generated from opensafely/research-template
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project.yaml
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/
project.yaml
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version: '3.0'
expectations:
population_size: 1000
actions:
# study cohort
generate_study_population_covid_admission:
run: cohortextractor:latest generate_cohort --study-definition study_definition_covid_admission
outputs:
highly_sensitive:
cohort: output/input_covid_admission.csv
process_1:
run: r:latest analysis/process_1.R
needs: [generate_study_population_covid_admission]
outputs:
highly_sensitive:
case: output/case_covid_icu_death.csv
# case2: output/case_covid_icu_death_2.csv
control: output/control_covid_hosp.csv
# control2: output/control_covid_hosp_2.csv
check_process_1:
run: r:latest -e 'rmarkdown::render("analysis/check_process_1.Rmd", knit_root_dir = "/workspace", output_dir = "output")'
needs: [generate_study_population_covid_admission]
outputs:
moderately_sensitive:
html: output/check_process_1.html
# matching
matching: # matching with replacement # died covid
run: r:latest -e 'rmarkdown::render("analysis/matching.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
needs: [process_1]
outputs:
moderately_sensitive:
html: output/matching.html
highly_sensitive:
rds1: output/matched_patients.rds
rds2: output/unmatched_patients.rds
csv: output/matched_patients_id.csv
check_unmatched:
run: r:latest -e 'rmarkdown::render("analysis/check_unmatched.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
needs: [matching]
outputs:
moderately_sensitive:
html: output/check_unmatched.html
extract_variables:
run: cohortextractor:latest generate_cohort --with-end-date-fix --study-definition study_definition_outcome
needs: [matching]
outputs:
highly_sensitive:
cohort: output/input_outcome.csv
process_Rmatching: # add variables
run: r:latest analysis/process_Rmatching.R
needs: [extract_variables,matching]
outputs:
highly_sensitive:
cohort1: output/matched_outcome.rds
rds1: output/abtype79.rds
rds2: output/comor17.rds
# main analysis
table1_round: # matching variables
run: r:latest analysis/table1.R
needs: [process_1,process_Rmatching]
outputs:
moderately_sensitive:
csv1: output/table1_unmatched.csv
csv2: output/table1_matched.csv
csv3: output/table1_random.csv
table2_round: # confounders
run: r:latest analysis/table2.R
needs: [process_Rmatching]
outputs:
moderately_sensitive:
csv1: output/table2_matched.csv
csv3: output/table2_random.csv
table3_round: # antibiotics
run: r:latest analysis/table3.R
needs: [process_Rmatching]
outputs:
moderately_sensitive:
csv1: output/table3.csv
csv3: output/table3_ab.csv
model:
run: r:latest analysis/model/model.R
needs: [process_Rmatching]
outputs:
moderately_sensitive:
csv1: output/model_1_crude.csv
csv2: output/model_1_adjusted.csv
model_2_3grp: # # abtype modeling
run: r:latest -e 'rmarkdown::render("analysis/model_2_3grp.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
needs: [process_Rmatching]
outputs:
moderately_sensitive:
html: output/model_2_3grp.html
model_2:
run: r:latest -e 'rmarkdown::render("analysis/model_2.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
needs: [process_Rmatching]
outputs:
moderately_sensitive:
html: output/model_2.html
# sensitivity analysis
model_subgroup:
run: r:latest analysis/model/model_subgroup.R
needs: [process_Rmatching]
outputs:
moderately_sensitive:
csv1.1: output/model_3_male_crude.csv
csv1.2: output/model_3_male_adjusted.csv
csv1.3: output/model_3_male_ab.csv
csv2.1: output/model_3_female_crude.csv
csv2.2: output/model_3_female_adjusted.csv
csv2.3: output/model_3_female_ab.csv
csv3.1: output/model_3_age1_crude.csv
csv3.2: output/model_3_age1_adjusted.csv
csv3.3: output/model_3_age1_ab.csv
csv4.1: output/model_3_age2_crude.csv
csv4.2: output/model_3_age2_adjusted.csv
csv4.3: output/model_3_age2_ab.csv
csv5.1: output/model_3_age3_crude.csv
csv5.2: output/model_3_age3_adjusted.csv
csv5.3: output/model_3_age3_ab.csv
csv6.1: output/model_3_age4_crude.csv
csv6.2: output/model_3_age4_adjusted.csv
csv6.3: output/model_3_age4_ab.csv
model_age_plot:
run: r:latest -e 'rmarkdown::render("analysis/model_age_plot.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
needs: [process_Rmatching]
outputs:
moderately_sensitive:
html: output/model_age_plot.html
model_gender_plot:
run: r:latest -e 'rmarkdown::render("analysis/model_gender_plot.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
needs: [process_Rmatching]
outputs:
moderately_sensitive:
html: output/model_gender_plot.html
model_time:
run: r:latest analysis/model/model_time.R
needs: [process_Rmatching]
outputs:
moderately_sensitive:
csv1.1: output/model_time_adj1.csv
csv1.2: output/model_time_adj2.csv
model_time_plot: # adjust for last AB time
run: r:latest -e 'rmarkdown::render("analysis/model_time_plot.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
needs: [process_Rmatching]
outputs:
moderately_sensitive:
html: output/model_time_plot.html
model_disease:
run: r:latest analysis/model/model_disease.R
needs: [process_Rmatching]
outputs:
moderately_sensitive:
csv1.1: output/model_disease_adj1.csv
csv1.2: output/model_disease_adj2.csv
model_disease_plot: # adjust for individual
run: r:latest -e 'rmarkdown::render("analysis/model_disease_plot.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
needs: [process_Rmatching]
outputs:
moderately_sensitive:
html: output/model_disease_plot.html
# model_wave: # separate wave
# run: r:latest -e 'rmarkdown::render("analysis/model_wave.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
# needs: [process_Rmatching]
# outputs:
# moderately_sensitive:
# html: output/model_wave.html
model_cca:
run: r:latest analysis/model/model_cca.R
needs: [process_Rmatching]
outputs:
moderately_sensitive:
csv1.1: output/model_cca_crude.csv
csv1.2: output/model_cca_adjusted.csv
model_complete_case_plot:
run: r:latest -e 'rmarkdown::render("analysis/model_complete_case_plot.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
needs: [process_Rmatching]
outputs:
moderately_sensitive:
html: output/model_complete_case_plot.html
# adjust for 6 weeks exclusion
extract_variables_6w:
run: cohortextractor:latest generate_cohort --study-definition study_definition_outcome_6w
needs: [matching]
outputs:
highly_sensitive:
cohort: output/input_outcome_6w.csv
process_Rmatching_6w: # add variables
run: r:latest analysis/process_Rmatching_6w.R
needs: [extract_variables_6w,matching,process_Rmatching]
outputs:
highly_sensitive:
cohort1: output/matched_outcome_6w.rds
model_6w:
run: r:latest analysis/model/model_6w.R
needs: [process_Rmatching_6w]
outputs:
moderately_sensitive:
csv1.1: output/model_6w_binary_adj1.csv
csv1.2: output/model_6w_total_adj1.csv
csv1.3: output/model_6w_types_adj1.csv
csv2.1: output/model_6w_binary_adj2.csv
csv2.2: output/model_6w_total_adj2.csv
csv2.3: output/model_6w_types_adj2.csv
model_6w_time:
run: r:latest analysis/model/model_6w_time.R
needs: [process_Rmatching_6w]
outputs:
moderately_sensitive:
csv1.1: output/model_6w_time_adj1.csv
csv1.2: output/model_6w_time_adj2.csv
model_6w_plot: # adjust for last AB time
run: r:latest -e 'rmarkdown::render("analysis/model_6w_plot.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
needs: [process_Rmatching_6w]
outputs:
moderately_sensitive:
html: output/model_6w_plot.html
# ongoing project
extract_variables_ab_yr1:
run: cohortextractor:latest generate_cohort --study-definition study_definition_ab_yr1
needs: [matching]
outputs:
highly_sensitive:
cohort: output/input_ab_yr1.csv
# sensitivity analysis - combine ICU+death outcome
generate_study_population_covid_admission_2:
run: cohortextractor:latest generate_cohort --study-definition study_definition_covid_admission_2
outputs:
highly_sensitive:
cohort: output/input_covid_admission_2.csv
process_2:
run: r:latest analysis/process_2.R
needs: [generate_study_population_covid_admission_2]
outputs:
highly_sensitive:
case: output/case_covid_icu_death_2.csv
control: output/control_covid_hosp_2.csv
case2: output/case_covid_icu_2.csv
matching_2:
run: r:latest -e 'rmarkdown::render("analysis/matching_2.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
needs: [process_2]
outputs:
moderately_sensitive:
html: output/matching_2.html
highly_sensitive:
rds1: output/matched_patients_2.rds
rds2: output/unmatched_patients_2.rds
csv: output/matched_patients_id_2.csv
extract_variables_2:
run: cohortextractor:latest generate_cohort --with-end-date-fix --study-definition study_definition_outcome_2
needs: [matching_2]
outputs:
highly_sensitive:
cohort: output/input_outcome_2.csv
process_Rmatching_2: # add variables
run: r:latest analysis/process_Rmatching_2.R
needs: [extract_variables_2,matching_2]
outputs:
highly_sensitive:
cohort1: output/matched_outcome_2.rds
rds1: output/abtype79_2.rds
rds2: output/comor17_2.rds
model_ICU_death:
run: r:latest analysis/model/model_ICU_death.R
needs: [process_Rmatching_2]
outputs:
moderately_sensitive:
csv1: output/model_1_crude_ICU_death.csv
csv2: output/model_1_adjusted_ICU_death.csv
model_2_ICU_death:
run: r:latest -e 'rmarkdown::render("analysis/model_2_ICU_death.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
needs: [process_Rmatching_2]
outputs:
moderately_sensitive:
html: output/model_2_ICU_death.html