Package index • transNetwork

Simulation

Functions for generating stochastic outbreaks and trees.

simulate_outbreak(): Simulate a Stochastic Outbreak
build_timetree(): Build a Time Tree via Neighbor-Joining
sim_phytree(): Simulate a Phylogenetic Tree from a Time Tree
add_coalescent_distance(): Add Coalescent Lag to Transmission Distances

Analysis & Metrics

Tools for summarizing MCMC output and calculating distances.

summary_betnet(): Summary and Parameter Estimation for BetNet Output
find_mrci(): Find the Most Recent Common Infector (MRCI)
find_infectors(): Trace Infection Ancestry
find_all_pairwise_distances(): Compute All Pairwise Transmission Distances

Data Conversion

Internal utilities for formatting and transforming data.

transmission_edges_matrixwiw(): Convert Who-Infected-Who Matrix to Edge List
ttree_from_transmission(): Convert Outbreak Data to a ttree Object

Visualization

Plotting transmission networks and timelines.

transplot(): Plot Transmission Networks