Reference

Core Functions
prepare_epifusion_tree()	Prepare a tree (or trees) for EpiFusion
generate_epifusion_XML()	Generate an EpiFusion XML file
run_epifusion()	Run EpiFusion from R
load_raw_epifusion()	Load results from EpiFusion folder into an R object
extract_posterior_epifusion()	Parse results from raw EpiFusion object into a R object with infection, Rt, cumulative infection and parameter posteriors
trajectory_table()	Extract a trajectory table from an EpiFusion posterior R object
Sample Datasets
baseline_dataset()	Load baseline simulated dataset for trying EpiFusion
sampling_dataset()	Load step-change in sampling simulated dataset for trying EpiFusion
Individual Result Loading Functions
load_acceptance()	Load acceptance rates from EpiFusion folder into an R object
load_beta_trajectories()	Load beta trajectories from EpiFusion output folder into a list of dataframes
load_cumulativeinfection_trajectories()	Load cumulative infections trajectories from EpiFusion output folder into a list of dataframes
load_fitted_epi_cases()	Load trajectories of fitted epidemiological cases from EpiFusion output folder into a list of dataframes
load_infection_trajectories()	Load infection trajectories from EpiFusion folder into a list of dataframes
load_likelihoods()	Load likelihood trace from each chain of an EpiFusion analysis
load_parameter_samples()	Load parameter samples from EpiFusion analysis
load_rt_trajectories()	Load Rt trajectories from EpiFusion folder into a list of dataframes
Plotting Functions
plot_likelihood_trace()	Plots the likelihood trace of the chains of an EpiFusion analysis
plot_parameter_trace()	Plot the parameter traces from a raw EpiFusion object
plot_trajectories()	Plot the trajectory posteriors from a parsed EpiFusion trajectory table
plot_chainwise_trajectories()	Plot the trajectory posteriors from a raw EpiFusion object separated by chain
Other Functions
calculate_daily_infections()	Calculate means and HPD intervals of new infections per day from the cumulative infections posterior samples