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_resources.qmd
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## Textbooks
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{width="60%"}
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## Papers and Articles {.smaller}
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### Modelling infectious disease transmission
- Grassly, N. C., & Fraser, C. (2008). Mathematical models of infectious disease transmission. Nature Reviews Microbiology, 6(6), 477–487. <https://doi.org/10.1038/nrmicro1845>
- Kirkeby, C., Brookes, V. J., Ward, M. P., Dürr, S., & Halasa, T. (2021). A practical introduction to mechanistic modeling of disease transmission in veterinary science. Frontiers in veterinary science, 7, 546651. <https://www.frontiersin.org/articles/10.3389/fvets.2020.546651/full>
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- Blackwood, J. C., & Childs, L. M. (2018). An introduction to compartmental modeling for the budding infectious disease modeler. <https://vtechworks.lib.vt.edu/items/61e9ca00-ef21-4356-bcd7-a9294a1d2f17>
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- Cobey, S. (2020). Modeling infectious disease dynamics. Science, 368(6492), 713–714. <https://doi.org/10.1126/science.abb5659>
- Bjørnstad, O. N., Shea, K., Krzywinski, M., & Altman, N. (2020). Modeling infectious epidemics. Nature Methods, 17(5), 455–456. <https://doi.org/10.1038/s41592-020-0822-z>
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- Bodner, K., Brimacombe, C., Chenery, E. S., Greiner, A., McLeod, A. M., Penk, S. R., & Soto, J. S. V. (2021). Ten simple rules for tackling your first mathematical models: A guide for graduate students by graduate students. PLOS Computational Biology, 17(1), e1008539. <https://doi.org/10.1371/journal.pcbi.1008539>
- Mishra, S., Fisman, D. N., & Boily, M.-C. (2011). The ABC of terms used in mathematical models of infectious diseases. Journal of Epidemiology & Community Health, 65(1), 87–94. <https://jech.bmj.com/content/65/1/87>
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- James, L. P., Salomon, J. A., Buckee, C. O., & Menzies, N. A. (2021). The Use and Misuse of Mathematical Modeling for Infectious Disease Policymaking: Lessons for the COVID-19 Pandemic. 41(4), 379–385. <https://doi.org/10.1177/0272989X21990391>
- Holmdah, I., & Buckee, C. (2020). Wrong but useful—What COVID-19 epidemiologic models can and cannot tell us. New England Journal of Medicine. <https://doi.org/10.1056/nejmp2009027>
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- Metcalf, C. J. E. E., Edmunds, W. J., & Lessler, J. (2015). Six challenges in modelling for public health policy. Epidemics, 10(2015), 93–96. <https://doi.org/10.1016/j.epidem.2014.08.008>
- Roberts, M., Andreasen, V., Lloyd, A., & Pellis, L. (2015). Nine challenges for deterministic epidemic models. Epidemics, 10(2015), 49–53. <https://doi.org/10.1016/j.epidem.2014.09.006>
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### Deriving and Interpreting R0 {.smaller}
- Jones, J. H. (2011). Notes On R0. Building, 1–19. <https://web.stanford.edu/\~jhj1/teachingdocs/Jones-on-R0.pdf>
- Diekmann, O., Heesterbeek, J. A. P., & Metz, J. A. J. (1990). On the definition and the computation of the basic reproduction ratio R0 in models for infectious diseases in heterogeneous populations. Journal of Mathematical Biology, 28(4), 365–382. <https://doi.org/10.1007/BF00178324>
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- Diekmann, O., Heesterbeek, J. A. P., & Roberts, M. G. (2010). The construction of next-generation matrices for compartmental epidemic models. Journal of the Royal Society Interface, 7(47), 873–885. <https://doi.org/10.1098/rsif.2009.0386>
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## Code repositories {.smaller}
- [epirecipes](http://epirecip.es/epicookbook/): Code for collate mathematical models of infectious disease transmission, with implementations in R, Python, and Julia.
- [Modeling Infectious Diseases in Humans and Animals](http://www.modelinginfectiousdiseases.org/): Code for the labelled programs in the book "Modeling Infectious Diseases in Humans and Animals". They are generally available as C++, Fortran and Matlab files.