# Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data

## Documentation for package ‘outbreaker2’ version 1.1.3

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

## Help Pages

bind_to_function | Encloses argument in a function's environment
cases_pal | Color palettes used in outbreaker
chains_pal | Color palettes used in outbreaker
create_config | Set and check parameter settings of outbreaker
create_param | Initializes outputs for outbreaker
custom_likelihoods | Customise likelihood functions for outbreaker
custom_moves | Customise samplers for outbreaker
custom_priors | Customise priors for outbreaker
fake_outbreak | Small simulated outbreak
get_cpp_api | Access internal C++ rountines used in outbreaker2
outbreaker | outbreaker2: main function for reconstructing disease outbreaks
outbreaker_chains | Basic methods for processing outbreaker results
outbreaker_data | Process input data for outbreaker
outbreaker_package | outbreaker2: a platform for disease outbreak reconstruction
outbreaker_palettes | Color palettes used in outbreaker
outbreaker_param | Initializes outputs for outbreaker
outbreaker_store | Initializes outputs for outbreaker
plot.outbreaker_chains | Basic methods for processing outbreaker results
print.custom_likelihoods | Customise likelihood functions for outbreaker
print.custom_priors | Customise priors for outbreaker
print.outbreaker_chains | Basic methods for processing outbreaker results
print.outbreaker_config | Set and check parameter settings of outbreaker
print.outbreaker_moves | Customise samplers for outbreaker
sim_ctd | Simulate contact data from a transmission tree
summary.outbreaker_chains | Basic methods for processing outbreaker results