Quantifying Pathogen Surveillance Using Temporal Genomic Data

Chan, Joseph M.; Rabadan, Raul

Comparison to diversity metrics. Other alternative methods of gauging sampling bias may exist. For instance, there are many diversity metrics in ecology, including Chao's estimate of asymptotic species richness (41) , and in information theory, techniques like Shannon's entropy, which was applied in Fig. 1C . In particular, it is well known that the empirical Shannon entropy of a sample underestimates the entropy of the true distribution. Bootstrapping techniques can be used to estimate the bias produced by a low number of sequences. This method is attractive for its ability to measure surveillance by assaying the diversity of a pathogen directly. However, like the phylogenetic and bar coding methods considered, implementation for a large number of trials is substantially more difficult, computationally expensive, and time-consuming.