# Reconstruction of Transmission Chains from Surveillance Data

## Documentation for package ‘o2geosocial’ version 1.1.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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