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 |