run_bacon: Run Bacon

In special-uor/ageR: Supervised Age Modelling

Run Bacon

Description

Run the function rbacon::Bacon(...).

Usage

run_bacon(
  wdir,
  entity,
  postbomb = 0,
  cc = 1,
  seed = NA,
  alt_depths = NULL,
  quiet = FALSE,
  core = NULL,
  depths_eval = NULL,
  hiatuses = NULL,
  sample_ids = NULL,
  unknown_age = NULL,
  coredir = NULL,
  acc.mean = 20,
  acc.shape = 1.5,
  ssize = 2000,
  th0 = c(),
  thick = 5,
  p = NULL,
  ...
)

Arguments

wdir	Path where input files are stored.
entity	Name of the entity.
postbomb	Use a postbomb curve for negative (i.e. postbomb) 14C ages. 0 = none, 1 = NH1, 2 = NH2, 3 = NH3, 4 = SH1-2, 5 = SH3.
cc	Calibration curve for C-14 dates: cc = 1 for IntCal20 (northern hemisphere terrestrial), cc = 2 for Marine20 (marine), cc = 3 for SHCal20 (southern hemisphere terrestrial). For dates that are already on the cal BP scale use cc = 0.
seed	Set see to reproduce results. This seed is used for C++ executions, if it is not assigned then the seed is set by the system.
alt_depths	List of arrays with new depths.
quiet	Boolean to hide status messages.
core	Data frame with the core's data.
depths_eval	Numeric array with the sampling depths.
hiatuses	Data frame containing information of hiatuses.
sample_ids	Numeric array with IDs for the sampling depths.
unknown_age	Data frame containing information of unused ages.
coredir	Folder where the core's files core are and/or will be located.
acc.mean	The accumulation rate prior consists of a gamma distribution with two parameters. Its mean is set by acc.mean (default acc.mean=20 yr/cm (or whatever age or depth units are chosen), which can be changed to, e.g., 5, 10 or 50 for different kinds of deposits). Multiple values can be given in case of hiatuses or boundaries, e.g., Bacon(hiatus.depths=23, acc.mean=c(5,20)).
acc.shape	The prior for the accumulation rate consists of a gamma distribution with two parameters. Its shape is set by acc.shape (default acc.shape=1.5; higher values result in more peaked shapes).
ssize	The approximate amount of iterations to store at the end of the MCMC run. Default 2000; decrease for faster (but less reliable) runs or increase for cores where the MCMC mixing (panel at upper-left corner of age-model graph) appears problematic.
th0	Starting years for the MCMC iterations.
thick	Bacon will divide the core into sections of equal thickness specified by thick (default thick = 5).
p	progressor object from the package progressr.
...	Optional parameters for rbacon::Bacon.

Value

Saves MC ensemble, bacon_chronology and AM plot.

References

Blauuw, M. et al., Bayesian Analysis 6, 457-474 (2011)

Blauuw, M. et al., rbacon (2019), R package version 2.3.9.1

Comas-Bru, L. et al., SISALv2: A comprehensive speleothem isotope database with multiple age-depth models, Earth Syst. Sci. Data Discuss (2020) https://doi.org/10.5194/essd-2020-39, https://github.com/paleovar/SISAL.AM

special-uor/ageR documentation built on July 10, 2024, 10:08 p.m.