Evaluating Transmission Reconstruction Accuracy

library(transNetwork)
library(TransPhylo)

Introduction

This vignette demonstrates how to evaluate the accuracy of the TransPhylo inference engine using the utility functions in transNetwork. We simulate a “ground truth” outbreak, perform Bayesian inference, and then compare the results to see how many infector-infectee pairs were correctly identified.

The Simulation Loop

In this example, we run numsim iterations. For each iteration, we simulate a small outbreak of 10 individuals.

set.seed(42)
numsim <- 10
accuracy_scores <- numeric(numsim)

for (i in 1:numsim) {
    # 1. Simulate an outbreak with R0 = 1.0 (infection_rate / removal_rate)
    outbreak <- simulate_outbreak(infection_rate = 3.0, removal_rate = 3.0, target_size = 10)
    numcase <- nrow(outbreak)

    # 2. Build the phylogenetic time tree (the input for TransPhylo)
    timetree <- build_timetree(outbreak, plot = FALSE)
    
    # 3. TransPhylo inference
    ptree <- TransPhylo::ptreeFromPhylo(timetree, dateLastSample = 2007.964)
    res <- TransPhylo::inferTTree(ptree, mcmcIterations = 10000, w.shape = 10, w.scale = 0.1, dateT = 2008)

    # 4. Process Who-Infected-Whom (WIW) matrix
    matrixwiw <- TransPhylo::computeMatWIW(res, burnin = 0.5)
    
    # Use transNetwork utility to convert matrix to edge list
    netedges <- transmission_edges_matrixwiw(matrixwiw)
    
    # 5. Calculate Accuracy
    # Compare the inferred infector (Column 2 of netedges) with the truth (Column 2 of outbreak)
    correct_matches <- length(which(as.numeric(netedges[, 2]) - outbreak[, 2] == 0)) 
    accuracy_scores[i] <- correct_matches / (numcase-1)
}
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Results and Analysis

Once the simulations are complete, we can calculate the mean accuracy. This metric represents the probability that the model correctly identifies the true source of infection for a given case.

mean_acc <- mean(accuracy_scores)
print(paste("Average Reconstruction Accuracy:", round(mean_acc, 3)))
#> [1] "Average Reconstruction Accuracy: 0.356"

Visualizing the Reconstructed Network

Finally, we can use transplot to visualize the network from the final simulation. In this plot, the source is highlighted in grey, and edge colors indicate the posterior probability of the transmission link.

# Plotting the last simulated network
transplot(netedges, style = 1)