Reference

All functions

clusterInfectors()

Clusters the infectors based on their transmission probabilities

estimateR()

Estimates the effective reproductive number

estimateRi()

Estimates individual-level reproductive numbers

estimateRt()

Estimates time-level reproductive numbers

estimateRtAvg()

Estimates the average effective reproductive number

estimateSI()

Estimates the generation/serial interval distribution

indData

Individual-level simulated outbreak dataset

indToPair()

Transforms a dataset of individuals to a dataset of pairs

nbHeatmap()

Plots a heatmap of the relative transmission probabilities

nbNetwork()

Plots a network of the relative transmission probabilities

nbProbabilities()

Estimates relative transmission probabilities

nbResults

Dataset with results of nbProbabilities

pairData

Pair-level simulated outbreak dataset

performNB()

Performs naive bayes classification

performPEM()

Executes the PEM algorthim to estimate the generation/serial interval distribution

plotRt()

Creates a plot of the effective reproductive number