- ident
The individual determination for which you want to plot the posterior
density estimate of the calendar age.
- output_data
The return value either from one of the Bayesian non-parametric DPMM
functions (PolyaUrnBivarDirichlet or WalkerBivarDirichlet); or
from the Poisson process modelling function (PPcalibrate).
- calibration_curve
This is usually not required since the name of the
calibration curve variable is saved in the output data. However, if the
variable with this name is no longer in your environment then you should pass
the calibration curve here. If provided, this should be a dataframe which
should contain at least 3 columns entitled calendar_age, c14_age and c14_sig.
This format matches intcal20.
- plot_14C_age
Whether to use the radiocarbon age (\({}^{14}\)C yr BP) as
the units of the y-axis in the plot. Defaults to TRUE. If FALSE uses
F\({}^{14}\)C concentration instead.
- plot_cal_age_scale
The calendar scale to use for the x-axis. Allowed values are
"BP", "AD" and "BC". The default is "BP" corresponding to plotting in cal yr BP.
- hist_resolution
The distance between histogram breaks when plotting the individual
posterior calendar age density. Default is 5.
- density_resolution
The distance between calendar ages for the returned smoothed calendar age
probability. Default is 1.
- interval_width
The confidence intervals to show for the calibration curve and
for the highest posterior density ranges.
Choose from one of "1sigma" (68.3%), "2sigma" (95.4%) and "bespoke". Default is "2sigma".
- bespoke_probability
The probability to use for the confidence interval
if "bespoke" is chosen above. E.g., if 0.95 is chosen, then the 95% confidence
interval is calculated. Ignored if "bespoke" is not chosen.
- n_burn
The number of MCMC iterations that should be discarded as burn-in (i.e.,
considered to be occurring before the MCMC has converged). This relates to the number
of iterations (n_iter) when running the original update functions (not the thinned output_data).
Any MCMC iterations before this are not used in the calculations. If not given, the first half of
the MCMC chain is discarded. Note: The maximum value that the function will allow is
n_iter - 100 * n_thin (where n_iter and n_thin are the arguments given to
PolyaUrnBivarDirichlet or WalkerBivarDirichlet)
which would leave only 100 of the (thinned) values in output_data.
- n_end
The iteration number of the last sample in output_data to use in the calculations.
Assumed to be the total number of (thinned) realisations stored if not given.
- show_hpd_ranges
Set to TRUE to also show the highest posterior density (HPD) range
on the plot.
- show_unmodelled_density
Set to TRUE to also show the unmodelled density (i.e., the
result of independent calibration using CalibrateSingleDetermination) on the plot.
Default is FALSE.
- plot_pretty
logical, defaulting to TRUE. If set TRUE then will select pretty plotting
margins (that create sufficient space for axis titles and rotates y-axis labels). If FALSE will
implement current user values.