# Tools for 'outbreaker2'

## Documentation for package ‘o2ools’ version 0.0.1

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

## Help Pages

augment_linelist | Append summaries of outbreaker results to a linelist
filter_chain | Filter chain by parameter threshold
get_accuracy | Calculate the accuracy of outbreak reconstruction
get_consensus | Get the consensus transmission tree
get_entropy | Compute the entropy of transmission trees
get_Ri | Compute case reproduction numbers (Ri) from outbreaker2 chains
get_si | Compute the serial interval (si) from transmission trees
get_trees | Extract posterior transmission trees
identify | Replace integers in outbreaker2 output with unique identifiers
linelist | Simulated linelist with group labels
out | outbreaker2 toy dataset
sample.outbreaker_chains | Sample rows from an outbreaker_chains object
ttable | Compute the transmission contingency table