach to age-depth modelling that uses Bayesian statistics to reconstruct accumulation histories for deposits, through combining radiocarbon and other dates with prior information on accumulation rates and their variability. See Blaauw & Christen (2011).

Authors:Maarten Blaauw [aut, cre], J. Andres Christen [aut, ctb, cph], Marco A. Aquino Lopez [aut], Judith Esquivel Vazquez [ctb], Oscar M. Gonzalez V. [ctb], Ted Belding [cph], James Theiler [cph], Brian Gough [cph], Charles Karney [cph]

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rbacon.pdf |rbacon.html✨
rbacon/json (API)
NEWS

# Install 'rbacon' in R:
install.packages('rbacon', repos = c('https://maarten14c.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/maarten14c/rbacon/issues

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

age-depth-modelbayesianholocenelakesocean-sedimentspeatradiocarbon-calibration

6.70 score 7 stars 1 packages 55 scripts 1.4k downloads 1 mentions 32 exports 53 dependencies

Last updated 2 months agofrom:31b283c957. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 28 2024
R-4.5-win-x86_64OKOct 28 2024
R-4.5-linux-x86_64OKOct 28 2024
R-4.4-win-x86_64OKOct 28 2024
R-4.4-mac-x86_64OKOct 28 2024
R-4.4-mac-aarch64OKOct 28 2024
R-4.3-win-x86_64OKOct 28 2024
R-4.3-mac-x86_64OKOct 28 2024
R-4.3-mac-aarch64OKOct 28 2024

Exports:A.modelledaccrate.ageaccrate.age.ghostaccrate.age.summaryaccrate.depthaccrate.depth.ghostaccrate.depth.summaryaccrates.coreadd.datesagedepthagemodel.itAgesOfEventsbackgroundBaconBacon.Age.dBacon.cleanupBacon.d.AgeBacon.histbacon2clamBaconvergencecalib.plotclam2bacondraw.pbmeasureddraw.pbmodelledflux.age.ghostproxy.ghostscissorsset.initvalssqueezestretchthinnertofu

Dependencies:askpassclassclassIntclicodacolorspacecurldata.tableDBIe1071fansifarverggplot2gluegtablehttrisobandjsonliteKernSmoothlabelinglatticelifecyclemagrittrMASSMatrixmgcvmimemunsellnlmeopensslpillarpkgconfigproxyR6RColorBrewerRcppricerintcalrlangrnaturalearthrnaturalearthdatas2scalessfsysterratibbleunitsutf8vctrsviridisLitewithrwk

rbacon

Rendered fromrbacon.Rmdusingknitr::rmarkdownon Oct 28 2024.

Last update: 2024-09-28
Started: 2023-08-13

Readme and manuals

Help Manual

Help pageTopics
Calculate modelled 210PbA.modelled
Obtain estimated accumulation rates for any age of a core.accrate.age
Plot a core's accumulation rates against calendar time.accrate.age.ghost
Provide a summary of the estimated accumulation rates for any age of a core.accrate.age.summary
Obtain estimated accumulation rates as for any depth of a core.accrate.depth
Plot modelled accumulation rates against the depths of a core.accrate.depth.ghost
Provide a summary of the estimated accumulation rates for any depth of a core.accrate.depth.summary
Provide a summary of the estimated accumulation rates for a range of core depthsaccrates.core
Add dates to age-depth plotsadd.dates
Plot an age-depth modelagedepth
Extract one age-model iterationagemodel.it
Event probabilities against calendar ageAgesOfEvents
calculate probabilities that Pb-210 data have reached background levelsbackground
Main age-depth modelling functionBacon
Output all ages for a single depth.Bacon.Age.d
Remove files made to produce the current core's age-depth model.Bacon.cleanup
Output all depths for a single age.Bacon.d.Age
Calculate age distributions of depths.Bacon.hist
Translate Bacon .csv files to clam .csv files.bacon2clam
Test to identify poorly mixed MCMC runs.Baconvergence
Plot the datescalib.plot
Translate clam .csv files to Bacon .csv files.clam2bacon
Plot the 210Pb datadraw.pbmeasured
Plot the 210Pb datadraw.pbmodelled
Plot flux rates for proxies.flux.age.ghost
Proxies analysed along the depths of a core can be plotted as 'proxy-ghost' graphs against calendar time while taking into account chronological uncertainties. Here darker grey indicates more likely calendar ages for specific proxy values.proxy.ghost
Remove the first n iterations.scissors
Set initial values for the Bacon MCMC run.set.initvals
Squeeze some depths of a coresqueeze
Stretch some depths of a corestretch
Thin iterations.thinner
Bacon for veganstofu