|
add_shaded_quantiles()
|
Add a shaded region showing the min/max 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()
|
Load Calibration 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()
|
Create simulated radiocarbon data |
|
summarize_bayesian_inference()
|
Calculate some key summary measures using the result of a call to
sample_theta |
|
summarize_trunc_gauss_mix_sample()
|
Identify growth periods and the peak value for a truncated Gaussian mixture |
|
vis_calib_curve()
|
Visualize the calibration curve with equifinal and non-equifinal time spans |