Lassa and Ebola workflows on main are broken because some markers were left in while closing previous PRs.
This PR is intended to fix them. As part of this, I have had to separate out code chunks from db_cleaning into smaller scripts and functions because the mammoth script was impossible to debug.
I have checked that the code now works for Lassa and SARS; still broken for Ebola for potentially some different reason.
I'll fix Ebola workflow separately and as part of that work package, also bring together the changed made for revision to the paper.
Lassa and Ebola workflows on main are broken because some markers were left in while closing previous PRs. This PR is intended to fix them. As part of this, I have had to separate out code chunks from db_cleaning into smaller scripts and functions because the mammoth script was impossible to debug. I have checked that the code now works for Lassa and SARS; still broken for Ebola for potentially some different reason. I'll fix Ebola workflow separately and as part of that work package, also bring together the changed made for revision to the paper.