In: Held, L., Hens, N., O'Neill, P., Wallinga, J. (Eds.): Handbook of infectious disease data analysis, 1–24
Chapman & Hall/CRC handbooks of modern statistical methods -
New York, Taylor & Francis Group (2019)
This chapter is concerned with methods for the analysis of data on outbreaks of infectious disease in which additional genomic information is available on the pathogen. Molecular typing data from viruses or bacteria isolated from individual patients can contain additional information on possible links in the contact network that have led to transmission. Higher similarity between isolates is likely indicative of a closer link in the transmission chain. Different approaches to modeling such data are reviewed, all of which have associated R packages.
Keywords: Europe, data analysis, epidemiology, infectious diseases, statistical analysis