All functions

add_shaded_quantiles()

assess_calib_curve_equif()

Assess the equifinality or time spans in the input radiocarbon calibration curve

calc_calib_curve_equif_dates()

Calculate equifinal dates for each point in the calibration curve

calc_calib_curve_frac_modern()

Calculation the calibration curve fraction modern value for the input calendar dates.

calc_gauss_mix_pdf()

Caculate the density of a possibly truncated Gaussian mixture

calc_gauss_mix_pdf_mat()

Calculate the density of a possibly truncated Gaussian mixture for a matrix of samples

calc_half_life_from_peak()

For each sample, calculate the time it takes for the density to decrease by half from the peak (or by another use-provided ratio)

calc_meas_matrix()

Calculate the measurement matrix given N observations and G grid points

calc_quantiles()

Calculate the quantiles for an input matrix X

calc_relative_density()

Calculate the relative density at two dates (or a range of dates / the peak)

calc_tau_range()

Calculate a calendar date range that spans the input radiocarbon measurements

calc_trapez_weights()

Calculate integration weights assuming the midpoint rule

calc_trunc_gauss_mix_neg_log_lik()

Calculate the negative log-likelihood of a truncuated Gaussian mixture fit

do_bayesian_inference()

Do Bayesian inference given a set of radiocarbon measurements (rc_meas) and a density model (density_model).

do_bayesian_summary()

Summarize the best model sampled by do_bayesian_inference

draw_rc_meas_using_date()

Simulate radiocarbon measurements from input calendar dates

extract_param()

Extract the Bayesian samples for a Gaussian mixture model generated by sample_theta

fit_trunc_gauss_mix()

Fit a truncated Gaussian mixture to radiocarbon data using the Hooke-Jeeves algorithm with multiple restarts

import_rc_data()

Import radiocarbon data from a .csv file

init_trunc_gauss_mix()

Do random number draws to initialize a truncated Gaussian mixture

intcal13

The IntCal13 calibration curve

intcal13_raw

The raw data for constructing the IntCal13 calibration curve

intcal20

The IntCal20 calibration curve

intcal20_raw

The raw data for constructing the IntCal20 calibration curve

is_th_reduced_valid()

A helper function to determine if the reduced form parameter vector is valid

load_calib_curve()

make_blank_density_plot()

Prepare a blank plot for showing densities

marine13

The Marine13 calibration curve

marine13_raw

The raw data for constructing the Marine13 calibration curve

marine20

The Marine20 calibration curve

phi2tau()

Find the calendar date from the fraction modern value given known bounding indices

plot_50_percent_quantile()

Plot the 50 percent quantile curve

plot_best_solution()

Plot the best model created by do_bayesian_inference

plot_known_sim_density()

Plot the known simulation density

plot_summed_density()

Plot the summed probability density function (SPDF)

sample_gauss_mix()

Sample from a possibly truncated Gaussian mixture

sample_theta()

Sample from the posterior of a density model for a set of radiocarbon measurements

sample_trunc_exp()

Sample from a truncated exponential distribution

set_calib_curve()

Set the radiocarbon calibration curve for an analysis

set_density_model()

Set the density model (density_model) for an analysis

set_rc_meas()

Set the radiocarbon measurements (rc_meas) for an analysis

set_sim()

Use the results of a simulation to set the radiocarbon measurements (rc_meas) for an analysis (and store the settings used to do the simulation)

shcal13

The SHCal13 Southern Hemisphere atmospheric radiocarbon calibration curve

shcal13_raw

The raw data for constructing the SHCal13 Southern Hemisphere atmospheric calibration curve

shcal20

The SHCal20 Southern Hemisphere atmospheric radiocarbon calibration curve

shcal20_raw

The raw data for constructing the SHCal20 Southern Hemisphere atmospheric calibration curve

simulate_rc_data()

summarize_bayesian_inference()
Calculate some key summary measures using the result of a call to sample_theta
summarize_trunc_gauss_mix_sample()
vis_calib_curve()