R/data_io_functions.R
set_rc_meas.RdThis is one of a set of helper functions for undertaking a typical analysis of radiocarbon dates. As the analysis proceeds, results are stored in a save file called analysis_name.rds in the folder data_dir. Where results are non-deterministic, random number seeds are set and stored to ensure that, even if processing is interrupted, results are fully reproducible.
There are, in fact, two distinct pipelines for (a) simulations and (b) analyses that use existing radiocarbon measurements saved in a .csv file. Since this is the first helper function used in the standard pipeline for using an input .csv file, that pipeline is described here. See set_sim for the pipeline when doing a simulation.
The standard pipeline for analyses that use an input data stored in a .csv file (see the vignette standard_pipeline for additional details):
(0) import_rc_data Import data from a .csv file using import_rc_data.
(1) set_rc_meas Use the data from the previous step to set the radiocarbon measurements to be used for this analysis
(2) calc_tau_range Determine the range of calendar dates that span the radiocarbon measurements (or specify the range directly)
(3) set_density_model Set the parametric model to be used for Bayesian inference. Currently, only a truncated Gaussian mixture is supported, which requires setting the calendar date range for truncation (likely using the result from step (3)) and choosing the number of mixture components, K. If K is a vector, Bayesian inference will be done for each element of the vector during step (5), do_bayesian_inference.
(4) set_calib_curve Set the calibration curve to be used for subsequent steps.
(5) do_bayesian_inference Call sample_theta to do the Bayesian inference for each model to check.
(6) do_bayesian_summary Calculate summary statistics for the best model sampled by calling do_bayesian_inference (the best model is the one with the best WAIC).
(7) plot_best_solution Create a plot of the best solution.
set_rc_meas(data_dir, analysis_name, rc_meas)
| data_dir | The directory in which to store analysis data |
|---|---|
| analysis_name | A unique name for a given analysis in data_dir |
| rc_meas | The radiocarbon measurements to use for this analysis (the format of rc_meas is as output by import_rc_data) |
import_rc_data() for the format of rc_meas'