Naive Bayes Transmission Analysis
Clusters the infectors based on their transmission probabilities
Estimates the effective reproductive number
Estimates individual-level reproductive numbers
Estimates time-level reproductive numbers
Estimates the average effective reproductive number
Estimates the generation/serial interval distribution
Transforms a dataset of individuals to a dataset of pairs
Plots a heatmap of the relative transmission probabilities
Plots a network of the relative transmission probabilities
Estimates relative transmission probabilities
Performs naive bayes classification
Executes the PEM algorthim to estimate the generation/serial interval ...
Creates a plot of the effective reproductive number
Estimates the relative transmission probabilities between cases in an infectious disease outbreak or cluster using naive Bayes. Included are various functions to use these probabilities to estimate transmission parameters such as the generation/serial interval and reproductive number as well as finding the contribution of covariates to the probabilities and visualizing results. The ideal use is for an infectious disease dataset with metadata on the majority of cases but more informative data such as contact tracing or pathogen whole genome sequencing on only a subset of cases. For a detailed description of the methods see Leavitt et al. (2020) <doi:10.1093/ije/dyaa031>.
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