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correlates_reporting_usgcove_archive
Reproducible reporting workflows for the immune correlates statistical analyses of the Moderna and Janssen COVID-19 vaccine efficacy trials by the USG/COVE Response Biostatistics Team [Archived 16 October 2021]
GNU General Public License v3.0
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remove auxiliary html helpers
#622
nhejazi
closed
2 years ago
0
add these back for now pending a better solution
#621
youyifong
closed
2 years ago
0
Updated assay_graphics for single timepoint modularity
#620
nhejazi
closed
2 years ago
1
write check for data for the new correlates reporting repo
#619
youyifong
opened
2 years ago
0
Modularized the remainder of cor_graphical. It should now build both cor reports.
#618
brianSimpkins
closed
2 years ago
2
Cleanup to prep for archiving
#617
nhejazi
closed
2 years ago
0
_common.R changes; hvtn705 cor_coxph
#616
youyifong
closed
2 years ago
0
change data_name to paste0(attr(config, "config"), "_data_processed.csv") so that they would work properly with the new _common.R
#615
youyifong
closed
2 years ago
0
delete folder recursively in makefile
#614
yiwenlu
closed
2 years ago
0
fix COR issue
#613
yiwenlu
closed
2 years ago
2
add multivariate cox model, driven by primary_assays in config.yml
#612
youyifong
closed
2 years ago
0
cor_threshold tweaks for reading data through _common.R
#611
youyifong
closed
2 years ago
0
bug fixes from moderna real data run
#610
youyifong
closed
2 years ago
0
generalize timepoint with tpeak/tinterm, simplify response call, add child report.rmd files
#609
yiwenlu
closed
2 years ago
3
reproduce Weiping's cove results
#608
youyifong
closed
2 years ago
0
Put data hash back in _common.R
#607
youyifong
closed
2 years ago
0
change where _common.R looks for real data; update where real moderna…
#606
youyifong
closed
2 years ago
0
delete fork; create new fork
#605
youyifong
closed
2 years ago
0
update cor_graphical to fix bugs under mock moderna
#604
youyifong
closed
2 years ago
0
comment out code that needs processed _params.Rdata
#603
youyifong
closed
2 years ago
0
add processed ensemble data with risk score to repo
#602
youyifong
closed
2 years ago
0
updated risk score so all subjects with Riskscorecohortflag==1 have risk score
#601
brborate
closed
2 years ago
0
updates
#600
youyifong
closed
2 years ago
0
data_processed_with_riskscore with all subjects; baseline positive subjects with NAs for risk score
#599
brborate
closed
2 years ago
0
move config for correlates analyses to _common.R
#598
youyifong
closed
2 years ago
0
A dummy PR to trigger travis build
#597
youyifong
closed
2 years ago
0
updated Riskscorecohortflag in baseline risk score code for COVE analysis
#596
brborate
closed
2 years ago
0
update mock raw data for cove and ensemble
#595
youyifong
closed
2 years ago
0
updated riskscorecohortflag for COVE within riskscore code
#594
brborate
closed
2 years ago
0
decouple code for data processing and correlates analyses?
#593
youyifong
closed
2 years ago
7
generalized configuration
#592
nhejazi
closed
2 years ago
5
convert cor_nonlinear
#591
youyifong
closed
2 years ago
0
change 29 to 14 in comments
#590
youyifong
closed
2 years ago
0
Revert "update marker data to international units in mock data, remove conversion from data processing; generalize captions and notes using config"
#589
youyifong
closed
2 years ago
0
Ensemble Cor Threshold changes
#588
Larsvanderlaan
closed
2 years ago
0
update marker data to international units in mock data, remove conversion from data processing; generalize captions and notes using config
#587
youyifong
closed
2 years ago
0
run report on real moderna data on cosrv
#586
youyifong
closed
2 years ago
2
move international unit conversion from data processing to data mapping
#585
youyifong
closed
2 years ago
3
using the future parallel processing framework to speed up cor_graphical
#584
youyifong
closed
2 years ago
0
Suppressing some cor_graphical warning messages
#583
brianSimpkins
closed
2 years ago
0
update report.rmd
#582
yiwenlu
closed
2 years ago
0
modularize rmd
#581
youyifong
closed
2 years ago
0
Update table numbering in cor_tabular
#580
cyu-hvtn
closed
2 years ago
1
Updates to `renv` and required packages
#579
nhejazi
closed
2 years ago
0
new chapter for graphical for time to event; fix table numbering by removing counterwithin
#578
youyifong
closed
2 years ago
0
update RhpcBLASctl version in renv.lock so that it can install; add two marker time point section to config
#577
youyifong
closed
2 years ago
0
add bookdown rendering to test_before_submit script
#576
youyifong
closed
2 years ago
0
Fix markdown debug message
#575
youyifong
closed
2 years ago
0
cor_tabular numbering within chapter
#574
youyifong
closed
2 years ago
2
Dehardcoded report for cor_threshold
#573
Larsvanderlaan
closed
2 years ago
0
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