Updates to NiV tasks after internal review#82
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- This should be read in as a dependency on the nipah_serology task
- Split short and long term tests into two seperate columns - Note, ggstar is required to generate different shapes to those used for parameter types
- Also breaks long lines
…c-ide/priority-pathogens into nipah_internal_review_updates
- Also coalesces param value and central so that central ranges have a point in the forest plot
- Matches other plots; note, legend is alphabetical rather than the forest plot sort order
- Consistent across plots; severe illness has a varb lower limit = 0
- Both the bsl plot and qa filtered plots are due to be removed
- This is no longer set to NA
- Replaces bsl with incp meta analysis - Restructures final figure - Removes orderly_artefacts for convience (properly listing them is a todo)
- Adds shared/nipah_raw_data.csv since download dep is now false; note the file was downloaded from REDCap at 18:38 on 20/03/2026
- No longer masked by MASS since bsl has been removed
- Now matches orderly artefact
- Removed so that the task completes; adding this back is a todo
- Neater for orderly run
- Prevents plot from showing - better for orderly run
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hi @tristan-myles unfortunately the workflow does not run for me and fails with the following error: This is in a fresh clone of the repo. Let's discuss after the break. |
- Note the file was downloaded from REDCap at 11:23 on 06/01/2026
- Duplicate individual plots being saved - this script needs to be refined
- Duplicate individual plots being saved
- Note: saved pdfs are large since maps are being saved
- Duplicate individual plots being saved
- Removes sero png plot dependency from map_alternate since it's not used
2 participants
! Please run all lines in the
nipah_workflow.Rfile to check this PR. !Far too many update to describe in detail - sorry!
Changes have only been made to NiV specific tasks, NiV specific cleaning, and NiV functions.
The workflow file has been updated to include all NiV tasks. The download dependency has also been set to False, and the raw data (downloaded from REDCap at 18:38, 20/03/2026) has been uploaded to shared. This will allow the task to be run by someone without API access to REDCap and ensures the reproducibility of our work independent of REDCap. If a change is made to the data on REDCap, e.g. new data added after review, update the workflow file by uncommenting the db_redcap_download task and set the download dependency to TRUE in db_extraction_prep.