Added estimating individual-level transmission vignette and poisson compound functions #15
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joshwlambert
added
documentation
This was referenced May 24, 2023
adamkucharski
approved these changes
May 26, 2023
Co-authored-by: Adam Kucharski <adam.kucharski@lshtm.ac.uk>
Co-authored-by: Adam Kucharski <adam.kucharski@lshtm.ac.uk>
Co-authored-by: Adam Kucharski <adam.kucharski@lshtm.ac.uk>
Co-authored-by: Adam Kucharski <adam.kucharski@lshtm.ac.uk>
Co-authored-by: Adam Kucharski <adam.kucharski@lshtm.ac.uk>
Co-authored-by: Adam Kucharski <adam.kucharski@lshtm.ac.uk>
Co-authored-by: Adam Kucharski <adam.kucharski@lshtm.ac.uk>
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This PR addresses #1 and #4.
It adds four new functions which calculate the density and cumulative distribution functions for the Poisson-lognormal and Poisson-Weibull compound distributions.
It adds a new vignette which outlines estimating the parameters for distribution models to understand whether individual-level transmission shows signatures of overdispersion (or superspreading), and how to use {superspreading} with {fitdistrplus} to compare models, including the Poisson compound distributions now included in the package.
Tests and function documentation have been added and updated in line with the changes above. The references JSON file has been updated to include the new papers cited by the new vignette.