Approximate Bayesian Computation

validate_abc()

Validate individual components of an ABC model

simulate_abc()

Simulate data for ABC inference using specified priors

run_abc()

Perform ABC on data generated by simulate_abc

Grid-based inference

simulate_grid()

Simulate values of summary statistics across a parameter grid

Genetic algorithms

compute_fitness()

Compute the fitness of the given parameter set against observed data

run_ga()

Run genetic algorithm (GA) inference of the parameters of the given model

ABC cross-validation and posterior checks

unpack()

Unpack demografr object into individual components of the abc package

cross_validate()

Perform cross-validation using the anc::cv4postpr function

select_model()

Perform selection between different ABC models

goodness_of_fit()

Peform a test of the goodness-of-fit of a given model

predict(<demografr_abc.abc>)

Generate summary statistics from the inferred posterior distribution of parameters

extract_prediction()

Unnest the predicted values of a given statistic from the simulated data

plot_prediction()

Plot the results of a posterior predictive check for a given summary statistic

Analysis of ABC inference results

extract_summary()

Extract table of estimated model parameters

extract_posterior()

Extract inferred posterior(s) as a standard data frame

plot_prior()

Plot prior distribution(s)

plot_posterior()

Plot posterior distribution of given parameters

plot(<demografr_abc.abc>)

Plot diagnostics of posterior distribution(s)

hist(<demografr_abc.abc>)

Plot histogram of posterior distribution(s)

Helper functions

summarise_data()

Apply summary statistic functions to the simulated data

simulate_model()

Simulate a single tree sequence from the given inference setup

combine_data()

Combine multiple individual ABC simulation runs into one

sample_prior()

Sample value from a given prior sampling formula object