Job request: 17594
- Organisation:
- ONS
- Workspace:
- covid_mental_health
- ID:
- fuyikvy3e2osahrp
This page shows the technical details of what happened when the authorised researcher Klaudia Rzepnicka requested one or more actions to be run against real patient data in the project, within a secure environment.
By cross-referencing the list of jobs with the
pipeline section below, you can infer what
security level
various outputs were written to. Researchers can never directly
view outputs marked as
highly_sensitive
;
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
-
- Job identifier:
-
kv74xmg7o5f7elqi
Pipeline
Show project.yaml
# describes how each step in your analysis should be run
version: '3.0'
expectations:
population_size: 1000
actions:
generate_wide_non_health:
run: cohortextractor:latest generate_cohort --study-definition study_definition_non_health --with-end-date-fix
outputs:
highly_sensitive:
cohort: output/input_non_health.csv
generate_wide_health_mh:
run: cohortextractor:latest generate_cohort --study-definition study_definition_health_mh --with-end-date-fix
outputs:
highly_sensitive:
cohort: output/input_health_mh.csv
generate_wide_health_non_mh:
run: cohortextractor:latest generate_cohort --study-definition study_definition_health_non_mh --with-end-date-fix
outputs:
highly_sensitive:
cohort: output/input_health_non_mh.csv
generate_wide_ons_cis_new:
run: >
databuilder:v0
generate-dataset
--output output/dataset_ons_cis_new.csv
analysis/dataset_definition_ons_cis_new.py
outputs:
highly_sensitive:
dataset: output/dataset_ons_cis_new.csv
combine_wide_data:
run: r:latest analysis/1_combine_wide_data.R
needs: [generate_wide_non_health, generate_wide_health_mh, generate_wide_health_non_mh, generate_wide_ons_cis_new]
outputs:
highly_sensitive:
cohort: output/input_cis_wide.csv
transform_cis_wide_to_long:
run: r:latest analysis/2_cis_wide_to_long.R
needs: [combine_wide_data]
outputs:
highly_sensitive:
cohort: output/input_cis_long.csv
reconcile_snomed_ctv3:
run: r:latest analysis/3_reconcile_snomed_ctv3.R
needs: [transform_cis_wide_to_long]
outputs:
highly_sensitive:
cohort: output/input_reconciled.csv
#bmi: output/bmi_summary_table_info_before_cap.csv
derive_exposed:
run: r:latest analysis/4_exposed_population.R
needs: [reconcile_snomed_ctv3]
outputs:
highly_sensitive:
cohort: output/cis_exposed.csv
derive_controls:
run: r:latest analysis/5_control_population.R
needs: [reconcile_snomed_ctv3]
outputs:
highly_sensitive:
cohort: output/cis_control.csv
perform_matching:
run: r:latest analysis/6_create_controls.R
needs: [derive_exposed, derive_controls]
outputs:
highly_sensitive:
incidence: output/incidence_group.csv
prevalence: output/prevalence_group.csv
#exacerbated: output/exacerbated_group.csv
testing_exposed_post_pre_matching:
run: r:latest analysis/6_6_pre_post_match_testing.R
needs: [derive_exposed, derive_controls,perform_matching]
outputs:
moderately_sensitive:
t1: output/dates_order_control.csv
t2: output/dates_order_exposed.csv
adjust_matched_groups:
run: r:latest analysis/7_adjust_groups.R
needs: [perform_matching]
outputs:
highly_sensitive:
incidence: output/adjusted_incidence_group.csv
prevalence: output/adjusted_prevalence_group.csv
descriptive_stats:
run: r:latest analysis/8_descriptive_statistics.R
needs: [adjust_matched_groups]
outputs:
moderately_sensitive:
incidence_cat_stats: output/1_descriptives_incidence_cat.csv
incidence_con_stats: output/2_descriptives_incidence_con.csv
prevalence_cat_stats: output/3_descriptives_prevalence_cat.csv
prevalence_con_stats: output/4_descriptives_prevalence_con.csv
cumulative_incidence:
run: r:latest analysis/9_cumulative_incidence_curves.R
needs: [adjust_matched_groups]
outputs:
highly_sensitive:
inc_t: output/incidence_t.csv
prev_t: output/prevalence_t.csv
moderately_sensitive:
inc_surv: output/incidence_surv.jpg
prev_surv: output/prevalence_surv.jpg
hazard_ratios:
run: r:latest analysis/10_new_hazard_ratio_code.R
needs: [cumulative_incidence]
outputs:
moderately_sensitive:
temp: output/5_cox_hazard_ratio_incidence_table.csv
temp2: output/6_cox_hazard_ratio_prevalence_table.csv
surv1: output/1_survfit_plot_incidence_noadj.jpg
surv2: output/2_survfit_plot_prevalence_noadj.jpg
surv3: output/3_survfit_plot_incidence_min.jpg
surv4: output/4_survfit_plot_prevalence_min.jpg
surv5: output/5_survfit_plot_incidence_full.jpg
surv6: output/6_survfit_plot_prevalence_full.jpg
shoen_1: output/inc_no_adj_schoenfeld_res.csv
shoen_2: output/inc_min_adj_schoenfeld_res.csv
shoen_3: output/inc_full_adj_schoenfeld_res.csv
shoen_4: output/prev_no_adj_schoenfeld_res.csv
shoen_5: output/prev_min_adj_schoenfeld_res.csv
shoen_6: output/prev_full_adj_schoenfeld_res.csv
shoen_jp1: output/inc_no_adj_schoenfeld_res.jpg
shoen_jp2: output/inc_min_adj_schoenfeld_res.jpg
shoen_jp3: output/inc_full_adj_schoenfeld_res.jpg
shoen_jp4: output/prev_no_adj_schoenfeld_res.jpg
shoen_jp5: output/prev_min_adj_schoenfeld_res.jpg
shoen_jp6: output/prev_full_adj_schoenfeld_res.jpg
distribution_of_follow_up_time:
run: r:latest analysis/11_distribution_of_follow_up_time.R
needs: [cumulative_incidence]
outputs:
moderately_sensitive:
distribution_inc: output/distribution_of_follow_up_time_incidence.jpg
distribution_prev: output/distribution_of_follow_up_time_prevalence.jpg
density1: output/distribution_of_follow_up_time_incidence_density.jpg
density2: output/distribution_of_follow_up_time_prevalence_density.jpg
event_rates_incidence:
run: r:latest analysis/12_event_rates_incidence.R
needs: [cumulative_incidence]
outputs:
moderately_sensitive:
incidence_event_rates: output/event_counts_and_rates_incidence.csv
event_rates_prevalence:
run: r:latest analysis/13_event_rates_prevalence.R
needs: [cumulative_incidence]
outputs:
moderately_sensitive:
incidence_event_rates: output/event_counts_and_rates_prevalence.csv
temporary_test_effects_of_time:
run: r:latest analysis/14_testing_waves.R
needs: [cumulative_incidence]
outputs:
moderately_sensitive:
d1: output/99_coeff_exposed_spline_time_fulladj_incidence.csv
d2: output/99_anova_exposed_spline_time_interactions.csv
d3: output/99_coeff_exposed_spline_time_fulladj_prev.csv
d4: output/99_anova_exposed_spline_time_fulladj_prev.csv
d5: output/99_coefficients_for_waves_incidence.csv
d6: output/99_anova_waves_time_interaction.csv
sc1: output/spline_interaction_inc_full_schoenfeld_res.csv
sc2: output/spline_interaction_inc_full_schoenfeld_res.jpg
sc3: output/spline_interaction_prev_full_schoenfeld_res.jpg
sc4: output/spline_interaction_prev_full_schoenfeld_res.csv
sc5: output/wave_interaction_inc_full_schoenfeld_res.jpg
sc6: output/wave_interaction_inc_full_schoenfeld_res.csv
emmeans:
run: r:latest analysis/15_emmeans.R
needs: [cumulative_incidence]
outputs:
moderately_sensitive:
d1: output/99_emmeans_incidence.csv
d2: output/99_emmeans_incidence.jpg
d3: output/99_emmeans_3df_incidence.csv
d4: output/99_emmeans_3df_incidence.jpg
d5: output/99_emmeans_4df_incidence.csv
d6: output/99_emmeans_4df_incidence.jpg
d7: output/BIC_all_3models.cvs
d8: output/different_degrees_of_freedom_avova_all_adjustments.cvs
hr_for_interaction_with_spline:
run: r:latest analysis/16_hr_for_interaction_with_spline.R
needs: [cumulative_incidence]
outputs:
moderately_sensitive:
d1: output/100_hazard_ratios_by_modifier_incidence.csv
d2: output/100_hazard_ratios_by_modifier_variable.jpg
Timeline
-
Created:
-
Started:
-
Finished:
-
Runtime: 00:00:28
These timestamps are generated and stored using the UTC timezone on the TPP backend.
Job information
- Status
-
Succeeded
- Backend
- TPP
- Workspace
- covid_mental_health
- Requested by
- Klaudia Rzepnicka
- Branch
- main
- Force run dependencies
- No
- Git commit hash
- e7a4ff2
- Requested actions
-
-
testing_exposed_post_pre_matching
-
Code comparison
Compare the code used in this Job Request