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- parameter_2_sample_paired_upper & parameter_2_sample_paired_lower mappings were switched around
- Mostly related to transmission parameters
- CovID: 271 - Quantile not extracted - Also updates existing Chua incubation period row - moved estimation method to parameter 2 since it relates to variability
- This is already done in the nipah cleaning task
- Adds SI plots - More cleaning and plot restructuring
- NA columns default to logical so cast as numeric
- Also updates missing uncertainty waterfall logic
- Varibility is always included as a dashed line
- Only quantile and range is provided with no central estimate
…hesis and script to run this for the nipah workflow
…tive (this may still cause issues if people run the workflow manually). Also will still need to add some pre-canned results
- Sorts by colour col and by central if sort=TRUE
- This is more stable than using the [table]_data_id
- Also adds to workflow
- Fix is based on existings changes made to lassa_functions, but unsure if this file should be changed since it impacts previous pathogens which use this file...
- This should not be changed for Nipah
- Range is more useful for meta analysis compared to IQR which was captured
… can run in reasonable time for orderly.
…pathogens into nipah_workflow
- CovID: 2931
sangeetabhatia03
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Jan 14, 2026
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sangeetabhatia03
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@tristan-myles i have tested that the workflow works for me. I have had to comment out a few lines that left graphic devices open; see commit #d5aa3b49f397e110eee15d5ed333005c635422a9 and make sure that you're happy with the edits.
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Still a WIP, but the initial skeleton of the work flow is contained in this PR.
It updates nipah_functions, with the key changes relating to updating the
data_curationandforest_plotfunctions.It adds Nipah specific cleaning. The order of pathogen specific cleaning is also updated in db_cleaning.
The order of parameter mappings are updated in shared/redcap_data/nipah/mapping_table.csv
NB,
priority-pathogens.Rprojis removed. This file should not be tracked. Please move your localpriority-pathogens.Rprojand copy it back into your folder after pulling this code.