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New package: creating discrete distributions with given average / quantiles #25

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mjrolland opened this issue Nov 11, 2020 · 3 comments

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@mjrolland
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It often happens that key epidemiological distributions of COVID-19 are reported in the literature, not as readily-useable distributions, but e.g. by specifying the mean, median, and given quantiles. Creating the corresponding discrete distribution e.g. from a Gamma or a Weibull can be tricky. It would be great to have a new package implementing these.

[impact: Delay distributions are used throughout epi analysis, e.g. in assessing transmissibility, or when forecasting cases or bed occupancy. This package would facilitate the use of published delays drastically. ]
[originally proposed by @thibautjombart]
[suggested repo: Do not know]
[additional notes: ]

@thibautjombart
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Note: a discussion, including code gists, was initiated on reconhub/covid19hub#4

@RMHogervorst
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If I may jump in here. Finding discrete values for a given mean/ median and standard deviation can be done using the SPRITE method https://hackernoon.com/introducing-sprite-and-the-case-of-the-carthorse-child-58683c2bfeb.
I think that method uses the normal distribution, but we could change that.

@RMHogervorst
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Wait maybe I'm confusing things here. You don't want the actual underlying numbers but a distribution description

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