hospitraceR detects transmission clusters of healthcare-associated pathogens by combining whole-genome sequencing data with patient location traces, surveillance cultures, and admission status.
Beyond clustering, the package can:
- compare two cluster assignments, both structurally and epidemiologically;
- categorize each patient’s transmission role and attempt to “explain” transmission scenarios in clusters using spatiotemporal overlap information;
- summarize per-cluster genetic distances and acquisition timing;
and more. See the introductory article for a guided introduction.
Plotting lives in the companion package hospitraceRVisualize.