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 |
|---|---|---|
| lk2hkmb7toos2ojd | succeeded | model |
Pipeline
Show Hide project.yaml
version: '3.0'
expectations:
population_size: 1000
actions:
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
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
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
table1: # matching var
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
# matching2: # matching with replacement # died any
# run: r:latest -e 'rmarkdown::render("analysis/matching2.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
# needs: [process_1]
# outputs:
# moderately_sensitive:
# html: output/matching2.html
# highly_sensitive:
# rds1: output/matched_patients_2.rds
# rds2: output/unmatched_patients_2.rds
# csv: output/matched_patients_id_2.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
# check_matching2:
# run: r:latest -e 'rmarkdown::render("analysis/check_matching2.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
# needs: [matching2]
# outputs:
# moderately_sensitive:
# html: output/check_matching2.html
extract_variables:
run: cohortextractor:latest generate_cohort --study-definition study_definition_outcome
needs: [matching]
outputs:
highly_sensitive:
cohort: output/input_outcome.csv
# extract_variables2:
# run: cohortextractor:latest generate_cohort --study-definition study_definition_outcome2
# needs: [matching2]
# outputs:
# highly_sensitive:
# cohort: output/input_outcome2.csv
# process_Rmatching: # add variables
# run: r:latest analysis/process_Rmatching.R
# needs: [extract_variables,matching]
# outputs:
# highly_sensitive:
# cohort1: output/matched_outcome.rds
# process_Rmatching2: # add variables
# run: r:latest analysis/process_Rmatching2.R
# needs: [extract_variables2,matching2]
# outputs:
# highly_sensitive:
# cohort1: output/matched_outcome2.rds
# check_input: #
# run: r:latest -e 'rmarkdown::render("analysis/check_input.Rmd", knit_root_dir = "/workspace", output_dir = "output")'
# needs: [process_Rmatching2,extract_variables2,matching2,process_Rmatching,extract_variables,matching,process_1, generate_study_population_covid_admission]
# outputs:
# moderately_sensitive:
# html: output/check_input.html
### for covid icu/ covid death
# 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
### for covid icu/ any death
### for covid icu/ covid death
# 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
State
State is inferred from the related Jobs.
Status: Succeeded
Timings
Timings set to UTC timezone.
- Created:
- Started:
- Finished:
- Runtime: 00:00:55