create_config |
Set and check parameter settings |
create_param |
Initializes outputs for outbreaker |
custom_likelihoods |
Customise likelihood functions for o2geosocial |
custom_moves |
Customise samplers for outbreaker |
custom_priors |
Customise priors for outbreaker |
outbreaker |
outbreaker: main function for reconstructing disease outbreaks |
outbreaker_chains |
Basic methods for processing outbreaker results |
outbreaker_data |
Process input data for outbreaker |
outbreaker_param |
Initializes outputs for outbreaker |
outbreaker_store |
Initializes outputs for outbreaker |
plot.outbreaker_chains |
Basic methods for processing outbreaker results |
pre_clustering |
Pre cluster cases in groups according using the genotypes and the arbitrary thresholds gamma (spatial) and delta (temporal). |
print.custom_likelihoods |
Customise likelihood functions for o2geosocial |
print.custom_priors |
Customise priors for outbreaker |
print.outbreaker_chains |
Basic methods for processing outbreaker results |
summary.outbreaker_chains |
Basic methods for processing outbreaker results |
toy_outbreak_long |
Simulated outbreaks |
toy_outbreak_short |
Simulated outbreaks |