Bayesian Reconstruction of Disease Outbreaks by Combining
Epidemiologic and Genomic Data
![[R logo]](../../../doc/html/Rlogo.svg)
![[Up]](../../../doc/html/left.jpg)
![[Top]](../../../doc/html/up.jpg)
Documentation for package ‘outbreaker2’ version 1.1.3
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 |