Job Request: 2576 u2vbo5byvxr56za5

This page shows the technical details of what happened when authorised researcher Will Hulme requested one or more actions to be run against real patient data in the COVID-19 Vaccine Effectiveness 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.

State

State is inferred from the related Jobs
Status: failed

Config

Backend: tpp
Workspace: covid-vaccine-effectiveness-research_main (main)
Creator: wjchulme
Force run dependencies?: False
Git Commit Hash: ff14ba0
Requested Actions:
  • models_in70s_coviddeath_any_all
  • report_ipw_in70s_coviddeath_any_all
  • report_in70s_coviddeath_any_all
  • models_in70s_coviddeath_pfizer_all
  • report_ipw_in70s_coviddeath_pfizer_all
  • report_in70s_coviddeath_pfizer_all
  • models_in70s_coviddeath_az_all
  • report_ipw_in70s_coviddeath_az_all
  • report_in70s_coviddeath_az_all

Timings

Created: 1 month, 2 weeks ago
Started: 1 month, 2 weeks ago
Finished: 1 month, 2 weeks ago
Runtime: 03:41:41

Pipeline

version: '3.0'

expectations:
population_size: 50000

actions:

design:
run: r:latest analysis/R/design.R
outputs:
moderately_sensitive:
metadata: output/metadata/metadata*
chars: output/metadata/baseline_characteristics.rds
formula: output/metadata/list_formula.rds
strata: output/metadata/list_strata.rds
reweight: output/metadata/reweight_death.rds


##############################################################################
##############################################################################
## VE in over 80s (over80s)
##############################################################################
##############################################################################

extract_over80s:
run: cohortextractor:latest generate_cohort --study-definition study_definition_over80s --output-format csv.gz
outputs:
highly_sensitive:
cohort: output/input_over80s.csv.gz

data_process_over80s:
run: r:latest analysis/R/data_process.R over80s
needs: [extract_over80s]
outputs:
highly_sensitive:
data: output/over80s/data/data_processed.rds

data_process_long_over80s:
run: r:latest analysis/R/data_process_long.R over80s
needs: [data_process_over80s]
outputs:
highly_sensitive:
data1: output/over80s/data/data_long_vax_dates.rds
data2: output/over80s/data/data_long_admission_dates.rds
data3: output/over80s/data/data_long_admission_infectious_dates.rds
data4: output/over80s/data/data_long_admission_noninfectious_dates.rds
data5: output/over80s/data/data_long_pr_probable_covid_dates.rds
data6: output/over80s/data/data_long_pr_suspected_covid_dates.rds
data7: output/over80s/data/data_long_postest_dates.rds

check_ethnicity_over80s:
run: r:latest analysis/R/check_ethnicity.R over80s
needs: [data_process_over80s]
outputs:
moderately_sensitive:
tab: output/over80s/data/ethnicity_table*.txt

data_properties_over80s:
run: r:latest analysis/R/data_properties.R output/over80s/data/data_processed.rds output/over80s/data_properties
needs: [data_process_over80s]
outputs:
moderately_sensitive:
datasummary: output/over80s/data_properties/data_processed*.txt

data_selection_over80s:
run: r:latest analysis/R/data_selection.R over80s
needs: [data_process_over80s]
outputs:
highly_sensitive:
data: output/over80s/data/data_cohort.rds
moderately_sensitive:
flow: output/over80s/data/flowchart.csv

descr_table1_over80s:
run: r:latest analysis/R/descr_table1.R over80s
needs: [design, data_selection_over80s]
outputs:
highly_sensitive:
rds: output/over80s/descriptive/tables/*.rds
moderately_sensitive:
html: output/over80s/descriptive/tables/table1.html

descr_irr_over80s:
run: r:latest analysis/R/descr_tableirr.R over80s
needs: [design, data_selection_over80s]
outputs:
moderately_sensitive:
tables: output/over80s/descriptive/tables/table_irr.html
csv: output/over80s/descriptive/tables/table_irr.csv

data_stset_over80s:
run: r:latest analysis/R/data_stset.R over80s 0.1
needs: [design, data_selection_over80s, data_process_long_over80s]
outputs:
highly_sensitive:
data1: output/over80s/data/data_fixed.rds
data2: output/over80s/data/data_tte.rds
data3: output/over80s/data/data_pt.rds

data_samples_over80s:
run: r:latest analysis/R/data_samples.R over80s 0.1
needs: [design, data_stset_over80s]
outputs:
highly_sensitive:
data: output/over80s/data/data_samples.rds

descr_preflight_over80s:
run: r:latest analysis/R/preflight.R over80s all 0.15
needs: [design, data_stset_over80s]
outputs:
moderately_sensitive:
html: output/over80s/descriptive/model-checks/*.html
csv: output/over80s/descriptive/model-checks/*.csv

descr_events_over80s:
run: r:latest analysis/R/descr_events.R over80s
needs: [design, data_stset_over80s]
outputs:
highly_sensitive:
rds: output/over80s/descriptive/plots/*.rds
moderately_sensitive:
plots: output/over80s/descriptive/plots/*.svg
tables: output/over80s/descriptive/tables/*.csv


# data_properties_over80s_fixed:
# run: r:latest analysis/R/data_properties.R output/over80s/data/data_wide_fixed.rds output/over80s/data_properties
# needs: [data_stset_over80s]
# outputs:
# moderately_sensitive:
# datasummary: output/over80s/data_properties/data_wide_fixed*.txt
#
# data_properties_over80s_tte:
# run: r:latest analysis/R/data_properties.R output/over80s/data/data_wide_tte.rds output/over80s/data_properties
# needs: [data_stset_over80s]
# outputs:
# moderately_sensitive:
# datasummary: output/over80s/data_properties/data_wide_tte*.txt


#######################################
## OVERALL MODELS: positive test, vax1 only (ignores second dose)
#######################################

## any vaccine

models_over80s_postest_any_all:
run: r:latest analysis/R/dose_1/model_msm.R over80s postest any all
needs: [design, data_stset_over80s, data_samples_over80s]
outputs:
highly_sensitive:
models: output/over80s/postest/any/all/*/model*.rds
data: output/over80s/postest/any/all/*/data*.rds
moderately_sensitive:
weights: output/over80s/postest/any/all/*/weights*

report_ipw_over80s_postest_any_all:
run: r:latest analysis/R/dose_1/report_ipw.R over80s postest any all
needs: [design, models_over80s_postest_any_all]
outputs:
highly_sensitive:
broom: output/over80s/postest/any/all/*/broom*.rds
gt: output/over80s/postest/any/all/*/gt*.rds
moderately_sensitive:
plots: output/over80s/postest/any/all/*/plot*.svg
tables: output/over80s/postest/any/all/*/tab*.html
data: output/over80s/postest/any/all/*/broom*.csv

report_over80s_postest_any_all:
run: r:latest analysis/R/dose_1/report_msm.R over80s postest any all
needs: [design, models_over80s_postest_any_all]
outputs:
moderately_sensitive:
plots: output/over80s/postest/any/all/*.svg
tables: output/over80s/postest/any/all/*.csv

## pfizer vaccine

models_over80s_postest_pfizer_all:
run: r:latest analysis/R/dose_1/model_msm.R over80s postest pfizer all
needs: [design, data_stset_over80s, data_samples_over80s]
outputs:
highly_sensitive:
models: output/over80s/postest/pfizer/all/*/model*.rds
data: output/over80s/postest/pfizer/all/*/data*.rds
moderately_sensitive:
weights: output/over80s/postest/pfizer/all/*/weights*

report_ipw_over80s_postest_pfizer_all:
run: r:latest analysis/R/dose_1/report_ipw.R over80s postest pfizer all
needs: [design, models_over80s_postest_pfizer_all]
outputs:
highly_sensitive:
broom: output/over80s/postest/pfizer/all/*/broom*.rds
gt: output/over80s/postest/pfizer/all/*/gt*.rds
moderately_sensitive:
plots: output/over80s/postest/pfizer/all/*/plot*.svg
tables: output/over80s/postest/pfizer/all/*/tab*.html
data: output/over80s/postest/pfizer/all/*/broom*.csv

report_over80s_postest_pfizer_all:
run: r:latest analysis/R/dose_1/report_msm.R over80s postest pfizer all
needs: [design, models_over80s_postest_pfizer_all]
outputs:
moderately_sensitive:
plots: output/over80s/postest/pfizer/all/*.svg
tables: output/over80s/postest/pfizer/all/*.csv

## az vaccine

models_over80s_postest_az_all:
run: r:latest analysis/R/dose_1/model_msm.R over80s postest az all
needs: [design, data_stset_over80s, data_samples_over80s]
outputs:
highly_sensitive:
models: output/over80s/postest/az/all/*/model*.rds
data: output/over80s/postest/az/all/*/data*.rds
moderately_sensitive:
weights: output/over80s/postest/az/all/*/weights*

report_ipw_over80s_postest_az_all:
run: r:latest analysis/R/dose_1/report_ipw.R over80s postest az all
needs: [design, models_over80s_postest_az_all]
outputs:
highly_sensitive:
broom: output/over80s/postest/az/all/*/broom*.rds
gt: output/over80s/postest/az/all/*/gt*.rds
moderately_sensitive:
plots: output/over80s/postest/az/all/*/plot*.svg
tables: output/over80s/postest/az/all/*/tab*.html
data: output/over80s/postest/az/all/*/broom*.csv

report_over80s_postest_az_all:
run: r:latest analysis/R/dose_1/report_msm.R over80s postest az all
needs: [design, models_over80s_postest_az_all]
outputs:
moderately_sensitive:
plots: output/over80s/postest/az/all/*.svg
tables: output/over80s/postest/az/all/*.csv


#######################################
## OVERALL MODELS: covid hospital admission, vax1 only (ignores second dose)
#######################################

## any vaccine

models_over80s_covidadmitted_any_all:
run: r:latest analysis/R/dose_1/model_msm.R over80s covidadmitted any all
needs: [design, data_stset_over80s, data_samples_over80s]
outputs:
highly_sensitive:
models: output/over80s/covidadmitted/any/all/*/model*.rds
data: output/over80s/covidadmitted/any/all/*/data*.rds
moderately_sensitive:
weights: output/over80s/covidadmitted/any/all/*/weights*

report_ipw_over80s_covidadmitted_any_all:
run: r:latest analysis/R/dose_1/report_ipw.R over80s covidadmitted any all
needs: [design, models_over80s_covidadmitted_any_all]
outputs:
highly_sensitive:
broom: output/over80s/covidadmitted/any/all/*/broom*.rds
gt: output/over80s/covidadmitted/any/all/*/gt*.rds
moderately_sensitive:
plots: output/over80s/covidadmitted/any/all/*/plot*.svg
tables: output/over80s/covidadmitted/any/all/*/tab*.html
data: output/over80s/covidadmitted/any/all/*/broom*.csv

report_over80s_covidadmitted_any_all:
run: r:latest analysis/R/dose_1/report_msm.R over80s covidadmitted any all
needs: [design, models_over80s_covidadmitted_any_all]
outputs:
moderately_sensitive:
plots: output/over80s/covidadmitted/any/all/*.svg
tables: output/over80s/covidadmitted/any/all/*.csv


## pfizer vaccine

models_over80s_covidadmitted_pfizer_all:
run: r:latest analysis/R/dose_1/model_msm.R over80s covidadmitted pfizer all
needs: [design, data_stset_over80s, data_samples_over80s]
outputs:
highly_sensitive:
models: output/over80s/covidadmitted/pfizer/all/*/model*.rds
data: output/over80s/covidadmitted/pfizer/all/*/data*.rds
moderately_sensitive:
weights: output/over80s/covidadmitted/pfizer/all/*/weights*

report_ipw_over80s_covidadmitted_pfizer_all:
run: r:latest analysis/R/dose_1/report_ipw.R over80s covidadmitted pfizer all
needs: [design, models_over80s_covidadmitted_pfizer_all]
outputs:
highly_sensitive:
broom: output/over80s/covidadmitted/pfizer/all/*/broom*.rds
gt: output/over80s/covidadmitted/pfizer/all/*/gt*.rds
moderately_sensitive:
plots: output/over80s/covidadmitted/pfizer/all/*/plot*.svg
tables: output/over80s/covidadmitted/pfizer/all/*/tab*.html
data: output/over80s/covidadmitted/pfizer/all/*/broom*.csv

report_over80s_covidadmitted_pfizer_all:
run: r:latest analysis/R/dose_1/report_msm.R over80s covidadmitted pfizer all
needs: [design, models_over80s_covidadmitted_pfizer_all]
outputs:
moderately_sensitive:
plots: output/over80s/covidadmitted/pfizer/all/*.svg
tables: output/over80s/covidadmitted/pfizer/all/*.csv

## az vaccine

models_over80s_covidadmitted_az_all:
run: r:latest analysis/R/dose_1/model_msm.R over80s covidadmitted az all
needs: [design, data_stset_over80s, data_samples_over80s]
outputs:
highly_sensitive:
models: output/over80s/covidadmitted/az/all/*/model*.rds
data: output/over80s/covidadmitted/az/all/*/data*.rds
moderately_sensitive:
weights: output/over80s/covidadmitted/az/all/*/weights*

report_ipw_over80s_covidadmitted_az_all:
run: r:latest analysis/R/dose_1/report_ipw.R over80s covidadmitted az all
needs: [design, models_over80s_covidadmitted_az_all]
outputs:
highly_sensitive:
broom: output/over80s/covidadmitted/az/all/*/broom*.rds
gt: output/over80s/covidadmitted/az/all/*/gt*.rds
moderately_sensitive:
plots: output/over80s/covidadmitted/az/all/*/plot*.svg
tables: output/over80s/covidadmitted/az/all/*/tab*.html
data: output/over80s/covidadmitted/az/all/*/broom*.csv

report_over80s_covidadmitted_az_all:
run: r:latest analysis/R/dose_1/report_msm.R over80s covidadmitted az all
needs: [design, models_over80s_covidadmitted_az_all]
outputs:
moderately_sensitive:
plots: output/over80s/covidadmitted/az/all/*.svg
tables: output/over80s/covidadmitted/az/all/*.csv



#######################################
## OVERALL MODELS: non-covid death, vax1 only (ignores second dose)
#######################################

## any vaccine

models_over80s_noncoviddeath_any_all:
run: r:latest analysis/R/dose_1/model_msm.R over80s noncoviddeath any all
needs: [design, data_stset_over80s, data_samples_over80s]
outputs:
highly_sensitive:
models: output/over80s/noncoviddeath/any/all/*/model*.rds
data: output/over80s/noncoviddeath/any/all/*/data*.rds
moderately_sensitive:
weights: output/over80s/noncoviddeath/any/all/*/weights*

report_ipw_over80s_noncoviddeath_any_all:
run: r:latest analysis/R/dose_1/report_ipw.R over80s noncoviddeath any all
needs: [design, models_over80s_noncoviddeath_any_all]
outputs:
highly_sensitive:
broom: output/over80s/noncoviddeath/any/all/*/broom*.rds
gt: output/over80s/noncoviddeath/any/all/*/gt*.rds
moderately_sensitive:
plots: output/over80s/noncoviddeath/any/all/*/plot*.svg
tables: output/over80s/noncoviddeath/any/all/*/tab*.html
data: output/over80s/noncoviddeath/any/all/*/broom*.csv


report_over80s_noncoviddeath_any_all:
run: r:latest analysis/R/dose_1/report_msm.R over80s noncoviddeath any all
needs: [design, models_over80s_noncoviddeath_any_all]
outputs:
moderately_sensitive:
plots: output/over80s/noncoviddeath/any/all/*.svg
tables: output/over80s/noncoviddeath/any/all/*.csv


## pfizer vaccine

models_over80s_noncoviddeath_pfizer_all:
run: r:latest analysis/R/dose_1/model_msm.R over80s noncoviddeath pfizer all
needs: [design, data_stset_over80s, data_samples_over80s]
outputs:
highly_sensitive:
models: output/over80s/noncoviddeath/pfizer/all/*/model*.rds
data: output/over80s/noncoviddeath/pfizer/all/*/data*.rds
moderately_sensitive:
weights: output/over80s/noncoviddeath/pfizer/all/*/weights*

report_ipw_over80s_noncoviddeath_pfizer_all:
run: r:latest analysis/R/dose_1/report_ipw.R over80s noncoviddeath pfizer all
needs: [design, models_over80s_noncoviddeath_pfizer_all]
outputs:
highly_sensitive:
broom: output/over80s/noncoviddeath/pfizer/all/*/broom*.rds
gt: output/over80s/noncoviddeath/pfizer/all/*/gt*.rds
moderately_sensitive:
plots: output/over80s/noncoviddeath/pfizer/all/*/plot*.svg
tables: output/over80s/noncoviddeath/pfizer/all/*/tab*.html
data: output/over80s/noncoviddeath/pfizer/all/*/broom*.csv

report_over80s_noncoviddeath_pfizer_all:
run: r:latest analysis/R/dose_1/report_msm.R over80s noncoviddeath pfizer all
needs: [design, models_over80s_noncoviddeath_pfizer_all]
outputs:
moderately_sensitive:
plots: output/over80s/noncoviddeath/pfizer/all/*.svg
tables: output/over80s/noncoviddeath/pfizer/all/*.csv

## az vaccine

models_over80s_noncoviddeath_az_all:
run: r:latest analysis/R/dose_1/model_msm.R over80s noncoviddeath az all
needs: [design, data_stset_over80s, data_samples_over80s]
outputs:
highly_sensitive:
models: output/over80s/noncoviddeath/az/all/*/model*.rds
data: output/over80s/noncoviddeath/az/all/*/data*.rds
moderately_sensitive:
weights: output/over80s/noncoviddeath/az/all/*/weights*

report_ipw_over80s_noncoviddeath_az_all:
run: r:latest analysis/R/dose_1/report_ipw.R over80s noncoviddeath az all
needs: [design, models_over80s_noncoviddeath_az_all]
outputs:
highly_sensitive:
broom: output/over80s/noncoviddeath/az/all/*/broom*.rds
gt: output/over80s/noncoviddeath/az/all/*/gt*.rds
moderately_sensitive:
plots: output/over80s/noncoviddeath/az/all/*/plot*.svg
tables: output/over80s/noncoviddeath/az/all/*/tab*.html
data: output/over80s/noncoviddeath/az/all/*/broom*.csv

report_over80s_noncoviddeath_az_all:
run: r:latest analysis/R/dose_1/report_msm.R over80s noncoviddeath az all
needs: [design, models_over80s_noncoviddeath_az_all]
outputs:
moderately_sensitive:
plots: output/over80s/noncoviddeath/az/all/*.svg
tables: output/over80s/noncoviddeath/az/all/*.csv




#######################################
## OVERALL MODELS: covid death, vax1 only (ignores second dose)
#######################################

## any vaccine

models_over80s_coviddeath_any_all:
run: r:latest analysis/R/dose_1/model_msm.R over80s coviddeath any all
needs: [design, data_stset_over80s, data_samples_over80s]
outputs:
highly_sensitive:
models: output/over80s/coviddeath/any/all/*/model*.rds
data: output/over80s/coviddeath/any/all/*/data*.rds
moderately_sensitive:
weights: output/over80s/coviddeath/any/all/*/weights*

report_ipw_over80s_coviddeath_any_all:
run: r:latest analysis/R/dose_1/report_ipw.R over80s coviddeath any all
needs: [design, models_over80s_coviddeath_any_all]
outputs:
highly_sensitive:
broom: output/over80s/coviddeath/any/all/*/broom*.rds
gt: output/over80s/coviddeath/any/all/*/gt*.rds
moderately_sensitive:
plots: output/over80s/coviddeath/any/all/*/plot*.svg
tables: output/over80s/coviddeath/any/all/*/tab*.html
data: output/over80s/coviddeath/any/all/*/broom*.csv

report_over80s_coviddeath_any_all:
run: r:latest analysis/R/dose_1/report_msm.R over80s coviddeath any all
needs: [design, models_over80s_coviddeath_any_all]
outputs:
moderately_sensitive:
plots: output/over80s/coviddeath/any/all/*.svg
tables: output/over80s/coviddeath/any/all/*.csv


## pfizer vaccine

models_over80s_coviddeath_pfizer_all:
run: r:latest analysis/R/dose_1/model_msm.R over80s coviddeath pfizer all
needs: [design, data_stset_over80s, data_samples_over80s]
outputs:
highly_sensitive:
models: output/over80s/coviddeath/pfizer/all/*/model*.rds
data: output/over80s/coviddeath/pfizer/all/*/data*.rds
moderately_sensitive:
weights: output/over80s/coviddeath/pfizer/all/*/weights*

report_ipw_over80s_coviddeath_pfizer_all:
run: r:latest analysis/R/dose_1/report_ipw.R over80s coviddeath pfizer all
needs: [design, models_over80s_coviddeath_pfizer_all]
outputs:
highly_sensitive:
broom: output/over80s/coviddeath/pfizer/all/*/broom*.rds
gt: output/over80s/coviddeath/pfizer/all/*/gt*.rds
moderately_sensitive:
plots: output/over80s/coviddeath/pfizer/all/*/plot*.svg
tables: output/over80s/coviddeath/pfizer/all/*/tab*.html
data: output/over80s/coviddeath/pfizer/all/*/broom*.csv

report_over80s_coviddeath_pfizer_all:
run: r:latest analysis/R/dose_1/report_msm.R over80s coviddeath pfizer all
needs: [design, models_over80s_coviddeath_pfizer_all]
outputs:
moderately_sensitive:
plots: output/over80s/coviddeath/pfizer/all/*.svg
tables: output/over80s/coviddeath/pfizer/all/*.csv

## az vaccine

models_over80s_coviddeath_az_all:
run: r:latest analysis/R/dose_1/model_msm.R over80s coviddeath az all
needs: [design, data_stset_over80s, data_samples_over80s]
outputs:
highly_sensitive:
models: output/over80s/coviddeath/az/all/*/model*.rds
data: output/over80s/coviddeath/az/all/*/data*.rds
moderately_sensitive:
weights: output/over80s/coviddeath/az/all/*/weights*

report_ipw_over80s_coviddeath_az_all:
run: r:latest analysis/R/dose_1/report_ipw.R over80s coviddeath az all
needs: [design, models_over80s_coviddeath_az_all]
outputs:
highly_sensitive:
broom: output/over80s/coviddeath/az/all/*/broom*.rds
gt: output/over80s/coviddeath/az/all/*/gt*.rds
moderately_sensitive:
plots: output/over80s/coviddeath/az/all/*/plot*.svg
tables: output/over80s/coviddeath/az/all/*/tab*.html
data: output/over80s/coviddeath/az/all/*/broom*.csv

report_over80s_coviddeath_az_all:
run: r:latest analysis/R/dose_1/report_msm.R over80s coviddeath az all
needs: [design, models_over80s_coviddeath_az_all]
outputs:
moderately_sensitive:
plots: output/over80s/coviddeath/az/all/*.svg
tables: output/over80s/coviddeath/az/all/*.csv



#######################################
## OVERALL MODELS: all-cause death, vax1 only (ignores second dose)
#######################################

## any vaccine

models_over80s_death_any_all:
run: r:latest analysis/R/dose_1/model_msm.R over80s death any all
needs: [design, data_stset_over80s, data_samples_over80s]
outputs:
highly_sensitive:
models: output/over80s/death/any/all/*/model*.rds
data: output/over80s/death/any/all/*/data*.rds
moderately_sensitive:
weights: output/over80s/death/any/all/*/weights*

report_ipw_over80s_death_any_all:
run: r:latest analysis/R/dose_1/report_ipw.R over80s death any all
needs: [design, models_over80s_death_any_all]
outputs:
highly_sensitive:
broom: output/over80s/death/any/all/*/broom*.rds
gt: output/over80s/death/any/all/*/gt*.rds
moderately_sensitive:
plots: output/over80s/death/any/all/*/plot*.svg
tables: output/over80s/death/any/all/*/tab*.html
data: output/over80s/death/any/all/*/broom*.csv

report_over80s_death_any_all:
run: r:latest analysis/R/dose_1/report_msm.R over80s death any all
needs: [design, models_over80s_death_any_all]
outputs:
moderately_sensitive:
plots: output/over80s/death/any/all/*.svg
tables: output/over80s/death/any/all/*.csv

## pfizer vaccine

models_over80s_death_pfizer_all:
run: r:latest analysis/R/dose_1/model_msm.R over80s death pfizer all
needs: [design, data_stset_over80s, data_samples_over80s]
outputs:
highly_sensitive:
models: output/over80s/death/pfizer/all/*/model*.rds
data: output/over80s/death/pfizer/all/*/data*.rds
moderately_sensitive:
weights: output/over80s/death/pfizer/all/*/weights*

report_ipw_over80s_death_pfizer_all:
run: r:latest analysis/R/dose_1/report_ipw.R over80s death pfizer all
needs: [design, models_over80s_death_pfizer_all]
outputs:
highly_sensitive:
broom: output/over80s/death/pfizer/all/*/broom*.rds
gt: output/over80s/death/pfizer/all/*/gt*.rds
moderately_sensitive:
plots: output/over80s/death/pfizer/all/*/plot*.svg
tables: output/over80s/death/pfizer/all/*/tab*.html
data: output/over80s/death/pfizer/all/*/broom*.csv

report_over80s_death_pfizer_all:
run: r:latest analysis/R/dose_1/report_msm.R over80s death pfizer all
needs: [design, models_over80s_death_pfizer_all]
outputs:
moderately_sensitive:
plots: output/over80s/death/pfizer/all/*.svg
tables: output/over80s/death/pfizer/all/*.csv

## az vaccine

models_over80s_death_az_all:
run: r:latest analysis/R/dose_1/model_msm.R over80s death az all
needs: [design, data_stset_over80s, data_samples_over80s]
outputs:
highly_sensitive:
models: output/over80s/death/az/all/*/model*.rds
data: output/over80s/death/az/all/*/data*.rds
moderately_sensitive:
weights: output/over80s/death/az/all/*/weights*

report_ipw_over80s_death_az_all:
run: r:latest analysis/R/dose_1/report_ipw.R over80s death az all
needs: [design, models_over80s_death_az_all]
outputs:
highly_sensitive:
broom: output/over80s/death/az/all/*/broom*.rds
gt: output/over80s/death/az/all/*/gt*.rds
moderately_sensitive:
plots: output/over80s/death/az/all/*/plot*.svg
tables: output/over80s/death/az/all/*/tab*.html
data: output/over80s/death/az/all/*/broom*.csv

report_over80s_death_az_all:
run: r:latest analysis/R/dose_1/report_msm.R over80s death az all
needs: [design, models_over80s_death_az_all]
outputs:
moderately_sensitive:
plots: output/over80s/death/az/all/*.svg
tables: output/over80s/death/az/all/*.csv



#######################################
## COMBINE OVERALL MODELS:
#######################################

# report_over80s_any_all:
# run: r:latest analysis/R/dose_1/report_alloutcomes.R over80s any all
# needs: [design, report_over80s_postest_any_all, report_over80s_covidadmitted_any_all, report_over80s_coviddeath_any_all, report_over80s_noncoviddeath_any_all, report_over80s_death_any_all]
# outputs:
# moderately_sensitive:
# plots: output/over80s/*any_all.svg
# tables: output/over80s/*any_all.csv
# html: output/over80s/*any_all.html
#
# report_over80s_pfizer_all:
# run: r:latest analysis/R/dose_1/report_alloutcomes.R over80s pfizer all
# needs: [design, report_over80s_postest_pfizer_all, report_over80s_covidadmitted_pfizer_all, report_over80s_coviddeath_pfizer_all, report_over80s_noncoviddeath_pfizer_all, report_over80s_death_pfizer_all]
# outputs:
# moderately_sensitive:
# plots: output/over80s/*pfizer_all.svg
# tables: output/over80s/*pfizer_all.csv
# html: output/over80s/*pfizer_all.html
#
# report_over80s_az_all:
# run: r:latest analysis/R/dose_1/report_alloutcomes.R over80s az all
# needs: [design, report_over80s_postest_az_all, report_over80s_covidadmitted_az_all, report_over80s_coviddeath_az_all, report_over80s_noncoviddeath_az_all, report_over80s_death_az_all]
# outputs:
# moderately_sensitive:
# plots: output/over80s/*az_all.svg
# tables: output/over80s/*az_all.csv
# html: output/over80s/*az_all.html


report_ipw_over80s_all:
run: r:latest analysis/R/dose_1/report_vaxmodel.R over80s death all
needs: [design, report_ipw_over80s_death_any_all, report_ipw_over80s_death_pfizer_all, report_ipw_over80s_death_az_all]
outputs:
moderately_sensitive:
svg: output/over80s/plot_vax1.svg
#html: output/over80s/tab_vax1.html
csv: output/over80s/tab_vax1.csv


report_over80s_all:
run: r:latest analysis/R/dose_1/report_alloutcomes_combined.R over80s all
needs: [design, report_over80s_postest_any_all, report_over80s_covidadmitted_any_all, report_over80s_coviddeath_any_all, report_over80s_noncoviddeath_any_all, report_over80s_death_any_all,
report_over80s_postest_pfizer_all, report_over80s_covidadmitted_pfizer_all, report_over80s_coviddeath_pfizer_all, report_over80s_noncoviddeath_pfizer_all, report_over80s_death_pfizer_all,
report_over80s_postest_az_all, report_over80s_covidadmitted_az_all, report_over80s_coviddeath_az_all, report_over80s_noncoviddeath_az_all, report_over80s_death_az_all]
outputs:
moderately_sensitive:
plots: output/over80s/*_all.svg
plots1: output/over80s/*_all.png
tables: output/over80s/*_all.csv






##############################################################################
##############################################################################
## VE in 70-79s
##############################################################################
##############################################################################

extract_in70s:
run: cohortextractor:latest generate_cohort --study-definition study_definition_in70s --output-format csv.gz
outputs:
highly_sensitive:
cohort: output/input_in70s.csv.gz

data_process_in70s:
run: r:latest analysis/R/data_process.R in70s
needs: [extract_in70s]
outputs:
highly_sensitive:
data: output/in70s/data/data_processed.rds

data_process_long_in70s:
run: r:latest analysis/R/data_process_long.R in70s
needs: [data_process_in70s]
outputs:
highly_sensitive:
data1: output/in70s/data/data_long_vax_dates.rds
data2: output/in70s/data/data_long_admission_dates.rds
data3: output/in70s/data/data_long_admission_infectious_dates.rds
data4: output/in70s/data/data_long_admission_noninfectious_dates.rds
data5: output/in70s/data/data_long_pr_probable_covid_dates.rds
data6: output/in70s/data/data_long_pr_suspected_covid_dates.rds
data7: output/in70s/data/data_long_postest_dates.rds

check_ethnicity_in70s:
run: r:latest analysis/R/check_ethnicity.R in70s
needs: [data_process_in70s]
outputs:
moderately_sensitive:
tab: output/in70s/data/ethnicity_table*.txt

data_properties_in70s:
run: r:latest analysis/R/data_properties.R output/in70s/data/data_processed.rds output/in70s/data_properties
needs: [data_process_in70s]
outputs:
moderately_sensitive:
datasummary: output/in70s/data_properties/data_processed*.txt

data_selection_in70s:
run: r:latest analysis/R/data_selection.R in70s
needs: [data_process_in70s]
outputs:
highly_sensitive:
data: output/in70s/data/data_cohort.rds
moderately_sensitive:
flow: output/in70s/data/flowchart.csv

descr_table1_in70s:
run: r:latest analysis/R/descr_table1.R in70s
needs: [design, data_selection_in70s]
outputs:
highly_sensitive:
rds: output/in70s/descriptive/tables/*.rds
moderately_sensitive:
html: output/in70s/descriptive/tables/table1.html

descr_irr_in70s:
run: r:latest analysis/R/descr_tableirr.R in70s
needs: [design, data_selection_in70s]
outputs:
moderately_sensitive:
tables: output/in70s/descriptive/tables/table_irr.html
csv: output/in70s/descriptive/tables/table_irr.csv

data_stset_in70s:
run: r:latest analysis/R/data_stset.R in70s 0.05
needs: [design, data_selection_in70s, data_process_long_in70s]
outputs:
highly_sensitive:
data1: output/in70s/data/data_fixed.rds
data2: output/in70s/data/data_tte.rds
data3: output/in70s/data/data_pt.rds

data_samples_in70s:
run: r:latest analysis/R/data_samples.R in70s 0.05
needs: [design, data_stset_in70s]
outputs:
highly_sensitive:
data: output/in70s/data/data_samples.rds

descr_preflight_in70s:
run: r:latest analysis/R/preflight.R in70s all 0.05
needs: [design, data_stset_in70s]
outputs:
moderately_sensitive:
html: output/in70s/descriptive/model-checks/*.html
csv: output/in70s/descriptive/model-checks/*.csv

descr_events_in70s:
run: r:latest analysis/R/descr_events.R in70s
needs: [design, data_stset_in70s]
outputs:
highly_sensitive:
rds: output/in70s/descriptive/plots/*.rds
moderately_sensitive:
plots: output/in70s/descriptive/plots/*.svg
tables: output/in70s/descriptive/tables/*.csv


# data_properties_in70s_fixed:
# run: r:latest analysis/R/data_properties.R output/in70s/data/data_wide_fixed.rds output/in70s/data_properties
# needs: [data_stset_in70s]
# outputs:
# moderately_sensitive:
# datasummary: output/in70s/data_properties/data_wide_fixed*.txt
#
# data_properties_in70s_tte:
# run: r:latest analysis/R/data_properties.R output/in70s/data/data_wide_tte.rds output/in70s/data_properties
# needs: [data_stset_in70s]
# outputs:
# moderately_sensitive:
# datasummary: output/in70s/data_properties/data_wide_tte*.txt


#######################################
## OVERALL MODELS: positive test, vax1 only (ignores second dose)
#######################################

## any vaccine

models_in70s_postest_any_all:
run: r:latest analysis/R/dose_1/model_msm.R in70s postest any all
needs: [design, data_stset_in70s, data_samples_in70s]
outputs:
highly_sensitive:
models: output/in70s/postest/any/all/*/model*.rds
data: output/in70s/postest/any/all/*/data*.rds
moderately_sensitive:
weights: output/in70s/postest/any/all/*/weights*

report_ipw_in70s_postest_any_all:
run: r:latest analysis/R/dose_1/report_ipw.R in70s postest any all
needs: [design, models_in70s_postest_any_all]
outputs:
highly_sensitive:
broom: output/in70s/postest/any/all/*/broom*.rds
gt: output/in70s/postest/any/all/*/gt*.rds
moderately_sensitive:
plots: output/in70s/postest/any/all/*/plot*.svg
tables: output/in70s/postest/any/all/*/tab*.html
data: output/in70s/postest/any/all/*/broom*.csv

report_in70s_postest_any_all:
run: r:latest analysis/R/dose_1/report_msm.R in70s postest any all
needs: [design, models_in70s_postest_any_all]
outputs:
moderately_sensitive:
plots: output/in70s/postest/any/all/*.svg
tables: output/in70s/postest/any/all/*.csv

## pfizer vaccine

models_in70s_postest_pfizer_all:
run: r:latest analysis/R/dose_1/model_msm.R in70s postest pfizer all
needs: [design, data_stset_in70s, data_samples_in70s]
outputs:
highly_sensitive:
models: output/in70s/postest/pfizer/all/*/model*.rds
data: output/in70s/postest/pfizer/all/*/data*.rds
moderately_sensitive:
weights: output/in70s/postest/pfizer/all/*/weights*

report_ipw_in70s_postest_pfizer_all:
run: r:latest analysis/R/dose_1/report_ipw.R in70s postest pfizer all
needs: [design, models_in70s_postest_pfizer_all]
outputs:
highly_sensitive:
broom: output/in70s/postest/pfizer/all/*/broom*.rds
gt: output/in70s/postest/pfizer/all/*/gt*.rds
moderately_sensitive:
plots: output/in70s/postest/pfizer/all/*/plot*.svg
tables: output/in70s/postest/pfizer/all/*/tab*.html
data: output/in70s/postest/pfizer/all/*/broom*.csv

report_in70s_postest_pfizer_all:
run: r:latest analysis/R/dose_1/report_msm.R in70s postest pfizer all
needs: [design, models_in70s_postest_pfizer_all]
outputs:
moderately_sensitive:
plots: output/in70s/postest/pfizer/all/*.svg
tables: output/in70s/postest/pfizer/all/*.csv

## az vaccine

models_in70s_postest_az_all:
run: r:latest analysis/R/dose_1/model_msm.R in70s postest az all
needs: [design, data_stset_in70s, data_samples_in70s]
outputs:
highly_sensitive:
models: output/in70s/postest/az/all/*/model*.rds
data: output/in70s/postest/az/all/*/data*.rds
moderately_sensitive:
weights: output/in70s/postest/az/all/*/weights*

report_ipw_in70s_postest_az_all:
run: r:latest analysis/R/dose_1/report_ipw.R in70s postest az all
needs: [design, models_in70s_postest_az_all]
outputs:
highly_sensitive:
broom: output/in70s/postest/az/all/*/broom*.rds
gt: output/in70s/postest/az/all/*/gt*.rds
moderately_sensitive:
plots: output/in70s/postest/az/all/*/plot*.svg
tables: output/in70s/postest/az/all/*/tab*.html
data: output/in70s/postest/az/all/*/broom*.csv

report_in70s_postest_az_all:
run: r:latest analysis/R/dose_1/report_msm.R in70s postest az all
needs: [design, models_in70s_postest_az_all]
outputs:
moderately_sensitive:
plots: output/in70s/postest/az/all/*.svg
tables: output/in70s/postest/az/all/*.csv


#######################################
## OVERALL MODELS: covid hospital admission, vax1 only (ignores second dose)
#######################################

## any vaccine

models_in70s_covidadmitted_any_all:
run: r:latest analysis/R/dose_1/model_msm.R in70s covidadmitted any all
needs: [design, data_stset_in70s, data_samples_in70s]
outputs:
highly_sensitive:
models: output/in70s/covidadmitted/any/all/*/model*.rds
data: output/in70s/covidadmitted/any/all/*/data*.rds
moderately_sensitive:
weights: output/in70s/covidadmitted/any/all/*/weights*

report_ipw_in70s_covidadmitted_any_all:
run: r:latest analysis/R/dose_1/report_ipw.R in70s covidadmitted any all
needs: [design, models_in70s_covidadmitted_any_all]
outputs:
highly_sensitive:
broom: output/in70s/covidadmitted/any/all/*/broom*.rds
gt: output/in70s/covidadmitted/any/all/*/gt*.rds
moderately_sensitive:
plots: output/in70s/covidadmitted/any/all/*/plot*.svg
tables: output/in70s/covidadmitted/any/all/*/tab*.html
data: output/in70s/covidadmitted/any/all/*/broom*.csv

report_in70s_covidadmitted_any_all:
run: r:latest analysis/R/dose_1/report_msm.R in70s covidadmitted any all
needs: [design, models_in70s_covidadmitted_any_all]
outputs:
moderately_sensitive:
plots: output/in70s/covidadmitted/any/all/*.svg
tables: output/in70s/covidadmitted/any/all/*.csv


## pfizer vaccine

models_in70s_covidadmitted_pfizer_all:
run: r:latest analysis/R/dose_1/model_msm.R in70s covidadmitted pfizer all
needs: [design, data_stset_in70s, data_samples_in70s]
outputs:
highly_sensitive:
models: output/in70s/covidadmitted/pfizer/all/*/model*.rds
data: output/in70s/covidadmitted/pfizer/all/*/data*.rds
moderately_sensitive:
weights: output/in70s/covidadmitted/pfizer/all/*/weights*

report_ipw_in70s_covidadmitted_pfizer_all:
run: r:latest analysis/R/dose_1/report_ipw.R in70s covidadmitted pfizer all
needs: [design, models_in70s_covidadmitted_pfizer_all]
outputs:
highly_sensitive:
broom: output/in70s/covidadmitted/pfizer/all/*/broom*.rds
gt: output/in70s/covidadmitted/pfizer/all/*/gt*.rds
moderately_sensitive:
plots: output/in70s/covidadmitted/pfizer/all/*/plot*.svg
tables: output/in70s/covidadmitted/pfizer/all/*/tab*.html
data: output/in70s/covidadmitted/pfizer/all/*/broom*.csv

report_in70s_covidadmitted_pfizer_all:
run: r:latest analysis/R/dose_1/report_msm.R in70s covidadmitted pfizer all
needs: [design, models_in70s_covidadmitted_pfizer_all]
outputs:
moderately_sensitive:
plots: output/in70s/covidadmitted/pfizer/all/*.svg
tables: output/in70s/covidadmitted/pfizer/all/*.csv

## az vaccine

models_in70s_covidadmitted_az_all:
run: r:latest analysis/R/dose_1/model_msm.R in70s covidadmitted az all
needs: [design, data_stset_in70s, data_samples_in70s]
outputs:
highly_sensitive:
models: output/in70s/covidadmitted/az/all/*/model*.rds
data: output/in70s/covidadmitted/az/all/*/data*.rds
moderately_sensitive:
weights: output/in70s/covidadmitted/az/all/*/weights*

report_ipw_in70s_covidadmitted_az_all:
run: r:latest analysis/R/dose_1/report_ipw.R in70s covidadmitted az all
needs: [design, models_in70s_covidadmitted_az_all]
outputs:
highly_sensitive:
broom: output/in70s/covidadmitted/az/all/*/broom*.rds
gt: output/in70s/covidadmitted/az/all/*/gt*.rds
moderately_sensitive:
plots: output/in70s/covidadmitted/az/all/*/plot*.svg
tables: output/in70s/covidadmitted/az/all/*/tab*.html
data: output/in70s/covidadmitted/az/all/*/broom*.csv

report_in70s_covidadmitted_az_all:
run: r:latest analysis/R/dose_1/report_msm.R in70s covidadmitted az all
needs: [design, models_in70s_covidadmitted_az_all]
outputs:
moderately_sensitive:
plots: output/in70s/covidadmitted/az/all/*.svg
tables: output/in70s/covidadmitted/az/all/*.csv



#######################################
## OVERALL MODELS: non-covid death, vax1 only (ignores second dose)
#######################################

## any vaccine

models_in70s_noncoviddeath_any_all:
run: r:latest analysis/R/dose_1/model_msm.R in70s noncoviddeath any all
needs: [design, data_stset_in70s, data_samples_in70s]
outputs:
highly_sensitive:
models: output/in70s/noncoviddeath/any/all/*/model*.rds
data: output/in70s/noncoviddeath/any/all/*/data*.rds
moderately_sensitive:
weights: output/in70s/noncoviddeath/any/all/*/weights*

report_ipw_in70s_noncoviddeath_any_all:
run: r:latest analysis/R/dose_1/report_ipw.R in70s noncoviddeath any all
needs: [design, models_in70s_noncoviddeath_any_all]
outputs:
highly_sensitive:
broom: output/in70s/noncoviddeath/any/all/*/broom*.rds
gt: output/in70s/noncoviddeath/any/all/*/gt*.rds
moderately_sensitive:
plots: output/in70s/noncoviddeath/any/all/*/plot*.svg
tables: output/in70s/noncoviddeath/any/all/*/tab*.html
data: output/in70s/noncoviddeath/any/all/*/broom*.csv


report_in70s_noncoviddeath_any_all:
run: r:latest analysis/R/dose_1/report_msm.R in70s noncoviddeath any all
needs: [design, models_in70s_noncoviddeath_any_all]
outputs:
moderately_sensitive:
plots: output/in70s/noncoviddeath/any/all/*.svg
tables: output/in70s/noncoviddeath/any/all/*.csv


## pfizer vaccine

models_in70s_noncoviddeath_pfizer_all:
run: r:latest analysis/R/dose_1/model_msm.R in70s noncoviddeath pfizer all
needs: [design, data_stset_in70s, data_samples_in70s]
outputs:
highly_sensitive:
models: output/in70s/noncoviddeath/pfizer/all/*/model*.rds
data: output/in70s/noncoviddeath/pfizer/all/*/data*.rds
moderately_sensitive:
weights: output/in70s/noncoviddeath/pfizer/all/*/weights*

report_ipw_in70s_noncoviddeath_pfizer_all:
run: r:latest analysis/R/dose_1/report_ipw.R in70s noncoviddeath pfizer all
needs: [design, models_in70s_noncoviddeath_pfizer_all]
outputs:
highly_sensitive:
broom: output/in70s/noncoviddeath/pfizer/all/*/broom*.rds
gt: output/in70s/noncoviddeath/pfizer/all/*/gt*.rds
moderately_sensitive:
plots: output/in70s/noncoviddeath/pfizer/all/*/plot*.svg
tables: output/in70s/noncoviddeath/pfizer/all/*/tab*.html
data: output/in70s/noncoviddeath/pfizer/all/*/broom*.csv

report_in70s_noncoviddeath_pfizer_all:
run: r:latest analysis/R/dose_1/report_msm.R in70s noncoviddeath pfizer all
needs: [design, models_in70s_noncoviddeath_pfizer_all]
outputs:
moderately_sensitive:
plots: output/in70s/noncoviddeath/pfizer/all/*.svg
tables: output/in70s/noncoviddeath/pfizer/all/*.csv

## az vaccine

models_in70s_noncoviddeath_az_all:
run: r:latest analysis/R/dose_1/model_msm.R in70s noncoviddeath az all
needs: [design, data_stset_in70s, data_samples_in70s]
outputs:
highly_sensitive:
models: output/in70s/noncoviddeath/az/all/*/model*.rds
data: output/in70s/noncoviddeath/az/all/*/data*.rds
moderately_sensitive:
weights: output/in70s/noncoviddeath/az/all/*/weights*

report_ipw_in70s_noncoviddeath_az_all:
run: r:latest analysis/R/dose_1/report_ipw.R in70s noncoviddeath az all
needs: [design, models_in70s_noncoviddeath_az_all]
outputs:
highly_sensitive:
broom: output/in70s/noncoviddeath/az/all/*/broom*.rds
gt: output/in70s/noncoviddeath/az/all/*/gt*.rds
moderately_sensitive:
plots: output/in70s/noncoviddeath/az/all/*/plot*.svg
tables: output/in70s/noncoviddeath/az/all/*/tab*.html
data: output/in70s/noncoviddeath/az/all/*/broom*.csv

report_in70s_noncoviddeath_az_all:
run: r:latest analysis/R/dose_1/report_msm.R in70s noncoviddeath az all
needs: [design, models_in70s_noncoviddeath_az_all]
outputs:
moderately_sensitive:
plots: output/in70s/noncoviddeath/az/all/*.svg
tables: output/in70s/noncoviddeath/az/all/*.csv




#######################################
## OVERALL MODELS: covid death, vax1 only (ignores second dose)
#######################################

## any vaccine

models_in70s_coviddeath_any_all:
run: r:latest analysis/R/dose_1/model_msm.R in70s coviddeath any all
needs: [design, data_stset_in70s, data_samples_in70s]
outputs:
highly_sensitive:
models: output/in70s/coviddeath/any/all/*/model*.rds
data: output/in70s/coviddeath/any/all/*/data*.rds
moderately_sensitive:
weights: output/in70s/coviddeath/any/all/*/weights*

report_ipw_in70s_coviddeath_any_all:
run: r:latest analysis/R/dose_1/report_ipw.R in70s coviddeath any all
needs: [design, models_in70s_coviddeath_any_all]
outputs:
highly_sensitive:
broom: output/in70s/coviddeath/any/all/*/broom*.rds
gt: output/in70s/coviddeath/any/all/*/gt*.rds
moderately_sensitive:
plots: output/in70s/coviddeath/any/all/*/plot*.svg
tables: output/in70s/coviddeath/any/all/*/tab*.html
data: output/in70s/coviddeath/any/all/*/broom*.csv

report_in70s_coviddeath_any_all:
run: r:latest analysis/R/dose_1/report_msm.R in70s coviddeath any all
needs: [design, models_in70s_coviddeath_any_all]
outputs:
moderately_sensitive:
plots: output/in70s/coviddeath/any/all/*.svg
tables: output/in70s/coviddeath/any/all/*.csv


## pfizer vaccine

models_in70s_coviddeath_pfizer_all:
run: r:latest analysis/R/dose_1/model_msm.R in70s coviddeath pfizer all
needs: [design, data_stset_in70s, data_samples_in70s]
outputs:
highly_sensitive:
models: output/in70s/coviddeath/pfizer/all/*/model*.rds
data: output/in70s/coviddeath/pfizer/all/*/data*.rds
moderately_sensitive:
weights: output/in70s/coviddeath/pfizer/all/*/weights*

report_ipw_in70s_coviddeath_pfizer_all:
run: r:latest analysis/R/dose_1/report_ipw.R in70s coviddeath pfizer all
needs: [design, models_in70s_coviddeath_pfizer_all]
outputs:
highly_sensitive:
broom: output/in70s/coviddeath/pfizer/all/*/broom*.rds
gt: output/in70s/coviddeath/pfizer/all/*/gt*.rds
moderately_sensitive:
plots: output/in70s/coviddeath/pfizer/all/*/plot*.svg
tables: output/in70s/coviddeath/pfizer/all/*/tab*.html
data: output/in70s/coviddeath/pfizer/all/*/broom*.csv

report_in70s_coviddeath_pfizer_all:
run: r:latest analysis/R/dose_1/report_msm.R in70s coviddeath pfizer all
needs: [design, models_in70s_coviddeath_pfizer_all]
outputs:
moderately_sensitive:
plots: output/in70s/coviddeath/pfizer/all/*.svg
tables: output/in70s/coviddeath/pfizer/all/*.csv

## az vaccine

models_in70s_coviddeath_az_all:
run: r:latest analysis/R/dose_1/model_msm.R in70s coviddeath az all
needs: [design, data_stset_in70s, data_samples_in70s]
outputs:
highly_sensitive:
models: output/in70s/coviddeath/az/all/*/model*.rds
data: output/in70s/coviddeath/az/all/*/data*.rds
moderately_sensitive:
weights: output/in70s/coviddeath/az/all/*/weights*

report_ipw_in70s_coviddeath_az_all:
run: r:latest analysis/R/dose_1/report_ipw.R in70s coviddeath az all
needs: [design, models_in70s_coviddeath_az_all]
outputs:
highly_sensitive:
broom: output/in70s/coviddeath/az/all/*/broom*.rds
gt: output/in70s/coviddeath/az/all/*/gt*.rds
moderately_sensitive:
plots: output/in70s/coviddeath/az/all/*/plot*.svg
tables: output/in70s/coviddeath/az/all/*/tab*.html
data: output/in70s/coviddeath/az/all/*/broom*.csv

report_in70s_coviddeath_az_all:
run: r:latest analysis/R/dose_1/report_msm.R in70s coviddeath az all
needs: [design, models_in70s_coviddeath_az_all]
outputs:
moderately_sensitive:
plots: output/in70s/coviddeath/az/all/*.svg
tables: output/in70s/coviddeath/az/all/*.csv



#######################################
## OVERALL MODELS: all-cause death, vax1 only (ignores second dose)
#######################################

## any vaccine

models_in70s_death_any_all:
run: r:latest analysis/R/dose_1/model_msm.R in70s death any all
needs: [design, data_stset_in70s, data_samples_in70s]
outputs:
highly_sensitive:
models: output/in70s/death/any/all/*/model*.rds
data: output/in70s/death/any/all/*/data*.rds
moderately_sensitive:
weights: output/in70s/death/any/all/*/weights*

report_ipw_in70s_death_any_all:
run: r:latest analysis/R/dose_1/report_ipw.R in70s death any all
needs: [design, models_in70s_death_any_all]
outputs:
highly_sensitive:
broom: output/in70s/death/any/all/*/broom*.rds
gt: output/in70s/death/any/all/*/gt*.rds
moderately_sensitive:
plots: output/in70s/death/any/all/*/plot*.svg
tables: output/in70s/death/any/all/*/tab*.html
data: output/in70s/death/any/all/*/broom*.csv

report_in70s_death_any_all:
run: r:latest analysis/R/dose_1/report_msm.R in70s death any all
needs: [design, models_in70s_death_any_all]
outputs:
moderately_sensitive:
plots: output/in70s/death/any/all/*.svg
tables: output/in70s/death/any/all/*.csv

## pfizer vaccine

models_in70s_death_pfizer_all:
run: r:latest analysis/R/dose_1/model_msm.R in70s death pfizer all
needs: [design, data_stset_in70s, data_samples_in70s]
outputs:
highly_sensitive:
models: output/in70s/death/pfizer/all/*/model*.rds
data: output/in70s/death/pfizer/all/*/data*.rds
moderately_sensitive:
weights: output/in70s/death/pfizer/all/*/weights*

report_ipw_in70s_death_pfizer_all:
run: r:latest analysis/R/dose_1/report_ipw.R in70s death pfizer all
needs: [design, models_in70s_death_pfizer_all]
outputs:
highly_sensitive:
broom: output/in70s/death/pfizer/all/*/broom*.rds
gt: output/in70s/death/pfizer/all/*/gt*.rds
moderately_sensitive:
plots: output/in70s/death/pfizer/all/*/plot*.svg
tables: output/in70s/death/pfizer/all/*/tab*.html
data: output/in70s/death/pfizer/all/*/broom*.csv

report_in70s_death_pfizer_all:
run: r:latest analysis/R/dose_1/report_msm.R in70s death pfizer all
needs: [design, models_in70s_death_pfizer_all]
outputs:
moderately_sensitive:
plots: output/in70s/death/pfizer/all/*.svg
tables: output/in70s/death/pfizer/all/*.csv

## az vaccine

models_in70s_death_az_all:
run: r:latest analysis/R/dose_1/model_msm.R in70s death az all
needs: [design, data_stset_in70s, data_samples_in70s]
outputs:
highly_sensitive:
models: output/in70s/death/az/all/*/model*.rds
data: output/in70s/death/az/all/*/data*.rds
moderately_sensitive:
weights: output/in70s/death/az/all/*/weights*

report_ipw_in70s_death_az_all:
run: r:latest analysis/R/dose_1/report_ipw.R in70s death az all
needs: [design, models_in70s_death_az_all]
outputs:
highly_sensitive:
broom: output/in70s/death/az/all/*/broom*.rds
gt: output/in70s/death/az/all/*/gt*.rds
moderately_sensitive:
plots: output/in70s/death/az/all/*/plot*.svg
tables: output/in70s/death/az/all/*/tab*.html
data: output/in70s/death/az/all/*/broom*.csv

report_in70s_death_az_all:
run: r:latest analysis/R/dose_1/report_msm.R in70s death az all
needs: [design, models_in70s_death_az_all]
outputs:
moderately_sensitive:
plots: output/in70s/death/az/all/*.svg
tables: output/in70s/death/az/all/*.csv



#######################################
## COMBINE OVERALL MODELS:
#######################################

# report_in70s_any_all:
# run: r:latest analysis/R/dose_1/report_alloutcomes.R in70s any all
# needs: [design, report_in70s_postest_any_all, report_in70s_covidadmitted_any_all, report_in70s_coviddeath_any_all, report_in70s_noncoviddeath_any_all, report_in70s_death_any_all]
# outputs:
# moderately_sensitive:
# plots: output/in70s/*any_all.svg
# tables: output/in70s/*any_all.csv
# html: output/in70s/*any_all.html
#
# report_in70s_pfizer_all:
# run: r:latest analysis/R/dose_1/report_alloutcomes.R in70s pfizer all
# needs: [design, report_in70s_postest_pfizer_all, report_in70s_covidadmitted_pfizer_all, report_in70s_coviddeath_pfizer_all, report_in70s_noncoviddeath_pfizer_all, report_in70s_death_pfizer_all]
# outputs:
# moderately_sensitive:
# plots: output/in70s/*pfizer_all.svg
# tables: output/in70s/*pfizer_all.csv
# html: output/in70s/*pfizer_all.html
#
# report_in70s_az_all:
# run: r:latest analysis/R/dose_1/report_alloutcomes.R in70s az all
# needs: [design, report_in70s_postest_az_all, report_in70s_covidadmitted_az_all, report_in70s_coviddeath_az_all, report_in70s_noncoviddeath_az_all, report_in70s_death_az_all]
# outputs:
# moderately_sensitive:
# plots: output/in70s/*az_all.svg
# tables: output/in70s/*az_all.csv
# html: output/in70s/*az_all.html


report_ipw_in70s_all:
run: r:latest analysis/R/dose_1/report_vaxmodel.R in70s death all
needs: [design, report_ipw_in70s_death_any_all, report_ipw_in70s_death_pfizer_all, report_ipw_in70s_death_az_all]
outputs:
moderately_sensitive:
svg: output/in70s/plot_vax1.svg
#html: output/in70s/tab_vax1.html
csv: output/in70s/tab_vax1.csv


report_in70s_all:
run: r:latest analysis/R/dose_1/report_alloutcomes_combined.R in70s all
needs: [design, report_in70s_postest_any_all, report_in70s_covidadmitted_any_all, report_in70s_coviddeath_any_all, report_in70s_noncoviddeath_any_all, report_in70s_death_any_all,
report_in70s_postest_pfizer_all, report_in70s_covidadmitted_pfizer_all, report_in70s_coviddeath_pfizer_all, report_in70s_noncoviddeath_pfizer_all, report_in70s_death_pfizer_all,
report_in70s_postest_az_all, report_in70s_covidadmitted_az_all, report_in70s_coviddeath_az_all, report_in70s_noncoviddeath_az_all, report_in70s_death_az_all]
outputs:
moderately_sensitive:
plots: output/in70s/*_all.svg
plots1: output/in70s/*_all.png
tables: output/in70s/*_all.csv




Jobs

ID Status Action
34jiqeeluza4627g succeeded models_in70s_coviddeath_any_all View
rlefmeo7slx7xp5v succeeded report_ipw_in70s_coviddeath_any_all View
dlkxvtgcoj7gtvtd succeeded report_in70s_coviddeath_any_all View
c4wwe7mjomh3qz5v succeeded models_in70s_coviddeath_pfizer_all View
se5csrmyqbialsyd succeeded report_ipw_in70s_coviddeath_pfizer_all View
m6sdvsfceibvg3e4 succeeded report_in70s_coviddeath_pfizer_all View
nikimikoltl3jijo failed models_in70s_coviddeath_az_all View
a3nwgp77owkct4le failed report_ipw_in70s_coviddeath_az_all View
u5fbwb3vyp2m5dfn failed report_in70s_coviddeath_az_all View