Tools for 'outbreaker2'
Append summaries of outbreaker results to a linelist
Compute entropy of a categorical variable
Filter chain by parameter threshold
Calculate the accuracy of outbreak reconstruction
Get the consensus transmission tree
Compute the entropy of transmission trees
Compute case reproduction numbers (Ri) from outbreaker2 chains
Compute the serial interval (si) from transmission trees
Extract posterior transmission trees
Replace integers in outbreaker2 output with unique identifiers
Check if the object conforms to linelist expectations
Check if an object is a data frame of class 'outbreaker_chains'
Sample rows from an outbreaker_chains object
Compute the transmission contingency table
Streamlines the post-processing, summarization, and visualization of 'outbreaker2' output via a suite of helper functions. Facilitates tidy manipulation of posterior samples, integration with case metadata, generation of diagnostic plots and summary statistics.
Useful links