Adds more Nipah tasks & workflow updates#80
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thomrawson merged 29 commits intomainfrom Feb 9, 2026
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- Seperate sub rate plot is commented out
- Prevents issues in Nipah_bsl_data_synthesis where MASS::select() masks dplyr::select()
- Ordering in the plot now matches the legend
- bsl sythensis: adds make posterior summary function which returns cdf draws - nipah bsl task: wraps chunks of the code so that the model doesn't need to be rerun, and adds new plots
- Two linetypes are uncertainty and variability
- metaprop has more specific text size updates compared to metamean
- Delays (CovID 2931), splits estimated and observed incubation periods and serial intervals - Serology (CovID 2892), typo in the paper for uncertainty lower bound
- This is a shared orderly resource
- Overhaul of precious main figure
- Note, this task was previously written to account for QA and non-QA plots, and this needs to be
updated since we now have a single non-QA version which we use.
- Specific updates:
- Reorders hospitalisation to outcome factor order
- Updates bsl plot to use the CDF version
- Groups symptom-onset-to-death with symptom-onset-to-outcome plot
- Adds discharge/recovery to symptom onset outcomes
- Facets symptom-onset-to-outcome and hospitalisation-to-outcome
- Adds serial interval panel
- Updates final figure formatting, including legend position and panel
layout
- Also applies legend formatting
- Also updates axis titles and label order in final plot
- Moves CFR meta analysis code from nipah_serology here - Adds cleaned outbreak data (read in from outbreaks) - Adds CFR deduplication for extracted parameters - Updates CFR forest plot to only show deduplicated estimates with QA alpha filtering - Adds percentage symptomatic panel
- Removed unnecessary mapping, CFR, and sero meta analysis code - Updates task to only create plots (3 individual plots and 1 combined patchwork plot which uses 2/3 individual plots) - Adds point size argument to forest plotting func
- Note, only metaprop is updated
- Also updates forest plots
- The bsl tasks loads MASS which is problematic since it masks dplr::select which isn't explicitly called throughout the remaining tasks. Detaching MASS was problematic since it's used by other packages, so an imperfect fix is applied. MASS also masks patchwork::area; the same fix was applied for completeness, but the area function is not used in any subsequent tasks.
- In anticipation of moving to new orderly version
- Need to decide how to deal with shape files - Current approach won't work due to an additional folder when the task is in draft (compared to running directly from src). Additionally, current approach is not good orderly practice, but we don't want the file to be copied each time as a shared resource.
- Incorrect artefact path (additional figures still need to be added), missing colour param, and incorrect plot var name
- Consistent with the other tasks, but this will be updated to orderly
- This is created in nipah_maps and copied to shared. This should be an orderly dependency but since we are not running nipah_maps as a task at the moment, using this approach as a temp fix.
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All seems to work for me! |
thomrawson
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Feb 9, 2026
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thomrawson
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All seems to work for me!
Needed for MERS too.
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Note all tasks still use orderly2, and will be updated to orderly in a future PR.