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https://github.com/sempwn/r_epidemiology
Introduction to epidemiological modelling using R
https://github.com/sempwn/r_epidemiology
epidemiology modelling r
Last synced: 2 months ago
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Introduction to epidemiological modelling using R
- Host: GitHub
- URL: https://github.com/sempwn/r_epidemiology
- Owner: sempwn
- License: mit
- Created: 2018-01-25T21:45:14.000Z (almost 7 years ago)
- Default Branch: master
- Last Pushed: 2024-07-17T18:55:12.000Z (6 months ago)
- Last Synced: 2024-10-12T01:22:28.901Z (3 months ago)
- Topics: epidemiology, modelling, r
- Language: R
- Size: 19.5 KB
- Stars: 6
- Watchers: 1
- Forks: 2
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# R_epidemiology
Introduction to epidemiological modelling using R. We'll be following a number
of papers and blogs in order to introduce a variety of mathematical epidemiology
methods.
## Previous Papers
* [Noncollapsibility, confounding, and sparse data bias](https://doi.org/10.1016/j.jclinepi.2021.06.007)
* June 2018 [An introduction to data imputation](http://www.stat.columbia.edu/%7Egelman/arm/missing.pdf)
* Feb 2018. [An introduction to infectious disease modelling](http://sbfnk.github.io/chennai-modelling/index.html)
* Jan 2018. [A clarification of transmission terms in host-microparasite models: numbers, densities and areas.](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2869860/)
* Nov 2017. [Perturbations in Epidemiological Models: When zombies attack, we can survive!](http://dx.doi.org/10.1080/23737867.2014.11414478 )
* Oct 2017. [Modelling and calibration of the hepatitis C epidemic in Australia.](https://www.ncbi.nlm.nih.gov/pubmed/19036911)
* Sep 2017. [Vicious and virtuous circles in the dynamics of infectious disease and the provision of health care: gonorrhea in Britain as an example.](https://www.ncbi.nlm.nih.gov/pubmed/16088832)
* July 2017. [Estimating the future burden of multidrug-resistant and extensively drug-resistant tuberculosis in India, the Philippines, Russia, and South Africa: a mathematical modelling study.](https://www.ncbi.nlm.nih.gov/pubmed/28499828)
* June 2017. [Optimizing an HIV testing program using a system dynamics model of the continuum of care](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4543429/pdf/10729_2014_Article_9312.pdf)
* May 2017. [Modeling influenza epidemics and pandemics: insights into the future of swine flu (H1N1)](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2715422/ )
## Proposed papers and tutorials
* [Estimating the fitness cost and benefit of cefixime resistance in Neisseria gonorrhoeae to inform prescription policy: A modelling study](http://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1002416&type=printable)
* [Introduction to POMP for partially observed data](http://kingaa.github.io/short-course/)
* [Epimodel R package](http://www.epimodel.org/index.html)
* [Principled Bayesian workflow](https://betanalpha.github.io/assets/case_studies/principled_bayesian_workflow.html)
* [Reflection on modern methods: a common error in the segmented regression parameterization of interrupted time-series analyses](https://academic.oup.com/ije/article/50/3/1011/5937253)
* [Philosophy and the practice of Bayesian statistics](http://www.stat.columbia.edu/~gelman/research/published/philosophy.pdf)
## R script examples
* [Comparison of marginal and total odds ratios](collapsible_odds_ratios.R)
* [Comparison between frequency-dependent and density-dependent transmission](frequency-density-dynamics-comparison.R)
* [Vaccination rate in SIR](simple_SIR.R)
* [Introduction to differential equations (Feb 2018)](introduction_to_differential_equations.R)
* [Introduction to data imputation (June 5th 2018)](introduction_to_data_imputation.R)
* [Introduction to data imputation (June 19th 2018)](introduction_to_probabilistic_record_linkages.R)