New tutorial: Network analysis for infectious disease spread#160
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rossbar wants to merge 7 commits into
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New tutorial: Network analysis for infectious disease spread#160rossbar wants to merge 7 commits into
rossbar wants to merge 7 commits into
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dschult
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May 23, 2026
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Nice -- Well written; topic is relevant and interesting; provides an avenue to explore both graphically and numerically/statistically; and shows some of the complexity and difficulty in approaching the question of estimating R_0.
I approve this PR. I left a comment below, mostly to have you look at that sentence again.
Co-authored-by: Dan Schult <dschult@colgate.edu>
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Last week I stumbled upon this paper, which ultimately led me down a rabbit hole w.r.t. the basic modeling of infectious disease with networks.
Given the accessibility of the data, it also struck me as a great candidate to try to reproduce some of the results in the paper. There's a lot more that could be done here (e.g. incorporating the temporal information to estimate the changes in R_0 of the course of the outbreak), but I wanted to keep the scope as narrow as possible to start.
Caveat: I am by no means an epidemiologist! The example is very simple, but some domain knowledge to validate/challenge some of the choices I made would be important. In particular, the choice to model the transmission network as a digraph (using the
degreefor the R_0 calculation) and relying onmeanandvaras estimates of the moments of the degree distribution deserve thorough attention.