MCMC R estimate documents MERS but variables indicate H5 flu

[joshwlambert]

The howto script to estimate R and k using MCMC documents that it uses MERS data, but the variable names in the script indicate H5 flu. This was a bit confusing so clarifying which data is used, or if the data is mock data to represent a certain scenario would be helpful.

CCing @adamkucharski as I believe you wrote the howto script originally.

[avallecam]

Is that branch related to the current entry published on the website? https://epiverse-trace.github.io/howto/analyses/quantify_transmission/reproduction_number_cluster_size.html

[adamkucharski]

Yep, that was a quick exploration of H5 on a branch, swapping out the MERS data for Indonesia H5 – the live website version is all MERS

[joshwlambert]

Apologies, I was directed to the script from a link and hadn't realised I wasn't on the main branch, thanks for the explanation and the link to the website version.

As this issue was opened based on my misunderstanding it can now be closed without any further actions.

Is it worth integrating the H5 example into the MERS example, either adding it below or having tab set code chunks to allow users to click between them? I'd be happy to make this addition if so.

[adamkucharski]

Yep, think it could be nice to have both examples, especially as H5 includes a prior (a bit like we have Ebola + COVID for the reconstructing infections howto)

[joshwlambert]

I've added the H5 example from the h5_example branch into the MERS example in PR #111.

@adamkucharski I noticed that the h5_example branch also has two other scripts that are not on main. Should these be merged to be available on the howto website?