[conspire] And why open source math in science papers is a good thing

[Deirdre Saoirse Moen]

https://smw.ch/article/doi/smw.2020.20336

> In the fitting procedure used in the manuscript Fig1c_Rscript.R (available at https://github.com/ehylau/COVID-19 <https://github.com/ehylau/COVID-19>), the following condition is used in the return line of the likelihood function:
>      return(-sum(lli[!is.infinite(lli)]))
> This condition will erroneously drop any data-point that has a probability of zero (and hence a log-probability of −∞) under the current model parameters. As the optimisation is initiated with a shift value of 2.5 days, two data-points (54 and 68) are dropped from the beginning of the fit procedure. This then leads to an erroneous maximum likelihood infectiousness profile, which is displayed in figure 1C of the original manuscript [1 <https://smw.ch/article/doi/smw.2020.20336#5573e39b6600496d40f493d00ec7658479a19607>].

paper tl;dr: infectivity date isn’t 2-3 days prior to symptom start, it’s 4-5.

Deirdre
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