correlates_reporting2-2.2.1.zip
correlates_reporting2-2.2.1
.Rbuildignore
73 Bytes
.Rprofile
26 Bytes
.gitignore
44.2 kB
.here
0 Bytes
.renvignore
36 Bytes
.travis.yml
2.4 kB
CONTRIBUTING.md
15.8 kB
DESCRIPTION
1.7 kB
LICENSE.md
34.9 kB
Makefile
2.1 kB
README.md
3.2 kB
_bookdown_cop.yml
397 Bytes
_bookdown_cop_binaryprinstrat.yml
343 Bytes
_bookdown_cor.yml
744 Bytes
_bookdown_cor_coxph.yml
558 Bytes
_bookdown_cor_graphical.yml
566 Bytes
_bookdown_cor_nonlinear.yml
566 Bytes
_bookdown_cor_tabular.yml
562 Bytes
_bookdown_cor_threshold.yml
564 Bytes
_bookdown_immuno.yml
374 Bytes
_bookdown_immuno_graphical.yml
347 Bytes
_bookdown_immuno_tabular.yml
341 Bytes
_build.sh
1.8 kB
_build_chapter.sh
840 Bytes
_common.R
53.0 kB
_deploy_reports.sh
2.0 kB
_output.yml
400 Bytes
_report_cop
.gitkeep
0 Bytes
_report_cor
.gitkeep
0 Bytes
appendix.Rmd
1.0 kB
aws_build_instructions.md
8.6 kB
book.bib
20.4 kB
config.yml
40.6 kB
cop_binaryprinstrat
.gitignore
41 Bytes
.here
0 Bytes
Makefile
1.4 kB
code
binary_correlate_VE_analysis.R
34.9 kB
figs
.gitkeep
0 Bytes
output
.gitkeep
0 Bytes
report.Rmd
1.1 kB
report_ensemble.Rmd
686 Bytes
report_mockensemble.Rmd
638 Bytes
report_sub.Rmd
1.8 kB
risk_plot1.Rmd
940 Bytes
cop_mediation
.gitignore
35 Bytes
.here
0 Bytes
Makefile
1.2 kB
README.md
1.4 kB
code
.gitkeep
0 Bytes
clean_data.R
3.1 kB
format_utils.R
1.3 kB
params.R
3.5 kB
run_analysis.R
4.1 kB
sl_screen_fn.R
4.5 kB
data_clean
.gitkeep
0 Bytes
figs
.gitkeep
0 Bytes
output
.gitkeep
0 Bytes
report.Rmd
2.5 kB
slurm
.gitkeep
0 Bytes
cop_prinstrat
.here
0 Bytes
Makefile
0 Bytes
README.md
371 Bytes
code
.gitkeep
0 Bytes
data_clean
.gitkeep
0 Bytes
figs
.gitkeep
0 Bytes
output
.gitkeep
0 Bytes
report.Rmd
101 Bytes
slurm
.gitkeep
0 Bytes
cop_stochastic
.gitignore
222 Bytes
.here
0 Bytes
Makefile
1.0 kB
README.md
490 Bytes
code
.gitkeep
0 Bytes
make_analysis_data.R
2.5 kB
make_sve_cop_figs.R
4.3 kB
params.R
2.2 kB
run_cop_analysis.R
3.4 kB
sl_lrnr_libs.R
4.3 kB
sve_utils.R
4.8 kB
data_clean
.gitkeep
0 Bytes
figs
.gitkeep
0 Bytes
output
.gitkeep
0 Bytes
report.Rmd
8.2 kB
slurm
.gitkeep
0 Bytes
run_mcop_analysis.sh
945 Bytes
cor_coxph
.gitignore
3.1 kB
.here
0 Bytes
Makefile
3.1 kB
README.md
338 Bytes
additional_model.Rmd
368 Bytes
code
.gitkeep
0 Bytes
cor_coxph.R
8.7 kB
cor_coxph_collate_meta_VE.R
15.2 kB
cor_coxph_forestplots_ows.R
13.1 kB
cor_coxph_marginalized_risk_bootstrap.R
17.1 kB
cor_coxph_marginalized_risk_no_marker.R
3.4 kB
cor_coxph_marginalized_risk_plotting.R
33.0 kB
cor_coxph_meta_VE_curves.R
26.5 kB
cor_coxph_misc.R
15.8 kB
cor_coxph_notrun.R
7.9 kB
cor_coxph_ph.R
22.1 kB
cor_coxph_samplesizeratio.R
2.1 kB
cor_graphical_time_to_event.R
2.6 kB
params.R
5.1 kB
collate_ensemble.Rmd
1.5 kB
cutpoints.Rmd
69 Bytes
data_clean
.gitkeep
0 Bytes
figs
.gitkeep
0 Bytes
forestplots_azd1222.Rmd
206 Bytes
forestplots_cove.Rmd
830 Bytes
forestplots_ensemble.Rmd
340 Bytes
forestplots_fig.Rmd
826 Bytes
forestplots_mockcove.Rmd
2.3 kB
forestplots_mockensemble.Rmd
1.8 kB
itxn_by_assays.Rmd
2.7 kB
meta_collate_sub0.Rmd
13.5 kB
meta_collate_sub1.Rmd
502 Bytes
meta_collate_sub10.Rmd
586 Bytes
meta_collate_sub11.Rmd
586 Bytes
meta_collate_sub2.Rmd
502 Bytes
meta_collate_sub3.Rmd
529 Bytes
meta_collate_sub4.Rmd
501 Bytes
meta_collate_sub5.Rmd
502 Bytes
meta_collate_sub6.Rmd
501 Bytes
meta_collate_sub7.Rmd
541 Bytes
meta_collate_sub8.Rmd
541 Bytes
meta_collate_sub9.Rmd
584 Bytes
meta_cve.Rmd
5.1 kB
multiple_regression.Rmd
1.2 kB
output
.gitkeep
0 Bytes
report.Rmd
2.2 kB
report_azd1222.Rmd
2.4 kB
report_by_COR.Rmd
6.2 kB
report_cove.Rmd
2.5 kB
report_ensemble.Rmd
1.1 kB
report_mockensemble.Rmd
795 Bytes
report_profiscov.Rmd
1.9 kB
report_vat08m.Rmd
862 Bytes
risk_plots_by_assays.Rmd
5.4 kB
slurm
.gitkeep
0 Bytes
verification
.gitignore
68 Bytes
cor_coxph_specifications.Rmd
378 Bytes
cor_coxph_validation.R
24.4 kB
specifications.rmd
9.2 kB
verification.Rmd
850 Bytes
verification_input
D29.rv.MockCOVE.Rdata
7.3 kB
D57.rv.MockCOVE.Rdata
7.3 kB
moderna_mock_data_processed_with_riskscore.csv
13.2 MB
specifications.html
633.6 kB
specifications.rmd
9.3 kB
verification_output
D29.mock.csv
8.9 kB
D57.mock.csv
8.8 kB
verification_plan.Rmd
4.0 kB
verification_report.Rmd
15.4 kB
verification_report.pdf
185.5 kB
cor_graphical
.gitignore
126 Bytes
.here
0 Bytes
Makefile
4.8 kB
README.md
610 Bytes
code
.gitkeep
0 Bytes
CoR_assay_graphics.R
14.2 kB
CoR_wrcdf_with_VE_lines.R
7.4 kB
cor_data_preprocess.R
20.9 kB
cor_data_preprocess_2.R
9.7 kB
cor_graphics_violin_scatter.R
29.1 kB
cor_process_function.R
5.2 kB
cor_wrcdf_plot_function.R
4.2 kB
covid_corr_plot_functions.R
36.4 kB
params.R
420 Bytes
data_clean
.gitkeep
0 Bytes
figs
.gitkeep
0 Bytes
report.Rmd
7.6 kB
report_boxplots.Rmd
370 Bytes
report_marker_rcdf.Rmd
381 Bytes
report_rcdf.Rmd
403 Bytes
report_sub1.Rmd
687 Bytes
report_sub2.Rmd
603 Bytes
report_sub3.Rmd
736 Bytes
slurm
.gitkeep
0 Bytes
verification
cor_graphical_specifications.md
19.3 kB
cor_graphical_verification_code.R
19.4 kB
verification.Rmd
2.9 kB
verification_plan.Rmd
4.9 kB
verification_report.Rmd
15.8 kB
verification_statistics.Rmd
2.9 kB
cor_nonlinear
.gitignore
38 Bytes
.here
0 Bytes
Makefile
1.4 kB
README.md
376 Bytes
code
.gitkeep
0 Bytes
cor_nonlinear.R
4.2 kB
cor_nonlinear_gam.R
7.5 kB
cor_nonlinear_step.R
5.4 kB
params.R
363 Bytes
data_clean
.gitkeep
0 Bytes
figs
.gitkeep
0 Bytes
output
.gitkeep
0 Bytes
D57
bootstrap_replicates_MockCOVE
5 Bytes
moderna_mock
D57
bootstrap_replicates_MockCOVE
5 Bytes
marginalized.risk.gam.MockCOVE.Rdata
1.5 MB
report.Rmd
1.4 kB
report_ensemble.Rmd
761 Bytes
report_mockensemble.Rmd
713 Bytes
report_sub.Rmd
521 Bytes
risk_plots.Rmd
859 Bytes
slurm
.gitkeep
0 Bytes
cor_surrogates
.gitignore
423 Bytes
.here
0 Bytes
Makefile
802 Bytes
README.md
1.1 kB
code
cor_surrogates_setup.R
42.7 kB
createRDAfiles_fromSLobjects.R
7.4 kB
cron_job.R
554 Bytes
day57or29analyses.R
6.8 kB
get_vimp.R
6.3 kB
get_vimp.sh
60 Bytes
manuscript_ROC_figure.R
3.8 kB
moderna_manuscript_figures.R
20.4 kB
post-hoc_analyses.R
4.1 kB
run_cvsl_varsets.R
5.7 kB
run_cvsl_varsets.sh
120 Bytes
run_n_check_cluster_jobs.R
4.0 kB
sl_screens.R
21.5 kB
submit_VIMPcluster_job.sh
213 Bytes
submit_cluster_job.sh
221 Bytes
tables_figures.R
32.5 kB
takingAverageofpredictions.R
2.6 kB
utils.R
41.2 kB
data_clean
.gitkeep
0 Bytes
figs
.gitkeep
0 Bytes
output
.gitkeep
0 Bytes
report.Rmd
564 Bytes
report.html
7.9 MB
report_sub.Rmd
40.8 kB
report_sub_HVTN705.Rmd
60.1 kB
report_sub_Moderna.Rmd
57.3 kB
requirements.txt
117 Bytes
verification
opt_surrogate_specification.Rmd
2.5 kB
opt_surrogate_specification.html
673.4 kB
specifications_optSurrogate.csv
12.4 kB
cor_tabular
.gitignore
56 Bytes
.here
0 Bytes
Makefile
1.8 kB
README.md
381 Bytes
code
.gitkeep
0 Bytes
make_functions.R
11.8 kB
make_table_all.R
37.5 kB
figs
.gitkeep
0 Bytes
header.tex
105 Bytes
output
.gitkeep
0 Bytes
report.Rmd
4.5 kB
slurm
.gitkeep
0 Bytes
verification
.gitignore
80 Bytes
.gitkeep
0 Bytes
cor_table_verification.Rmd
23.8 kB
table_specifications_cor.html
641.0 kB
verification.Rmd
1.5 kB
verification_plan.Rmd
3.9 kB
verification_report.Rmd
4.6 kB
cor_threshold
.gitignore
563 Bytes
.here
0 Bytes
Makefile
3.6 kB
README.md
3.1 kB
code
.gitkeep
0 Bytes
Run_Threshold_analysis.R
7.1 kB
clean_data.R
3.7 kB
learners.R
1.9 kB
nonsurvival_version
Run_Threshold_analysis.R
3.4 kB
clean_data.R
3.5 kB
learners.R
1.8 kB
plotting.R
1.6 kB
plotting_helpers.R
13.0 kB
tmleThresh.R
28.2 kB
old_code
Threshold_searching_analysis.R
23.6 kB
params.R
3.2 kB
params_old.R
6.7 kB
plotting.R
1.4 kB
plotting_helpers.R
9.1 kB
survivalThresh
Pooled_hazards.R
9.8 kB
Threshold_survivalCR.R
15.6 kB
fitting_likelihood.R
5.7 kB
sl3_learner_helpers.R
13.2 kB
survival_helper_functions.R
3.5 kB
targeting_functions.R
22.4 kB
task_generators.R
3.7 kB
tmleThresh.R
28.3 kB
data_clean
.gitkeep
0 Bytes
Thresholds_by_marker
.gitkeep
0 Bytes
figs
.gitkeep
0 Bytes
pointwise_CI
.gitkeep
0 Bytes
output
.gitkeep
0 Bytes
simultaneous_CI
.gitkeep
0 Bytes
output
.gitkeep
0 Bytes
report.Rmd
6.6 kB
slurm
.gitkeep
0 Bytes
sub_report.Rmd
2.4 kB
data_clean
.gitignore
28 Bytes
AZChAd26UKphase3FengetalCorrelates.csv
304 Bytes
janssen_pooled_mock_data_processed_with_riskscore.csv
16.4 MB
moderna_mock_data_processed_with_riskscore.csv
13.9 MB
design_doc_oss.md
4.2 kB
immuno_graphical
.gitignore
114 Bytes
.here
0 Bytes
Makefile
1.5 kB
README.md
2.7 kB
code
.gitkeep
0 Bytes
covid_corr_plot_functions.R
43.7 kB
descriptive_graphics_data_preprocess.R
9.9 kB
descriptive_graphics_demographic_strata.R
21.8 kB
descriptive_graphics_two_phase_plots.R
19.1 kB
ggally_cor_resample.R
14.5 kB
make_assay_lim.R
5.2 kB
params.R
4.1 kB
data_clean
.gitkeep
0 Bytes
figs
.gitkeep
0 Bytes
demographics
.gitkeep
0 Bytes
output
.gitkeep
0 Bytes
report.Rmd
23.1 kB
report_box.Rmd
424 Bytes
report_box_demographic.Rmd
477 Bytes
report_box_neg_vs_pos.Rmd
425 Bytes
report_pair_by_assay.Rmd
607 Bytes
report_pair_by_time.Rmd
516 Bytes
report_rcdf.Rmd
503 Bytes
report_rcdf_demographic.Rmd
424 Bytes
report_scatter.Rmd
393 Bytes
slurm
.gitkeep
0 Bytes
verification
.gitignore
32 Bytes
graphical_specifications.md
11.4 kB
immuno_graphical_verification_code.R
19.7 kB
verification.Rmd
3.1 kB
verification_plan.Rmd
4.9 kB
verification_report.Rmd
14.9 kB
verification_statistics.Rmd
5.9 kB
immuno_tabular
.gitignore
56 Bytes
.here
0 Bytes
Makefile
969 Bytes
README.md
381 Bytes
code
.gitkeep
0 Bytes
make_clean_data.R
5.3 kB
make_functions.R
11.5 kB
make_parameters.R
12.9 kB
make_table_all.R
25.7 kB
data_clean
.gitkeep
0 Bytes
figs
.gitkeep
0 Bytes
output
.gitkeep
0 Bytes
report.Rmd
4.0 kB
slurm
.gitkeep
0 Bytes
verification
.gitignore
80 Bytes
.gitkeep
0 Bytes
immuno_table_verification.Rmd
50.5 kB
table_specifications_immuno.html
654.3 kB
verification.Rmd
1.4 kB
verification_plan.Rmd
3.9 kB
verification_report.Rmd
8.4 kB
index_cop.Rmd
3.0 kB
index_cor.Rmd
3.5 kB
index_immuno.Rmd
3.0 kB
latex
krantz.cls
61.0 kB
preamble.tex
2.4 kB
references.Rmd
188 Bytes
renv
.gitignore
39 Bytes
activate.R
18.3 kB
settings.dcf
192 Bytes
renv.lock
61.0 kB
run_azd1222
261 Bytes
run_cove
254 Bytes
run_ensembleall
409 Bytes
run_ensembleallseniornonsenior
519 Bytes
run_hvtn705
257 Bytes
run_one
264 Bytes
run_prevent19
251 Bytes
run_profiscov
268 Bytes
run_vat08m_naive
348 Bytes
run_vat08m_nonnaive
350 Bytes
run_vat08mall
363 Bytes
test_before_submit
243 Bytes