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To support an education project around neglected infectious diseases in Sub-Saharan Africa, I aim to estimate and report some very basic epidemiological models in R to build intuition and understanding with the students.

I have been searching for a little bit (to no avail) - does anyone know of basic R-based modules / models (compartmental or agent-based) that I could use? For example - SIR models similar to these Python models (http://wiki.deductivethinking.com/wiki/Program_3.1)

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Good epidemiology packages for R to look at (I only included R packages curated in CRAN task views):

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epitools: Epidemiology Tools is another good one.

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You could try the pomp package. The last pages of its vignettes show how to create SIR models of varying complexity.

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