rebase oropouche-analysis branch#81

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ruthmccabe wants to merge 445 commits into

oropouche-analysisfrom

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Commits on Apr 16, 2025

Fixes mapping table bug
tristan-myles
committed

Commits on Apr 17, 2025

Merge pull request #67 from mrc-ide/prepare-redcap-updates
sangeetabhatia03
authored

Commits on May 6, 2025

update to plotting function and add tasks to workflow
Kelly McCain
committed
more cleaning - filter out papers that shouldn't have been included, fix errors in locations/countries/denominators/numerators/dates, etc
Kelly McCain
committed
fixes to delay and genomic and R plots, move legend inside; remove filter to only % for zcs
Kelly McCain
committed
fine tuning summary plots, rfs, outbreaks
Kelly McCain
committed
fix dates for latex tables; small edits
Kelly McCain
committed
handle units for inverse params
Kelly McCain
committed

Commits on May 12, 2025

Commits on May 13, 2025

Commits on May 15, 2025

Merge pull request #69 from mrc-ide/prepare-redcap-id-log-update
sangeetabhatia03
authored

Commits on May 16, 2025

Edits to make Zika run
sangeetabhatia03
committed
add serop and other pars tasks + other changes
Kelly McCain
committed
update extraction task
Kelly McCain
committed
Merge branch 'zika' of https://github.com/mrc-ide/priority-pathogens into zika
Kelly McCain
committed

Commits on May 22, 2025

allow changing labels in meta-analysis plot
Kelly McCain
committed
edits to serop tasks; add country and sample type stratification to meta-analysis plots
Kelly McCain
committed

Commits on May 23, 2025

Commits on May 30, 2025

Commits on Jun 2, 2025

updates to location and country labels and plotting function; fix R and delays plots
Kelly McCain
committed

Commits on Jun 3, 2025

update language to use probability isntead of risk or rate
Kelly McCain
committed
fix genomic parameters; and do calculation for plotting, change latex table country to location and country
Kelly McCain
committed

Commits on Jun 4, 2025

update annotation of summary plot
Kelly McCain
committed
fix location of legend for czs plot and add funnel plots
Kelly McCain
committed
clean up latex tables
Kelly McCain
committed
clean up genomic plots
Kelly McCain
committed
change risk to probability, fix mistakes
Kelly McCain
committed
add small space in x axis plotting function
Kelly McCain
committed

Commits on Jun 5, 2025

Commits on Jun 6, 2025

updates to serop, R, czs outputs
Kelly McCain
committed
change plot colors; remove filtering of parameters from figure; fix bug in prep data that duplicated qa_score col for genomic df
Kelly McCain
committed

Commits on Jun 10, 2025

Commits on Jun 11, 2025

Commits on Jun 12, 2025

add in the czs cleaning code and associated file; update plots in czs task
Kelly McCain
committed
update cleaned data and add to compilation task
Kelly McCain
committed

Commits on Jun 18, 2025

outbreak location and country cleaning
Kelly McCain
committed

Commits on Jun 19, 2025

Adds more param cleaning
tristan-myles
committed

Commits on Jun 20, 2025

Commits on Jun 25, 2025

Merge pull request #70 from mrc-ide/nipah_workflow
sangeetabhatia03
authored

Commits on Jun 29, 2025

Commits on Jun 30, 2025

updates to czs meta-analysis
Kelly McCain
committed
Merge branch 'zika' of github.com:mrc-ide/priority-pathogens into zika
tristan-myles
committed
commit Rproj id
Kelly McCain
committed
Merge branch 'zika' of https://github.com/mrc-ide/priority-pathogens into zika
Kelly McCain
committed

Commits on Jul 4, 2025

add missing czs probabilities; change to pregnancy loss; updates to the czs plots
Kelly McCain
committed

Commits on Jul 8, 2025

Clean up user env by removing added location
sangeetabhatia03
committed
add oxtraction prep
Kelly McCain
committed
Merge branch 'zika' of https://github.com/mrc-ide/priority-pathogens into zika
Kelly McCain
committed
add facet_by_trimester
Kelly McCain
committed

Commits on Jul 14, 2025

remove unneeded variables for final datasets
Kelly McCain
committed
update to fixing files (from a long time ago)
Kelly McCain
committed

Commits on Sep 11, 2025

Change "probability" to "proportion" and remove duplicated cleaning (now in csv file of checked vars)
Kelly McCain
committed

Commits on Sep 12, 2025

update to data_curation task to reflect removal of _2 variables
Kelly McCain
committed
add zika vignette
Kelly McCain
committed

Commits on Sep 22, 2025

remove zika-specific statements as no longer needed
Kelly McCain
committed
vignette updates
Kelly McCain
committed
remove unneeded function
Kelly McCain
committed
clean up workflow script
Kelly McCain
committed
update gitignore
Kelly McCain
committed
Add shapefiles and update serop task to work with shapefiles.
Kelly McCain
committed
make zika-specific forest plot function and update code with new function name
Kelly McCain
committed

Commits on Sep 23, 2025

remove the sars task
Kelly McCain
committed
remove printing of sero plot
Kelly McCain
committed
add webshot2 package to sars vignette
Kelly McCain
committed
Update error message for existing output folder
sangeetabhatia03
authored
Merge pull request #71 from mrc-ide/zika
sangeetabhatia03
authored
update data_curation to be data_curation_zika
Kelly McCain
committed

Commits on Sep 24, 2025

Commits on Oct 20, 2025

Commits on Oct 23, 2025

Commits on Dec 1, 2025

Adds sort option to forest plot
tristan-myles
committed

Commits on Dec 2, 2025

Commits on Jan 6, 2026

Commits on Jan 7, 2026

Commits on Jan 14, 2026

Commits on Jan 26, 2026

Adds bsl plot and linetype to legend
tristan-myles
committed

Commits on Feb 2, 2026

Commits on Feb 3, 2026

Commits on Feb 9, 2026

Merge pull request #80 from mrc-ide/nipah_workflow_updates
thomrawson
authored