This page shows the technical details of what happened when authorised researcher rriefu requested one or more actions to be run against real patient data in the BRIT Antibiotic Research project, within a secure environment.
By cross-referencing the indicated Requested Actions with the Pipeline section below, you can infer what
security level various outputs were written to. Outputs
marked as highly_sensitive
can never be viewed directly by a
researcher; they can only request that code runs against them. Outputs marked as moderately_sensitive
can be
viewed by an approved researcher by logging into a highly secure environment. Only outputs marked as
moderately_sensitive
can be requested for release to the public, via a controlled output review service.
Jobs
ID | Status | Action |
---|---|---|
7d5xm4n2jqksjf6l | failed | model |
Pipeline
Show Hide project.yaml
version: '3.0'
expectations:
population_size: 1000
actions:
generate_study_population_covid_primarycare:
run: cohortextractor:latest generate_cohort --study-definition study_definition_covid_primarycare
outputs:
highly_sensitive:
cohort: output/input_covid_primarycare.csv
generate_study_population_covid_SGSS:
run: cohortextractor:latest generate_cohort --study-definition study_definition_covid_SGSS
outputs:
highly_sensitive:
cohort: output/input_covid_SGSS.csv
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: # Covid ons death
run: r:latest analysis/process_1.R
needs: [generate_study_population_covid_primarycare, generate_study_population_covid_SGSS,generate_study_population_covid_admission]
outputs:
highly_sensitive:
case: output/case_covid_hosp.csv
control: output/control_covid_infection.csv
matching: #R MatchIt matching with replacement
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_cases.rds
csv: output/matched_patients_id.csv
extract_variables:
run: cohortextractor:latest generate_cohort --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
cohort2: output/matched_outcome_check.rds # filter died $ de-regist again
rds1: output/abtype79.rds
rds2: output/comor17.rds
table1: # compare before & after matching
run: r:latest -e 'rmarkdown::render("analysis/table1.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
needs: [process_1,process_Rmatching]
outputs:
moderately_sensitive:
html: output/table1.html
table2: # confounders
run: r:latest -e 'rmarkdown::render("analysis/table2.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
needs: [process_Rmatching]
outputs:
moderately_sensitive:
html: output/table2.html
table2_ab: # ab
run: r:latest -e 'rmarkdown::render("analysis/table2_ab.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
needs: [process_Rmatching]
outputs:
moderately_sensitive:
html: output/table2_ab.html
model:
run: r:latest -e 'rmarkdown::render("analysis/model.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
needs: [process_Rmatching]
outputs:
moderately_sensitive:
html: output/model.html
################# check ok###########
process_2: # died any cause
run: r:latest analysis/process_2.R
needs: [generate_study_population_covid_primarycare, generate_study_population_covid_SGSS]
outputs:
highly_sensitive:
control: output/control_covid_infection_2.csv
check_input: #
run: r:latest -e 'rmarkdown::render("analysis/check_input.Rmd", knit_root_dir = "/workspace", output_dir = "output")'
needs: [process_Rmatching,process_2,extract_variables,matching,process_matching,extract_variables_outcome_2_2,extract_variables_outcome_2_4,extract_variables_outcome_2_6,matching_2,process_1,generate_study_population_covid_primarycare, generate_study_population_covid_SGSS]
outputs:
moderately_sensitive:
html: output/check_input.html
# OS matching without replacement, ratio 2-4-6
matching_2:
run: python:latest python analysis/matching_outcome_2.py
needs: [process_1]
outputs:
moderately_sensitive:
matching_report2: output/matching_report_infection_hosp_2.txt
matching_report4: output/matching_report_infection_hosp_4.txt
matching_report6: output/matching_report_infection_hosp_6.txt
highly_sensitive:
combined2: output/matched_combined_infection_hosp_2.csv
combined4: output/matched_combined_infection_hosp_4.csv
combined6: output/matched_combined_infection_hosp_6.csv
extract_variables_outcome_2_2:
run: cohortextractor:latest generate_cohort --study-definition study_definition_outcome_2_2
needs: [matching_2]
outputs:
highly_sensitive:
cohort: output/input_outcome_2_2.csv
extract_variables_outcome_2_4:
run: cohortextractor:latest generate_cohort --study-definition study_definition_outcome_2_4
needs: [matching_2]
outputs:
highly_sensitive:
cohort: output/input_outcome_2_4.csv
extract_variables_outcome_2_6:
run: cohortextractor:latest generate_cohort --study-definition study_definition_outcome_2_6
needs: [matching_2]
outputs:
highly_sensitive:
cohort: output/input_outcome_2_6.csv
check_matching_2:
run: r:latest -e 'rmarkdown::render("analysis/check_matching_2.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
needs: [matching_2]
outputs:
moderately_sensitive:
html: output/check_matching_2.html
process_matching: # add variables
run: r:latest analysis/process_matching.R
needs: [extract_variables_outcome_2_6,extract_variables_outcome_2_4,extract_variables_outcome_2_2,matching_2]
outputs:
highly_sensitive:
cohort1: output/matched_outcome_2.csv
cohort2: output/matched_outcome_4.csv
cohort3: output/matched_outcome_6.csv
check_exposures_6:
run: r:latest -e 'rmarkdown::render("analysis/check_exposures_6.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
needs: [process_matching]
outputs:
moderately_sensitive:
html: output/check_exposures_6.html
check_exposures_4:
run: r:latest -e 'rmarkdown::render("analysis/check_exposures_4.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
needs: [process_matching]
outputs:
moderately_sensitive:
html: output/check_exposures_4.html
check_exposures_2:
run: r:latest -e 'rmarkdown::render("analysis/check_exposures_2.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
needs: [process_matching]
outputs:
moderately_sensitive:
html: output/check_exposures_2.html
# # R MatchIt
# matching: # matching with replacement
# 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_matching:
run: r:latest -e 'rmarkdown::render("analysis/check_matching.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
needs: [matching]
outputs:
moderately_sensitive:
html: output/check_matching.html
# extract_variables:
# run: cohortextractor:latest generate_cohort --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
check_exposures_cont: # continuous variables
run: r:latest -e 'rmarkdown::render("analysis/check_exposures_cont.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
needs: [process_Rmatching]
outputs:
moderately_sensitive:
html: output/check_exposures_cont.html
check_exposures_cat: # category variables
run: r:latest -e 'rmarkdown::render("analysis/check_exposures_cat.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
needs: [process_Rmatching]
outputs:
moderately_sensitive:
html: output/check_exposures_cat.html
modeling: # ab level
run: r:latest -e 'rmarkdown::render("analysis/modeling.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
needs: [process_Rmatching]
outputs:
moderately_sensitive:
html: output/modeling.html
modeling2: # ab level+ CCI + covid vaccine
run: r:latest -e 'rmarkdown::render("analysis/modeling2.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
needs: [process_Rmatching]
outputs:
moderately_sensitive:
html: output/modeling2.html
modeling3: # all
run: r:latest -e 'rmarkdown::render("analysis/modeling3.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
needs: [process_Rmatching]
outputs:
moderately_sensitive:
html: output/modeling3.html
describe_ab:
run: r:latest -e 'rmarkdown::render("analysis/describe_ab.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
needs: [process_Rmatching]
outputs:
moderately_sensitive:
html: output/describe_ab.html
# abtype modeling
modeling4: # all
run: r:latest -e 'rmarkdown::render("analysis/modeling4.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
needs: [process_Rmatching]
outputs:
moderately_sensitive:
html: output/modeling4.html
# broad ab modeling
modeling5: # all
run: r:latest -e 'rmarkdown::render("analysis/modeling5.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
needs: [process_Rmatching]
outputs:
moderately_sensitive:
html: output/modeling5.html
# unmatched controls
extract_variables_unmatched:
run: cohortextractor:latest generate_cohort --study-definition study_definition_unmatched
needs: [process_1]
outputs:
highly_sensitive:
cohort: output/input_unmatched.csv
process_unmatched: # add variables
run: r:latest analysis/process_unmatched.R
needs: [extract_variables_unmatched]
outputs:
highly_sensitive:
cohort1: output/unmatched_outcome.rds
# check_exposures_cont_unmatched: # continuous variables
# run: r:latest -e 'rmarkdown::render("analysis/check_exposures_cont_unmatched.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
# needs: [process_unmatched]
# outputs:
# moderately_sensitive:
# html: output/check_exposures_cont_unmatched.html
check_exposures_cat_unmatched: # category variables
run: r:latest -e 'rmarkdown::render("analysis/check_exposures_cat_unmatched.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
needs: [process_unmatched]
outputs:
moderately_sensitive:
html: output/check_exposures_cat_unmatched.html