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