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project.yaml
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project.yaml
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version: '3.0'
expectations:
population_size: 5000
actions:
## # # # # # # # # # # # # # # # # # # #
## # # # # # # # # # # # # # # # # # # #
## Data extraction
## # # # # # # # # # # # # # # # # # # #
## # # # # # # # # # # # # # # # # # # #
generate_study_population:
run: cohortextractor:latest generate_cohort --study-definition study_definition --output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/input.csv.gz
generate_study_population_flowchart:
run: cohortextractor:latest generate_cohort --study-definition study_definition_flowchart --output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/input_flowchart.csv.gz
generate_study_population_pax_trt:
run: cohortextractor:latest generate_cohort --study-definition study_definition_pax_trt --output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/input_pax_trt.csv.gz
## # # # # # # # # # # # # # # # # # # #
## # # # # # # # # # # # # # # # # # # #
## Data cleaning and description
## # # # # # # # # # # # # # # # # # # #
## # # # # # # # # # # # # # # # # # # #
data_process:
run: r:latest analysis/data_process.R
needs: [generate_study_population]
outputs:
highly_sensitive:
data1: output/data/data_processed.rds
data2: output/data/data_processed_grace6.rds
data3: output/data/data_processed_grace7.rds
data4: output/data/data_processed_grace8.rds
data1_excl: output/data/data_processed_excl_contraindicated.rds
data2_excl: output/data/data_processed_excl_contraindicated_grace6.rds
data3_excl: output/data/data_processed_excl_contraindicated_grace7.rds
data4_excl: output/data/data_processed_excl_contraindicated_grace8.rds
rds1: output/data_properties/n_excluded.rds
rds2: output/data_properties/n_excluded_contraindicated.rds
data_process_flowchart:
run: r:latest analysis/data_process_flowchart.R
needs: [generate_study_population_flowchart]
outputs:
highly_sensitive:
data: output/data/data_flowchart_processed.rds
data_properties:
run: r:latest analysis/data_properties/data_properties.R output/data/data_processed.rds output/data_properties
needs: [data_process]
outputs:
moderately_sensitive:
txt1: output/data_properties/data_processed_skim.txt
txt2: output/data_properties/data_processed_coltypes.txt
txt3: output/data_properties/data_processed_tabulate.txt
create_flowchart:
run: r:latest analysis/flowchart.R
needs: [data_process_flowchart, data_process]
outputs:
moderately_sensitive:
csv1: output/flowchart/flowchart.csv
csv2: output/flowchart/flowchart_redacted.csv
## # # # # # # # # # # # # # # # # # # #
## # # # # # # # # # # # # # # # # # # #
## Descriptive analyses
## # # # # # # # # # # # # # # # # # # #
## # # # # # # # # # # # # # # # # # # #
describe_distr_trt_init:
run: r:latest analysis/descriptives/describe_distr_trt_init.R
needs: [data_process]
outputs:
moderately_sensitive:
csv1: output/descriptives/distr_pax_init.csv
csv2: output/descriptives/distr_pax_init_red.csv
describe_outcomes_in_trt_window:
run: r:latest analysis/descriptives/describe_outcomes_in_trt_window.R
needs: [data_process]
outputs:
moderately_sensitive:
csv1: output/descriptives/outcomes_in_trt_window.csv
csv2: output/descriptives/outcomes_in_trt_window_red.csv
csv3: output/descriptives/outcomes_day0.csv
describe_prop_trt:
run: r:latest analysis/descriptives/describe_prop_trt.R
needs: [data_process]
outputs:
moderately_sensitive:
csv1: output/descriptives/prop_trt.csv
csv2: output/descriptives/prop_trt_red.csv
describe_trt_contra:
run: r:latest analysis/descriptives/describe_trt_contra.R
needs: [data_process]
outputs:
moderately_sensitive:
csv1: output/descriptives/trt_contra.csv
csv2: output/descriptives/trt_contra_red.csv
csvs1: output/descriptives/n_codes_*.csv
describe_trt_preds_all_ci_pax:
run: r:latest analysis/descriptives/describe_trt_preds.R all_ci Paxlovid
needs: [data_process]
outputs:
highly_sensitive:
model1: output/descriptives/psModel_Paxlovid_all_ci.rds
moderately_sensitive:
csv1: output/descriptives/psDens_untrimmed_Paxlovid_all_ci.csv
csv2: output/descriptives/psDens_trimmed_Paxlovid_all_ci.csv
csv3: output/descriptives/psCoefs_Paxlovid_all_ci.csv
csv4: output/descriptives/trimming_descriptives_Paxlovid_all_ci.csv
describe_trt_preds_all_ci_sot:
run: r:latest analysis/descriptives/describe_trt_preds.R all_ci Sotrovimab
needs: [data_process]
outputs:
highly_sensitive:
data1: output/descriptives/psModel_Sotrovimab_all_ci.rds
moderately_sensitive:
csv1: output/descriptives/psDens_untrimmed_Sotrovimab_all_ci.csv
csv2: output/descriptives/psDens_trimmed_Sotrovimab_all_ci.csv
csv3: output/descriptives/psCoefs_Sotrovimab_all_ci.csv
csv4: output/descriptives/trimming_descriptives_Sotrovimab_all_ci.csv
describe_trt_preds_all_ci_mol:
run: r:latest analysis/descriptives/describe_trt_preds.R all_ci Molnupiravir
needs: [data_process]
outputs:
highly_sensitive:
data1: output/descriptives/psModel_Molnupiravir_all_ci.rds
moderately_sensitive:
csv1: output/descriptives/psDens_untrimmed_Molnupiravir_all_ci.csv
csv2: output/descriptives/psDens_trimmed_Molnupiravir_all_ci.csv
csv3: output/descriptives/psCoefs_Molnupiravir_all_ci.csv
csv4: output/descriptives/trimming_descriptives_Molnupiravir_all_ci.csv
visualise_trt_preds_dens:
run: r:latest analysis/descriptives/visualise_trt_preds_dens.R
needs: [describe_trt_preds_all_ci_pax, describe_trt_preds_all_ci_sot, describe_trt_preds_all_ci_mol]
outputs:
moderately_sensitive:
png1: output/descriptives/psOverlap_untrimmed_*_all_ci.png
png2: output/descriptives/psOverlap_trimmed_*_all_ci.png
create_table1:
run: r:latest analysis/descriptives/table1.R
needs: [data_process]
outputs:
moderately_sensitive:
csv1: output/tables/table1.csv
csv2: output/tables/table1_red.csv
csv3: output/tables/table1_red_unf.csv
csv4: output/tables/table1_full.csv
csv5: output/tables/table1_full_red.csv
csv6: output/tables/table1_full_red_unf.csv
csv7: output/tables/table1_trt_untrt.csv
csv8: output/tables/table1_trt_untrt_red.csv
csv9: output/tables/table1_trt_untrt_red_unf.csv
create_table1_stratified_by_3months:
run: r:latest analysis/descriptives/table1_subsets.R
needs: [data_process]
outputs:
moderately_sensitive:
csv1: output/tables/stratified_3months/table1.csv
csv2: output/tables/stratified_3months/table1_red.csv
csv3: output/tables/stratified_3months/table1_red_unf.csv
csv4: output/tables/stratified_3months/table1_full.csv
csv5: output/tables/stratified_3months/table1_full_red.csv
csv6: output/tables/stratified_3months/table1_full_red_unf.csv
csv7: output/tables/stratified_3months/table1_trt_untrt.csv
csv8: output/tables/stratified_3months/table1_trt_untrt_red.csv
csv9: output/tables/stratified_3months/table1_trt_untrt_red_unf.csv
describe_trt_groups:
run: r:latest analysis/descriptives/describe_trt_groups.R
needs: [data_process]
outputs:
moderately_sensitive:
csv1: output/descriptives/trt_groups.csv
csv2: output/descriptives/trt_groups_red.csv
describe_fup_outcomes:
run: r:latest analysis/descriptives/describe_fup_outcomes.R
needs: [data_process]
outputs:
moderately_sensitive:
csv1: output/descriptives/overview_fup_outcomes.csv
csv2: output/descriptives/overview_fup_outcomes_red.csv
describe_postest_pop:
run: r:latest analysis/descriptives/describe_postest_pop.R
needs: [data_process]
outputs:
moderately_sensitive:
csv1: output/descriptives/postest_pop.csv
csv2: output/descriptives/postest_pop_red.csv
## # # # # # # # # # # # # # # # # # # #
## # # # # # # # # # # # # # # # # # # #
## Sequential trials - DATA PREP
## # # # # # # # # # # # # # # # # # # #
## # # # # # # # # # # # # # # # # # # #
data_select_and_simplify:
run: r:latest analysis/seq_trials/select_and_simplify_data.R
needs: [data_process]
outputs:
highly_sensitive:
data1: output/data/data_processed_excl_contraindicated.feather
data_prepare_seq_trials_month:
run: r:latest analysis/seq_trials/prepare_data.R --period=month
needs: [data_select_and_simplify]
outputs:
highly_sensitive:
data1: output/data/data_seq_trials_monthly.feather
## # # # # # # # # # # # # # # # # # # #
## # # # # # # # # # # # # # # # # # # #
## Sequential trials - DESCRIPTIVES
## # # # # # # # # # # # # # # # # # # #
## # # # # # # # # # # # # # # # # # # #
describe_size_trials_month:
run: r:latest analysis/seq_trials/descriptives/describe_size_trials.R --period=month
needs: [data_prepare_seq_trials_month]
outputs:
moderately_sensitive:
csv1: output/seq_trials/descriptives/data_flow_seq_trials_monthly.csv
csv2: output/seq_trials/descriptives/data_flow_seq_trials_monthly_red.csv
create_flow_diagram:
run: r:latest analysis/seq_trials/descriptives/create_flow_diagram.R
needs: [data_select_and_simplify, data_prepare_seq_trials_month]
outputs:
moderately_sensitive:
csv1: output/seq_trials/descriptives/flow_diagram/flow_diagram_monthly.csv
csv2: output/seq_trials/descriptives/flow_diagram/flow_diagram_monthly_red.csv
estimate_crude_survival:
run: r:latest analysis/seq_trials/descriptives/estimate_crude_survival.R
needs: [data_select_and_simplify, data_prepare_seq_trials_month]
outputs:
moderately_sensitive:
csv1: output/seq_trials/descriptives/survival/surv_main.csv
csv2: output/seq_trials/descriptives/survival/surv_by_period.csv
csv3: output/seq_trials/descriptives/survival/surv_by_trial.csv
## # # # # # # # # # # # # # # # # # # #
## # # # # # # # # # # # # # # # # # # #
## Sequential trials - ITT
## # # # # # # # # # # # # # # # # # # #
## # # # # # # # # # # # # # # # # # # #
plot_km:
run: r:latest analysis/seq_trials/km.R
--plot TRUE
needs: [data_prepare_seq_trials_month]
outputs:
moderately_sensitive:
csv1: output/seq_trials/descriptives/survival/km_estimates.csv
csv2: output/seq_trials/descriptives/survival/km_estimates_red.csv
csv3: output/seq_trials/descriptives/survival/km_estimates_red2.csv
plot1: output/seq_trials/descriptives/survival/km_estimates.png
plot2: output/seq_trials/descriptives/survival/km_estimates_red.png
plot_km_by_period:
run: r:latest analysis/seq_trials/km.R
--plot TRUE
--subgroups period
needs: [data_prepare_seq_trials_month]
outputs:
moderately_sensitive:
csv1: output/seq_trials/descriptives/survival/km_estimates_period.csv
csv2: output/seq_trials/descriptives/survival/km_estimates_period_red.csv
csv3: output/seq_trials/descriptives/survival/km_estimates_period_red2.csv
plot1: output/seq_trials/descriptives/survival/km_estimates_period.png
plot2: output/seq_trials/descriptives/survival/km_estimates_period_red.png
run_itt_analysis_simple:
run: r:latest analysis/seq_trials/itt_analysis.R --model=simple
needs: [data_prepare_seq_trials_month]
outputs:
highly_sensitive:
rds1: output/seq_trials/itt/itt_fit_simple.rds
rds2: output/seq_trials/itt/itt_vcov_simple.rds
moderately_sensitive:
csv1: output/seq_trials/itt/itt_fit_simple.csv
csv2: output/seq_trials/itt/itt_glance_simple.csv
txt: output/seq_trials/itt/log/itt_log_simple.txt
run_itt_analysis_interaction_period:
run: r:latest analysis/seq_trials/itt_analysis.R --model=interaction_period
needs: [data_prepare_seq_trials_month]
outputs:
highly_sensitive:
rds1: output/seq_trials/itt/itt_fit_interaction_period.rds
rds2: output/seq_trials/itt/itt_vcov_interaction_period.rds
moderately_sensitive:
csv1: output/seq_trials/itt/itt_fit_interaction_period.csv
csv2: output/seq_trials/itt/itt_glance_interaction_period.csv
txt: output/seq_trials/itt/log/itt_log_interaction_period.txt
run_itt_analysis_interaction_trial:
run: r:latest analysis/seq_trials/itt_analysis.R --model=interaction_trial
needs: [data_prepare_seq_trials_month]
outputs:
highly_sensitive:
rds1: output/seq_trials/itt/itt_fit_interaction_trial.rds
rds2: output/seq_trials/itt/itt_vcov_interaction_trial.rds
moderately_sensitive:
csv1: output/seq_trials/itt/itt_fit_interaction_trial.csv
csv2: output/seq_trials/itt/itt_glance_interaction_trial.csv
txt: output/seq_trials/itt/log/itt_log_interaction_trial.txt
run_itt_analysis_interaction_all:
run: r:latest analysis/seq_trials/itt_analysis.R --model=interaction_all
needs: [data_prepare_seq_trials_month]
outputs:
highly_sensitive:
rds1: output/seq_trials/itt/itt_fit_interaction_all.rds
rds2: output/seq_trials/itt/itt_vcov_interaction_all.rds
moderately_sensitive:
csv1: output/seq_trials/itt/itt_fit_interaction_all.csv
csv2: output/seq_trials/itt/itt_glance_interaction_all.csv
txt: output/seq_trials/itt/log/itt_log_interaction_all.txt
run_itt_analysis_crude:
run: r:latest analysis/seq_trials/itt_analysis.R --model=crude
needs: [data_prepare_seq_trials_month]
outputs:
highly_sensitive:
rds1: output/seq_trials/itt/itt_fit_crude.rds
rds2: output/seq_trials/itt/itt_vcov_crude.rds
moderately_sensitive:
csv1: output/seq_trials/itt/itt_fit_crude.csv
csv2: output/seq_trials/itt/itt_glance_crude.csv
txt: output/seq_trials/itt/log/itt_log_crude.txt
run_itt_analysis_crude_period:
run: r:latest analysis/seq_trials/itt_analysis.R --model=crude_period
needs: [data_prepare_seq_trials_month]
outputs:
highly_sensitive:
rds1: output/seq_trials/itt/itt_fit_crude_period.rds
rds2: output/seq_trials/itt/itt_vcov_crude_period.rds
moderately_sensitive:
csv1: output/seq_trials/itt/itt_fit_crude_period.csv
csv2: output/seq_trials/itt/itt_glance_crude_period.csv
txt: output/seq_trials/itt/log/itt_log_crude_period.txt
run_itt_analysis_crude_trial:
run: r:latest analysis/seq_trials/itt_analysis.R --model=crude_trial
needs: [data_prepare_seq_trials_month]
outputs:
highly_sensitive:
rds1: output/seq_trials/itt/itt_fit_crude_trial.rds
rds2: output/seq_trials/itt/itt_vcov_crude_trial.rds
moderately_sensitive:
csv1: output/seq_trials/itt/itt_fit_crude_trial.csv
csv2: output/seq_trials/itt/itt_glance_crude_trial.csv
txt: output/seq_trials/itt/log/itt_log_crude_trial.txt
create_surv_curves_itt_simple:
run: r:latest analysis/seq_trials/itt_curves.R --model=simple
needs: [data_prepare_seq_trials_month, run_itt_analysis_simple]
outputs:
moderately_sensitive:
csv1: output/seq_trials/itt/curves/itt_survcurves_simple.csv
csv2: output/seq_trials/itt/curves/itt_diffcurve_simple.csv
## # # # # # # # # # # # # # # # # # # #
## # # # # # # # # # # # # # # # # # # #
## Sequential trials - PP
## # # # # # # # # # # # # # # # # # # #
## # # # # # # # # # # # # # # # # # # #
run_pp_analysis_simple:
run: r:latest analysis/seq_trials/pp_analysis.R --model=simple
needs: [data_prepare_seq_trials_month]
outputs:
highly_sensitive:
rds1: output/seq_trials/pp/pp_fit_simple.rds
rds2: output/seq_trials/pp/pp_vcov_simple.rds
moderately_sensitive:
csv1: output/seq_trials/pp/pp_fit_simple.csv
csv2: output/seq_trials/pp/pp_glance_simple.csv
txt: output/seq_trials/pp/log/pp_log_simple.txt