Phylogeographic Analysis Similars - Agent Based Simulations

This dataset provides high-resolution, synthetic transmission networks generated as the foundational layer for the PhyloGeographic Analysis Similars (PhyloGAS) framework. PhyloGAS is an open-source benchmarking ecosystem designed to quantify the performance and observational biases of public health genomic surveillance pipelines (e.g., Nextstrain, ClusterTracker). Because the absolute "ground truth" of a viral outbreak—exactly who infected whom and when—is never perfectly known in real-world scenarios, testing the accuracy of phylodynamic reconstruction tools is a significant challenge. This dataset provides that ground truth.The disease model, importation schedule, and other Ephiper parameter settings are documented at https://github.com/NSSAC/PhyloGAS Contents of this Dataset:The initial version of this repository contains the outputs generated by the EpiHiper Agent-Based Model (ABM), more may be added over time. The primary data structures are detailed transmission dendrograms (event logs representing the exact transmission chain between simulated individuals over time). This initial release contains one baseline simulation replicate for six specific U.S. states. This includes the five states representing the CDC's Pathogen Genomics Centers of Excellence (PGCOE): Georgia (GA), Massachusetts (MA), Minnesota (MN), Virginia (VA), Washington (WA). These datasets were produced using:Biocomplexity Institute Synthetic Populatons v2.4.0 https://dataverse.lib.virginia.edu/dataverse/biocomplexityEpiHiper version: v2.0 https://github.com/NSSAC/EpiHiper