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VirologyCharite / SARS-CoV-2-VL-paper

Data and files from the May 25, 2021 SARS-CoV-2 viral load and infectiousness paper
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missing files #1

Closed sbfnk closed 3 years ago

sbfnk commented 3 years ago

Congratulations on this impressive work and getting the paper out.

I've tried to reproduce the analysis by rendering ExtendedMethods.Rmd but ran into an error here because the referenced file does not exist in the repo: https://github.com/VirologyCharite/SARS-CoV-2-VL-paper/blob/3aca779c084c6b61cc7adea0bfaf7dcc6808b112/utils.R#L816

Could this be added?

terrycojones commented 3 years ago

Hi Sebastian. Thank you, and thanks for pointing out the omission - sorry for the inconvenience. The file has been added.

sbfnk commented 3 years ago

Slowly making my way through the markdown, it seems to me that

CP/stan/TC_APGHB117_simple_shiftw25o.stan

is also missing, referenced here: https://github.com/VirologyCharite/SARS-CoV-2-VL-paper/blob/cc080de24f4361db904136279b7843c538e5806d/ExtendedMethods.Rmd#L1394

gbiele commented 3 years ago

Thanks for pointing this out. The content of this file is in the section "5 Stan model for time course estimation" of the R-markdown, but we'll also upload the file in a moment.

PS: depending on the system you are working on, fitting this model will take a while. To fully reproduce the results, the model will be fit with the full data set, and also for people with at least 4, at least 5, ... data points.