generated from opensafely/research-template
/
project.yaml
1149 lines (1006 loc) · 39.5 KB
/
project.yaml
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version: '3.0'
expectations:
population_size: 30000
actions:
### study cohort ###
generate_study_population_case:
run: cohortextractor:latest generate_cohort --study-definition study_definition_case
outputs:
highly_sensitive:
cohort: output/input_case.csv
generate_study_population_case_test:
run: cohortextractor:latest generate_cohort --study-definition study_definition_case_test
outputs:
highly_sensitive:
cohort: output/input_case_test.csv
generate_study_population_control_1:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_1
outputs:
highly_sensitive:
cohort: output/input_control_1.csv
generate_study_population_control_2:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_2
outputs:
highly_sensitive:
cohort: output/input_control_2.csv
generate_study_population_control_3:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_3
outputs:
highly_sensitive:
cohort: output/input_control_3.csv
generate_study_population_control_4:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_4
outputs:
highly_sensitive:
cohort: output/input_control_4.csv
generate_study_population_control_5:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_5
outputs:
highly_sensitive:
cohort: output/input_control_5.csv
generate_study_population_control_6:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_6
outputs:
highly_sensitive:
cohort: output/input_control_6.csv
generate_study_population_control_7:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_7
outputs:
highly_sensitive:
cohort: output/input_control_7.csv
generate_study_population_control_8:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_8
outputs:
highly_sensitive:
cohort: output/input_control_8.csv
case_check:
run: r:latest analysis/case_check.R
needs: [generate_study_population_case]
outputs:
highly_sensitive:
cohort: output/case_ch.csv
moderately_sensitive:
table1: output/case_check.csv
table2: output/case_frequency_check.csv
sepsis_trend:
run: r:latest analysis/sepsis_trend.R
needs: [case_check]
outputs:
moderately_sensitive:
plot1: output/figure_2.1.jpeg
plot2: output/figure_2.2.jpeg
plot3: output/figure_2.3.jpeg
table1: output/figure_2.3_table.csv
generate_study_population:
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-01-01 to 2022-12-31 by month" --skip-existing --output-dir=output/measures --output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/measures/input_*.csv.gz
generate_measures:
run: cohortextractor:latest generate_measures --study-definition study_definition --skip-existing --output-dir=output/measures
needs: [generate_study_population]
outputs:
moderately_sensitive:
measure_csv: output/measures/measure_*.csv
sepsis_trend_rate:
run: r:latest analysis/sepsis_trend_rate.R
needs: [case_check,generate_measures]
outputs:
moderately_sensitive:
plot1: output/figure_rate.jpeg
table1: output/figure_rate_table.csv
sepsis_trend_rate_com:
run: r:latest analysis/sepsis_trend_rate_com.R
needs: [case_check,generate_measures]
outputs:
moderately_sensitive:
plot1: output/figure_rate_com.jpeg
sepsis_trend_rate_hos:
run: r:latest analysis/sepsis_trend_rate_hos.R
needs: [case_check,generate_measures]
outputs:
moderately_sensitive:
plot1: output/figure_rate_hos.jpeg
process1:
run: r:latest analysis/process1.R
needs: [case_check,generate_study_population_control_1,generate_study_population_control_2,
generate_study_population_control_3,generate_study_population_control_4,generate_study_population_control_5,
generate_study_population_control_6,generate_study_population_control_7,generate_study_population_control_8]
outputs:
highly_sensitive:
cohort1: output/case_191.csv
cohort2: output/case_192.csv
cohort3: output/case_201.csv
cohort4: output/case_202.csv
cohort5: output/case_211.csv
cohort6: output/case_212.csv
cohort7: output/case_221.csv
cohort8: output/case_222.csv
cohort9: output/control_191.csv
cohort10: output/control_192.csv
cohort11: output/control_201.csv
cohort12: output/control_202.csv
cohort13: output/control_211.csv
cohort14: output/control_212.csv
cohort15: output/control_221.csv
cohort16: output/control_222.csv
matching1:
run: python:latest python analysis/matching1.py
needs: [process1]
outputs:
highly_sensitive:
table1: output/matched_cases_191.csv
table2: output/matched_matches_191.csv
table3: output/matched_combined_191.csv
table4: output/matched_cases_192.csv
table5: output/matched_matches_192.csv
table6: output/matched_combined_192.csv
moderately_sensitive:
report1: output/matching_report_191.txt
report2: output/matching_report_192.txt
matching2:
run: python:latest python analysis/matching2.py
needs: [process1]
outputs:
highly_sensitive:
table1: output/matched_cases_201.csv
table2: output/matched_matches_201.csv
table3: output/matched_combined_201.csv
table4: output/matched_cases_202.csv
table5: output/matched_matches_202.csv
table6: output/matched_combined_202.csv
moderately_sensitive:
report1: output/matching_report_201.txt
report2: output/matching_report_202.txt
matching3:
run: python:latest python analysis/matching3.py
needs: [process1]
outputs:
highly_sensitive:
table1: output/matched_cases_211.csv
table2: output/matched_matches_211.csv
table3: output/matched_combined_211.csv
table4: output/matched_cases_212.csv
table5: output/matched_matches_212.csv
table6: output/matched_combined_212.csv
moderately_sensitive:
report1: output/matching_report_211.txt
report2: output/matching_report_212.txt
matching4:
run: python:latest python analysis/matching4.py
needs: [process1]
outputs:
highly_sensitive:
table1: output/matched_cases_221.csv
table2: output/matched_matches_221.csv
table3: output/matched_combined_221.csv
moderately_sensitive:
report1: output/matching_report_221.txt
process_covidinclude:
run: r:latest analysis/process_covidinclude.R
needs: [generate_study_population_case]
outputs:
highly_sensitive:
cohort: output/case_covidinclude.csv
moderately_sensitive:
table1: output/case_frequency_check1.csv
table2: output/case_frequency_check2.csv
sepsis_trend_rate_covidinclude:
run: r:latest analysis/sepsis_trend_rate_covidinclude.R
needs: [process_covidinclude,generate_measures]
outputs:
moderately_sensitive:
plot1: output/figure_rate_covidinclude.jpeg
table1: output/figure_rate_covidinclude_table.csv
plot2: output/figure_rate_covidinclude_com.jpeg
plot3: output/figure_rate_covidinclude_hos.jpeg
process_noexclude:
run: r:latest analysis/process_noexclude.R
needs: [generate_study_population_case]
outputs:
moderately_sensitive:
plot1: output/figure_noexclude.jpeg
table1: output/figure_noexclude_table.csv
process2_idextraction:
run: r:latest analysis/process2_idextraction.R
needs: [matching1,matching2,matching3,matching4]
outputs:
highly_sensitive:
cohort: output/case_id.csv
generate_study_population_variables:
run: cohortextractor:latest generate_cohort --study-definition study_definition_variables
needs: [process2_idextraction]
outputs:
highly_sensitive:
cohort: output/input_variables.csv
process3_idextraction:
run: r:latest analysis/process3_idextraction.R
needs: [matching1,matching2,matching3,matching4]
outputs:
highly_sensitive:
cohort1: output/control_id_191.csv
cohort2: output/control_id_192.csv
cohort3: output/control_id_201.csv
cohort4: output/control_id_202.csv
cohort5: output/control_id_211.csv
cohort6: output/control_id_212.csv
cohort7: output/control_id_221.csv
generate_study_population_control_var_191:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_var_191
needs: [process3_idextraction]
outputs:
highly_sensitive:
cohort: output/input_control_var_191.csv
generate_study_population_control_var_192:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_var_192
needs: [process3_idextraction]
outputs:
highly_sensitive:
cohort: output/input_control_var_192.csv
generate_study_population_control_var_201:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_var_201
needs: [process3_idextraction]
outputs:
highly_sensitive:
cohort: output/input_control_var_201.csv
generate_study_population_control_var_202:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_var_202
needs: [process3_idextraction]
outputs:
highly_sensitive:
cohort: output/input_control_var_202.csv
generate_study_population_control_var_211:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_var_211
needs: [process3_idextraction]
outputs:
highly_sensitive:
cohort: output/input_control_var_211.csv
generate_study_population_control_var_212:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_var_212
needs: [process3_idextraction]
outputs:
highly_sensitive:
cohort: output/input_control_var_212.csv
generate_study_population_control_var_221:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_var_221
needs: [process3_idextraction]
outputs:
highly_sensitive:
cohort: output/input_control_var_221.csv
process_data:
run: r:latest analysis/data_process.R
needs: [generate_study_population_variables]
outputs:
highly_sensitive:
rds: output/processed/input_case_data.rds
process_data_control:
run: r:latest analysis/data_process_control.R
needs: [generate_study_population_control_var_191,generate_study_population_control_var_192,
generate_study_population_control_var_201,generate_study_population_control_var_202,
generate_study_population_control_var_211,generate_study_population_control_var_212,
generate_study_population_control_var_221]
outputs:
highly_sensitive:
rds: output/processed/input_control_data.rds
# Skim data
skim_data_case:
run: r:latest analysis/data_skim.R output/processed/input_case_data.rds output/data_properties
needs: [process_data]
outputs:
moderately_sensitive:
txt1: output/data_properties/input_case_data_skim.txt
txt2: output/data_properties/input_case_data_coltypes.txt
txt3: output/data_properties/input_case_data_tabulate.txt
skim_data_control:
run: r:latest analysis/data_skim.R output/processed/input_control_data.rds output/data_properties
needs: [process_data_control]
outputs:
moderately_sensitive:
txt1: output/data_properties/input_control_data_skim.txt
txt2: output/data_properties/input_control_data_coltypes.txt
txt3: output/data_properties/input_control_data_tabulate.txt
extract_case_ab_6w:
run: cohortextractor:latest generate_cohort --study-definition study_definition_case_ab
needs: [process2_idextraction]
outputs:
highly_sensitive:
cohort: output/input_case_ab.csv
extract_control_ab_6w_191:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_ab_191
needs: [process3_idextraction]
outputs:
highly_sensitive:
cohort: output/input_control_ab_191.csv
extract_control_ab_6w_192:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_ab_192
needs: [process3_idextraction]
outputs:
highly_sensitive:
cohort: output/input_control_ab_192.csv
extract_control_ab_6w_201:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_ab_201
needs: [process3_idextraction]
outputs:
highly_sensitive:
cohort: output/input_control_ab_201.csv
extract_control_ab_6w_202:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_ab_202
needs: [process3_idextraction]
outputs:
highly_sensitive:
cohort: output/input_control_ab_202.csv
extract_control_ab_6w_211:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_ab_211
needs: [process3_idextraction]
outputs:
highly_sensitive:
cohort: output/input_control_ab_211.csv
extract_control_ab_6w_212:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_ab_212
needs: [process3_idextraction]
outputs:
highly_sensitive:
cohort: output/input_control_ab_212.csv
extract_control_ab_6w_221:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_ab_221
needs: [process3_idextraction]
outputs:
highly_sensitive:
cohort: output/input_control_ab_221.csv
process_ab_case:
run: r:latest analysis/process_ab_case.R
needs: [extract_case_ab_6w]
outputs:
highly_sensitive:
rds: output/processed/input_case_ab.rds
process_ab_control:
run: r:latest analysis/process_ab_control.R
needs: [extract_control_ab_6w_191,extract_control_ab_6w_192,extract_control_ab_6w_201,
extract_control_ab_6w_202,extract_control_ab_6w_211,extract_control_ab_6w_212,extract_control_ab_6w_221]
outputs:
highly_sensitive:
rds: output/processed/input_control_ab.rds
check_age_dist:
run: r:latest analysis/check_age_dist.R
needs: [matching1,matching2,matching3,matching4]
outputs:
moderately_sensitive:
plot1: output/case_18.jpeg
extract_case_var_add:
run: cohortextractor:latest generate_cohort --study-definition study_definition_case_var_add
needs: [process2_idextraction]
outputs:
highly_sensitive:
cohort: output/input_case_var_add.csv
extract_case_var_add_191:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_var_add_191
needs: [process3_idextraction]
outputs:
highly_sensitive:
cohort: output/input_control_var_add_191.csv
extract_case_var_add_192:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_var_add_192
needs: [process3_idextraction]
outputs:
highly_sensitive:
cohort: output/input_control_var_add_192.csv
extract_case_var_add_201:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_var_add_201
needs: [process3_idextraction]
outputs:
highly_sensitive:
cohort: output/input_control_var_add_201.csv
extract_case_var_add_202:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_var_add_202
needs: [process3_idextraction]
outputs:
highly_sensitive:
cohort: output/input_control_var_add_202.csv
extract_case_var_add_211:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_var_add_211
needs: [process3_idextraction]
outputs:
highly_sensitive:
cohort: output/input_control_var_add_211.csv
extract_case_var_add_212:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_var_add_212
needs: [process3_idextraction]
outputs:
highly_sensitive:
cohort: output/input_control_var_add_212.csv
extract_case_var_add_221:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_var_add_221
needs: [process3_idextraction]
outputs:
highly_sensitive:
cohort: output/input_control_var_add_221.csv
process_model_var:
run: r:latest analysis/process_model_var.R
needs: [matching1,matching2,matching3,matching4,
process_data,process_data_control,
process_ab_case,process_ab_control,
process_ab_case_6w,process_ab_control_6w,
extract_case_var_add,extract_case_var_add_191,
extract_case_var_add_192,extract_case_var_add_201,
extract_case_var_add_202,extract_case_var_add_211,
extract_case_var_add_212,extract_case_var_add_221]
outputs:
highly_sensitive:
rds1: output/processed/input_model_c_h.rds
rds2: output/processed/input_model_c.rds
rds3: output/processed/input_model_h.rds
process_table_1:
run: r:latest analysis/Table1.R
needs: [process_model_var]
outputs:
moderately_sensitive:
table1: output/table_1_case.csv
table2: output/table_1_control.csv
process_table_1_separate:
run: r:latest analysis/Table1_separate.R
needs: [process_model_var]
outputs:
moderately_sensitive:
table1: output/table_1_case_com.csv
table2: output/table_1_control_com.csv
table3: output/table_1_case_hos.csv
table4: output/table_1_control_hos.csv
process_table_1_byimd:
run: r:latest analysis/Table1_byimd.R
needs: [process_model_var]
outputs:
moderately_sensitive:
table1: output/table_1_imd1_case.csv
table2: output/table_1_imd2_case.csv
table3: output/table_1_imd3_case.csv
table4: output/table_1_imd4_case.csv
table5: output/table_1_imd5_case.csv
table6: output/table_1_imd1_control.csv
table7: output/table_1_imd2_control.csv
table8: output/table_1_imd3_control.csv
table9: output/table_1_imd4_control.csv
table10: output/table_1_imd5_control.csv
model_crude_ch:
run: r:latest analysis/model_crude_ch.R
needs: [process_model_var]
outputs:
moderately_sensitive:
table1: output/crude_model_result.csv
highly_sensitive:
rds1: output/processed/input_crude_model_ch.rds
model_crude_c:
run: r:latest analysis/model_crude_c.R
needs: [process_model_var]
outputs:
moderately_sensitive:
table1: output/crude_model_result_c.csv
highly_sensitive:
rds1: output/processed/input_crude_model_c.rds
model_crude_h:
run: r:latest analysis/model_crude_h.R
needs: [process_model_var]
outputs:
moderately_sensitive:
table1: output/crude_model_result_h.csv
highly_sensitive:
rds1: output/processed/input_crude_model_h.rds
model_crude_plot:
run: r:latest analysis/model_crude_plot.R
needs: [model_crude_h,model_crude_c,model_crude_ch]
outputs:
moderately_sensitive:
table1: output/crude_plota.csv
table2: output/crude_plotb.csv
Figure_2A_crude:
run: r:latest analysis/Figure_2A_crude.R
needs: [model_crude_plot]
outputs:
moderately_sensitive:
plot1: output/Figure_2A_crude_1.jpeg
plot2: output/Figure_2A_crude_2.jpeg
Figure_2B_crude:
run: r:latest analysis/Figure_2B_crude.R
needs: [model_crude_plot]
outputs:
moderately_sensitive:
plot2: output/Figure_2B_crude.jpeg
Figure_2C_crude:
run: r:latest analysis/Figure_2C_crude.R
needs: [model_crude_plot]
outputs:
moderately_sensitive:
plot2: output/Figure_2C_crude.jpeg
Figure_2D_crude:
run: r:latest analysis/Figure_2D_crude.R
needs: [model_crude_plot]
outputs:
moderately_sensitive:
plot2: output/Figure_2D_crude.jpeg
Figure_2E_crude:
run: r:latest analysis/Figure_2E_crude.R
needs: [model_crude_plot]
outputs:
moderately_sensitive:
plot2: output/Figure_2E_crude.jpeg
model_adjusted_plot:
run: r:latest analysis/model_adjusted_plot.R
needs: [process_model_var]
outputs:
moderately_sensitive:
table6: output/adjusted_plotimd.csv
table1: output/adjusted_plota.csv
table2: output/adjusted_plotb.csv
table3: output/adjusted_plotc.csv
table4: output/adjusted_plotd.csv
table5: output/adjusted_plote.csv
Figure_2A:
run: r:latest analysis/Figure_2A.R
needs: [model_adjusted_plot]
outputs:
moderately_sensitive:
plot1: output/Figure_2A_adjusted_1.jpeg
plot2: output/Figure_2A_adjusted_2.jpeg
Figure_2B:
run: r:latest analysis/Figure_2B.R
needs: [model_adjusted_plot]
outputs:
moderately_sensitive:
plot2: output/Figure_2B_adjusted.jpeg
Figure_2C:
run: r:latest analysis/Figure_2C.R
needs: [model_adjusted_plot]
outputs:
moderately_sensitive:
plot2: output/Figure_2C_adjusted.jpeg
Figure_2D:
run: r:latest analysis/Figure_2D.R
needs: [model_adjusted_plot]
outputs:
moderately_sensitive:
plot2: output/Figure_2D_adjusted.jpeg
Figure_2E:
run: r:latest analysis/Figure_2E.R
needs: [model_adjusted_plot]
outputs:
moderately_sensitive:
plot2: output/Figure_2E_adjusted.jpeg
model_adjusted_plot_type:
run: r:latest analysis/model_adjusted_plot_type.R
needs: [process_model_var]
outputs:
moderately_sensitive:
table6: output/adjusted_type_plotimd.csv
table1: output/adjusted_type_plota.csv
table2: output/adjusted_type_plotb.csv
table3: output/adjusted_type_plotc.csv
table4: output/adjusted_type_plotd.csv
table5: output/adjusted_type_plote.csv
Figure_2E_type:
run: r:latest analysis/Figure_2E_type.R
needs: [model_adjusted_plot_type]
outputs:
moderately_sensitive:
plot2: output/Figure_2E_adjusted_type.jpeg
model_imd:
run: r:latest analysis/model_imd.R
needs: [process_model_var]
outputs:
moderately_sensitive:
table1: output/imd_model.csv
table2: output/imd_model_covid.csv
table3: output/imd_model_cardiometabolic.csv
Figure_2_IMD:
run: r:latest analysis/Figure_2_IMD.R
needs: [model_imd]
outputs:
moderately_sensitive:
plot1: output/Figure_2_IMD.jpeg
Figure_2_IMD_crude:
run: r:latest analysis/Figure_2_IMD_crude.R
needs: [model_imd]
outputs:
moderately_sensitive:
plot1: output/Figure_2_IMD_crude.jpeg
Figure_2_IMD_combine:
run: r:latest analysis/Figure_2_IMD_combine.R
needs: [model_imd,model_adjusted_plot]
outputs:
moderately_sensitive:
plot1: output/Figure_2_IMD_combine.jpeg
mortality_rate:
run: r:latest analysis/mortality_rate.R
needs: [process_model_var]
outputs:
moderately_sensitive:
table1: output/model_mortality.csv
mortality_model_time:
run: r:latest analysis/mortality_model_time.R
needs: [process_model_var]
outputs:
moderately_sensitive:
table1: output/model_mortality_1.csv
table2: output/model_mortality_2.csv
table3: output/model_mortality_3.csv
table4: output/model_mortality_all.csv
plot_mortality_model:
run: r:latest -e 'rmarkdown::render("analysis/mortality_model_plot.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
needs: [mortality_model_time]
outputs:
moderately_sensitive:
csv: output/mortality_model_plot.html
mortality_table:
run: r:latest analysis/mortality_table.R
needs: [process_model_var]
outputs:
moderately_sensitive:
table1: output/mortality_table_all.csv
table2: output/mortality_table_c.csv
table3: output/mortality_table_h.csv
age_check:
run: r:latest analysis/age_check.R
needs: [process_model_var]
outputs:
moderately_sensitive:
plot1: output/age_check_1.jpeg
plot2: output/age_check_2.jpeg
model_adjusted_clinical:
run: r:latest analysis/model_adjusted_clinical.R
needs: [process_model_var]
outputs:
moderately_sensitive:
table6: output/adjusted_clinical_1.csv
table1: output/adjusted_clinical_2.csv
table2: output/adjusted_clinical_3.csv
Figure_adjusted_clinical:
run: r:latest -e 'rmarkdown::render("analysis/Figure_adjusted_clinical.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
needs: [model_adjusted_clinical]
outputs:
moderately_sensitive:
csv: output/Figure_adjusted_clinical.html
Figure_crude_demo:
run: r:latest -e 'rmarkdown::render("analysis/Figure_crude_demo.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
needs: [model_crude_plot]
outputs:
moderately_sensitive:
csv: output/Figure_crude_demo.html
Figure_crude_clinical:
run: r:latest -e 'rmarkdown::render("analysis/Figure_crude_clinical.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
needs: [model_crude_plot]
outputs:
moderately_sensitive:
csv: output/Figure_crude_clinical.html
### adjusted model in period 1/2/3 ###
model_adjusted_clinical_period_1:
run: r:latest analysis/model_adjusted_clinical_period_1.R
needs: [process_model_var]
outputs:
moderately_sensitive:
table6: output/adjusted_clinical_1_period_1.csv
table1: output/adjusted_clinical_2_period_1.csv
table2: output/adjusted_clinical_3_period_1.csv
model_adjusted_clinical_period_2:
run: r:latest analysis/model_adjusted_clinical_period_2.R
needs: [process_model_var]
outputs:
moderately_sensitive:
table6: output/adjusted_clinical_1_period_2.csv
table1: output/adjusted_clinical_2_period_2.csv
table2: output/adjusted_clinical_3_period_2.csv
model_adjusted_clinical_period_3:
run: r:latest analysis/model_adjusted_clinical_period_3.R
needs: [process_model_var]
outputs:
moderately_sensitive:
table6: output/adjusted_clinical_1_period_3.csv
table1: output/adjusted_clinical_2_period_3.csv
table2: output/adjusted_clinical_3_period_3.csv
Figure_adjusted_clinical_period_1:
run: r:latest -e 'rmarkdown::render("analysis/Figure_adjusted_clinical_period_1.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
needs: [model_adjusted_clinical_period_1]
outputs:
moderately_sensitive:
csv: output/Figure_adjusted_clinical_period_1.html
Figure_adjusted_clinical_period_2:
run: r:latest -e 'rmarkdown::render("analysis/Figure_adjusted_clinical_period_2.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
needs: [model_adjusted_clinical_period_2]
outputs:
moderately_sensitive:
csv: output/Figure_adjusted_clinical_period_2.html
Figure_adjusted_clinical_period_3:
run: r:latest -e 'rmarkdown::render("analysis/Figure_adjusted_clinical_period_3.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
needs: [model_adjusted_clinical_period_3]
outputs:
moderately_sensitive:
csv: output/Figure_adjusted_clinical_period_3.html
### crude model in period 1/2/3 ###
model_crude_ch_period_1:
run: r:latest analysis/model_crude_ch_period_1.R
needs: [process_model_var]
outputs:
moderately_sensitive:
table1: output/crude_model_result_period_1.csv
highly_sensitive:
rds1: output/processed/input_crude_model_ch_period_1.rds
model_crude_ch_period_2:
run: r:latest analysis/model_crude_ch_period_2.R
needs: [process_model_var]
outputs:
moderately_sensitive:
table1: output/crude_model_result_period_2.csv
highly_sensitive:
rds1: output/processed/input_crude_model_ch_period_2.rds
model_crude_ch_period_3:
run: r:latest analysis/model_crude_ch_period_3.R
needs: [process_model_var]
outputs:
moderately_sensitive:
table1: output/crude_model_result_period_3.csv
highly_sensitive:
rds1: output/processed/input_crude_model_ch_period_3.rds
model_crude_c_period_1:
run: r:latest analysis/model_crude_c_period_1.R
needs: [process_model_var]
outputs:
moderately_sensitive:
table1: output/crude_model_result_c_period_1.csv
highly_sensitive:
rds1: output/processed/input_crude_model_c_period_1.rds
model_crude_c_period_2:
run: r:latest analysis/model_crude_c_period_2.R
needs: [process_model_var]
outputs:
moderately_sensitive:
table1: output/crude_model_result_c_period_2.csv
highly_sensitive:
rds1: output/processed/input_crude_model_c_period_2.rds
model_crude_c_period_3:
run: r:latest analysis/model_crude_c_period_3.R
needs: [process_model_var]
outputs:
moderately_sensitive:
table1: output/crude_model_result_c_period_3.csv
highly_sensitive:
rds1: output/processed/input_crude_model_c_period_3.rds
model_crude_h_period_1:
run: r:latest analysis/model_crude_h_period_1.R
needs: [process_model_var]
outputs:
moderately_sensitive:
table1: output/crude_model_result_h_period_1.csv
highly_sensitive:
rds1: output/processed/input_crude_model_h_period_1.rds
model_crude_h_period_2:
run: r:latest analysis/model_crude_h_period_2.R
needs: [process_model_var]
outputs:
moderately_sensitive:
table1: output/crude_model_result_h_period_2.csv
highly_sensitive:
rds1: output/processed/input_crude_model_h_period_2.rds
model_crude_h_period_3:
run: r:latest analysis/model_crude_h_period_3.R
needs: [process_model_var]
outputs:
moderately_sensitive:
table1: output/crude_model_result_h_period_3.csv
highly_sensitive:
rds1: output/processed/input_crude_model_h_period_3.rds
model_crude_plot_period_1:
run: r:latest analysis/model_crude_plot_period_1.R
needs: [model_crude_h_period_1,model_crude_c_period_1,model_crude_ch_period_1]
outputs:
moderately_sensitive:
table1: output/crude_plota_period_1.csv
table2: output/crude_plotb_period_1.csv
model_crude_plot_period_2:
run: r:latest analysis/model_crude_plot_period_2.R
needs: [model_crude_h_period_2,model_crude_c_period_2,model_crude_ch_period_2]
outputs:
moderately_sensitive:
table1: output/crude_plota_period_2.csv
table2: output/crude_plotb_period_2.csv
model_crude_plot_period_3:
run: r:latest analysis/model_crude_plot_period_3.R
needs: [model_crude_h_period_3,model_crude_c_period_3,model_crude_ch_period_3]
outputs:
moderately_sensitive:
table1: output/crude_plota_period_3.csv
table2: output/crude_plotb_period_3.csv
Figure_crude_clinical_period_1:
run: r:latest -e 'rmarkdown::render("analysis/Figure_crude_clinical_period_1.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
needs: [model_crude_plot_period_1]
outputs:
moderately_sensitive:
csv: output/Figure_crude_clinical_period_1.html
Figure_crude_clinical_period_2:
run: r:latest -e 'rmarkdown::render("analysis/Figure_crude_clinical_period_2.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
needs: [model_crude_plot_period_2]
outputs:
moderately_sensitive:
csv: output/Figure_crude_clinical_period_2.html
Figure_crude_clinical_period_3:
run: r:latest -e 'rmarkdown::render("analysis/Figure_crude_clinical_period_3.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
needs: [model_crude_plot_period_3]
outputs:
moderately_sensitive:
csv: output/Figure_crude_clinical_period_3.html
Figure_crude_demo_period_1:
run: r:latest -e 'rmarkdown::render("analysis/Figure_crude_demo_period_1.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
needs: [model_crude_plot_period_1]
outputs:
moderately_sensitive:
csv: output/Figure_crude_demo_period_1.html
Figure_crude_demo_period_2:
run: r:latest -e 'rmarkdown::render("analysis/Figure_crude_demo_period_2.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
needs: [model_crude_plot_period_2]
outputs:
moderately_sensitive:
csv: output/Figure_crude_demo_period_2.html
Figure_crude_demo_period_3:
run: r:latest -e 'rmarkdown::render("analysis/Figure_crude_demo_period_3.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
needs: [model_crude_plot_period_3]
outputs:
moderately_sensitive:
csv: output/Figure_crude_demo_period_3.html
### extract ab from -42days to index date
extract_case_ab_in6w:
run: cohortextractor:latest generate_cohort --study-definition study_definition_case_ab_6w
needs: [process2_idextraction]
outputs:
highly_sensitive:
cohort: output/input_case_ab_6w.csv
extract_control_ab_in6w_191:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_ab_6w_191
needs: [process3_idextraction]
outputs:
highly_sensitive:
cohort: output/input_control_ab_6w_191.csv
extract_control_ab_in6w_192:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_ab_6w_192
needs: [process3_idextraction]
outputs:
highly_sensitive:
cohort: output/input_control_ab_6w_192.csv
extract_control_ab_in6w_201:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_ab_6w_201
needs: [process3_idextraction]
outputs:
highly_sensitive:
cohort: output/input_control_ab_6w_201.csv
extract_control_ab_in6w_202:
run: cohortextractor:latest generate_cohort --study-definition study_definition_control_ab_6w_202
needs: [process3_idextraction]
outputs:
highly_sensitive:
cohort: output/input_control_ab_6w_202.csv
extract_control_ab_in6w_211: