generated from opensafely/research-template
/
project.yaml
129 lines (116 loc) · 5.7 KB
/
project.yaml
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version: '3.0'
expectations:
population_size: 50000
actions:
generate_study_population_control:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control
outputs:
highly_sensitive:
cohort: output/input_control.csv
generate_study_population_treatment:
run: cohortextractor:latest generate_cohort --study-definition study_definition_treatment
outputs:
highly_sensitive:
cohort: output/input_treatment.csv
generate_study_population_treatment_sensitivity:
run: cohortextractor:latest generate_cohort --study-definition study_definition_treatment_sensitivity
outputs:
highly_sensitive:
cohort: output/input_treatment_sensitivity.csv
data_properties:
run: r:latest analysis/data_properties.R output/input_control.csv output/input_treatment.csv output/data_properties
needs: [generate_study_population_control, generate_study_population_treatment]
outputs:
moderately_sensitive:
cohort: output/data_properties/input*.txt
define_covariates_combine:
run: stata-mp:latest analysis/004_define_covariates_combine.do
needs: [generate_study_population_control, generate_study_population_treatment, generate_study_population_treatment_sensitivity]
outputs:
highly_sensitive:
log: logs/cleaning_dataset_combine.log
data: output/data/main.dta
data1: output/data/sensitivity_analysis.dta
baseline_characteristic:
run: stata-mp:latest analysis/101_baseline_characteristics.do
needs: [define_covariates_combine]
outputs:
moderately_sensitive:
log: logs/baseline_characterisitcs.log
data: output/tables/baseline_allpts.csv
data1: output/tables/baseline_allpts_sensitivity.csv
cox_model:
run: stata-mp:latest analysis/204_cox_model.do
needs: [define_covariates_combine]
outputs:
moderately_sensitive:
log: logs/cox_model.log
data: output/tables/cox_model_summary.csv
data1: output/tables/cox_model_disease.csv
data2: output/tables/cox_model_rates.csv
data3: output/tables/cox_model_rates_round.csv
data4: output/tables/cox_model_summary_sens_1.csv
data5: output/tables/cox_model_disease_sens_1.csv
data6: output/tables/cox_model_rates_sens_1.csv
data7: output/tables/cox_model_rates_round_sens_1.csv
data8: output/tables/cox_model_summary_sens_2.csv
data9: output/tables/cox_model_summary_sens_4.csv
data10: output/tables/cox_model_rates_sens_4.csv
data11: output/tables/cox_model_rates_round_sens_4.csv
data12: output/tables/cox_model_summary_sens_5.csv
data13: output/tables/cox_model_rates_sens_5.csv
data14: output/tables/cox_model_rates_round_sens_5.csv
data15: output/tables/cox_model_summary_sens_6.csv
data16: output/tables/cox_model_rates_sens_6.csv
data17: output/tables/cox_model_rates_round_sens_6.csv
schoenfield_ae_all: output/figures/schoenfield_ae_all.svg
schoenfield_ae_all_serious: output/figures/schoenfield_ae_all_serious.svg
schoenfield_ae_spc_all: output/figures/schoenfield_ae_spc_all.svg
schoenfield_ae_spc_serious: output/figures/schoenfield_ae_spc_serious.svg
schoenfield_ae_drug_all: output/figures/schoenfield_ae_drug_all.svg
schoenfield_ae_drug_serious: output/figures/schoenfield_ae_drug_serious.svg
schoenfield_ae_imae_all: output/figures/schoenfield_ae_imae_all.svg
schoenfield_ae_imae_serious: output/figures/schoenfield_ae_imae_serious.svg
loglog_plot_ae_all: output/figures/loglog_plot_ae_all.svg
loglog_plot_ae_all_serious: output/figures/loglog_plot_ae_all_serious.svg
loglog_plot_ae_spc_all: output/figures/loglog_plot_ae_spc_all.svg
loglog_plot_ae_spc_serious: output/figures/loglog_plot_ae_spc_serious.svg
loglog_plot_ae_drug_all: output/figures/loglog_plot_ae_drug_all.svg
loglog_plot_ae_drug_serious: output/figures/loglog_plot_ae_drug_serious.svg
loglog_plot_ae_imae_all: output/figures/loglog_plot_ae_imae_all.svg
loglog_plot_ae_imae_serious: output/figures/loglog_plot_ae_imae_serious.svg
PS_model:
run: stata-mp:latest analysis/304_ps_model.do
needs: [define_covariates_combine]
outputs:
moderately_sensitive:
log: logs/ps_model.log
data: output/tables/cox_propensity.csv
histogram_agesex: output/figures/histogram_agesex.svg
histogram_adj: output/figures/histogram_adj.svg
histogram_adj2: output/figures/histogram_adj2.svg
histogram_adj3: output/figures/histogram_adj3.svg
histogram_adj4: output/figures/histogram_adj4.svg
balance_agesex: output/figures/balance_agesex.svg
balance_adj: output/figures/balance_adj.svg
balance_adj2: output/figures/balance_adj2.svg
balance_adj3: output/figures/balance_adj3.svg
balance_adj4: output/figures/balance_adj4.svg
preceed_rate:
run: stata-mp:latest analysis/405_preceeding_rate.do
needs: [define_covariates_combine]
outputs:
moderately_sensitive:
log: logs/preceed_rate.log
data: output/tables/comparator_rates.csv
data1: output/tables/comparator_rates_round.csv
redacted_table:
run: stata-mp:latest analysis/501_redacted_table.do
needs: [define_covariates_combine]
outputs:
moderately_sensitive:
log1: logs/redacted_table.log
data: output/tables/baseline_table_redact_bydrug.csv
data1: output/tables/baseline_table_redact_mean.csv
data2: output/tables/baseline_table_redact_bydrug_sens.csv
data3: output/tables/baseline_table_redact_mean_sens.csv