Job Request: 2968 a57uepyzzfjswg6y

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: succeeded

Config

Backend: tpp
Workspace: covid-vaccine-effectiveness-research_positivity (positivity)
Creator: wjchulme
Force run dependencies?: False
Git Commit Hash: 0f0063b
Requested Actions:
  • model_in70s_all_any_death
  • report_ipw_in70s_all_any_death
  • report_msm_in70s_all_any_death
  • report_incidence_in70s_all_any_death

Timings

Created: 1 week ago
Started: 1 week ago
Finished: 1 week ago
Runtime: 02:27:26

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
exclude_recentpostest: output/metadata/exclude_recentpostest.rds

## ####################################
## over80s
## ####################################

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

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
datavaxlong: output/over80s/data/data_long_vax_dates.rds
datavaxwide: output/over80s/data/data_wide_vax_dates.rds

data_process_long_over80s:
run: r:latest analysis/R/data_process_long.R over80s
needs:
- data_process_over80s
outputs:
highly_sensitive:
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

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:
txt: 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:
cohort: output/over80s/data/data_cohort.rds
moderately_sensitive:
flow: output/over80s/data/flowchart.csv

data_stset_over80s:
run: r:latest analysis/R/data_stset.R over80s
needs:
- design
- data_selection_over80s
- data_process_long_over80s
outputs:
highly_sensitive:
fixed: output/over80s/data/data_fixed.rds
tte: output/over80s/data/data_tte.rds
pt: 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

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

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_tableirrold_over80s:
run: r:latest analysis/R/descr_tableirr.R over80s FALSE
needs:
- design
- data_selection_over80s
outputs:
moderately_sensitive:
html: output/over80s/descriptive/tables/table_irr_old.html
csv: output/over80s/descriptive/tables/table_irr_old.csv

descr_tableirr_over80s:
run: r:latest analysis/R/descr_tableirr_lite.R over80s FALSE
needs:
- design
- data_selection_over80s
outputs:
moderately_sensitive:
html: output/over80s/descriptive/tables/table_irr.html
csv: output/over80s/descriptive/tables/table_irr.csv

descr_tableirr_exclude_over80s:
run: r:latest analysis/R/descr_tableirr_lite.R over80s TRUE
needs:
- design
- data_selection_over80s
outputs:
moderately_sensitive:
html: output/over80s/descriptive/tables/table_irr_exclude_recentpostest.html
csv: output/over80s/descriptive/tables/table_irr_exclude_recentpostest.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

## ####################################
## All
## ####################################

model_over80s_all_any_postest:
run: r:latest analysis/R/dose_1/model_msm.R over80s all any postest
needs:
- design
- data_stset_over80s
- data_samples_over80s
outputs:
highly_sensitive:
models: output/over80s/all/any/postest/model*.rds
data: output/over80s/all/any/postest/data*.rds
moderately_sensitive:
weights: output/over80s/all/any/postest/weights*

report_ipw_over80s_all_any_postest:
run: r:latest analysis/R/dose_1/report_ipw.R over80s all any postest
needs:
- design
- model_over80s_all_any_postest
outputs:
highly_sensitive:
broom: output/over80s/all/any/postest/broom*.rds
moderately_sensitive:
data: output/over80s/all/any/postest/broom*.csv

report_msm_over80s_all_any_postest:
run: r:latest analysis/R/dose_1/report_msm.R over80s all any postest
needs:
- design
- model_over80s_all_any_postest
outputs:
moderately_sensitive:
svg: output/over80s/all/any/postest/VE_plot.svg
png: output/over80s/all/any/postest/VE_plot.png
tables: output/over80s/all/any/postest/estimates*.csv

report_incidence_over80s_all_any_postest:
run: r:latest analysis/R/dose_1/report_incidence.R over80s all any postest
needs:
- design
- model_over80s_all_any_postest
outputs:
highly_sensitive:
data: output/over80s/all/any/postest/data_incidence.rds
moderately_sensitive:
cmlsvg: output/over80s/all/any/postest/cml_incidence*.svg
cmlpng: output/over80s/all/any/postest/cml_incidence*.png
trendsvg: output/over80s/all/any/postest/time*.svg
trendpng: output/over80s/all/any/postest/time*.png

model_over80s_all_pfizer_postest:
run: r:latest analysis/R/dose_1/model_msm.R over80s all pfizer postest
needs:
- design
- data_stset_over80s
- data_samples_over80s
outputs:
highly_sensitive:
models: output/over80s/all/pfizer/postest/model*.rds
data: output/over80s/all/pfizer/postest/data*.rds
moderately_sensitive:
weights: output/over80s/all/pfizer/postest/weights*

report_ipw_over80s_all_pfizer_postest:
run: r:latest analysis/R/dose_1/report_ipw.R over80s all pfizer postest
needs:
- design
- model_over80s_all_pfizer_postest
outputs:
highly_sensitive:
broom: output/over80s/all/pfizer/postest/broom*.rds
moderately_sensitive:
data: output/over80s/all/pfizer/postest/broom*.csv

report_msm_over80s_all_pfizer_postest:
run: r:latest analysis/R/dose_1/report_msm.R over80s all pfizer postest
needs:
- design
- model_over80s_all_pfizer_postest
outputs:
moderately_sensitive:
svg: output/over80s/all/pfizer/postest/VE_plot.svg
png: output/over80s/all/pfizer/postest/VE_plot.png
tables: output/over80s/all/pfizer/postest/estimates*.csv

report_incidence_over80s_all_pfizer_postest:
run: r:latest analysis/R/dose_1/report_incidence.R over80s all pfizer postest
needs:
- design
- model_over80s_all_pfizer_postest
outputs:
highly_sensitive:
data: output/over80s/all/pfizer/postest/data_incidence.rds
moderately_sensitive:
cmlsvg: output/over80s/all/pfizer/postest/cml_incidence*.svg
cmlpng: output/over80s/all/pfizer/postest/cml_incidence*.png
trendsvg: output/over80s/all/pfizer/postest/time*.svg
trendpng: output/over80s/all/pfizer/postest/time*.png

model_over80s_all_az_postest:
run: r:latest analysis/R/dose_1/model_msm.R over80s all az postest
needs:
- design
- data_stset_over80s
- data_samples_over80s
outputs:
highly_sensitive:
models: output/over80s/all/az/postest/model*.rds
data: output/over80s/all/az/postest/data*.rds
moderately_sensitive:
weights: output/over80s/all/az/postest/weights*

report_ipw_over80s_all_az_postest:
run: r:latest analysis/R/dose_1/report_ipw.R over80s all az postest
needs:
- design
- model_over80s_all_az_postest
outputs:
highly_sensitive:
broom: output/over80s/all/az/postest/broom*.rds
moderately_sensitive:
data: output/over80s/all/az/postest/broom*.csv

report_msm_over80s_all_az_postest:
run: r:latest analysis/R/dose_1/report_msm.R over80s all az postest
needs:
- design
- model_over80s_all_az_postest
outputs:
moderately_sensitive:
svg: output/over80s/all/az/postest/VE_plot.svg
png: output/over80s/all/az/postest/VE_plot.png
tables: output/over80s/all/az/postest/estimates*.csv

report_incidence_over80s_all_az_postest:
run: r:latest analysis/R/dose_1/report_incidence.R over80s all az postest
needs:
- design
- model_over80s_all_az_postest
outputs:
highly_sensitive:
data: output/over80s/all/az/postest/data_incidence.rds
moderately_sensitive:
cmlsvg: output/over80s/all/az/postest/cml_incidence*.svg
cmlpng: output/over80s/all/az/postest/cml_incidence*.png
trendsvg: output/over80s/all/az/postest/time*.svg
trendpng: output/over80s/all/az/postest/time*.png

model_over80s_all_any_covidadmitted:
run: r:latest analysis/R/dose_1/model_msm.R over80s all any covidadmitted
needs:
- design
- data_stset_over80s
- data_samples_over80s
outputs:
highly_sensitive:
models: output/over80s/all/any/covidadmitted/model*.rds
data: output/over80s/all/any/covidadmitted/data*.rds
moderately_sensitive:
weights: output/over80s/all/any/covidadmitted/weights*

report_ipw_over80s_all_any_covidadmitted:
run: r:latest analysis/R/dose_1/report_ipw.R over80s all any covidadmitted
needs:
- design
- model_over80s_all_any_covidadmitted
outputs:
highly_sensitive:
broom: output/over80s/all/any/covidadmitted/broom*.rds
moderately_sensitive:
data: output/over80s/all/any/covidadmitted/broom*.csv

report_msm_over80s_all_any_covidadmitted:
run: r:latest analysis/R/dose_1/report_msm.R over80s all any covidadmitted
needs:
- design
- model_over80s_all_any_covidadmitted
outputs:
moderately_sensitive:
svg: output/over80s/all/any/covidadmitted/VE_plot.svg
png: output/over80s/all/any/covidadmitted/VE_plot.png
tables: output/over80s/all/any/covidadmitted/estimates*.csv

report_incidence_over80s_all_any_covidadmitted:
run: r:latest analysis/R/dose_1/report_incidence.R over80s all any covidadmitted
needs:
- design
- model_over80s_all_any_covidadmitted
outputs:
highly_sensitive:
data: output/over80s/all/any/covidadmitted/data_incidence.rds
moderately_sensitive:
cmlsvg: output/over80s/all/any/covidadmitted/cml_incidence*.svg
cmlpng: output/over80s/all/any/covidadmitted/cml_incidence*.png
trendsvg: output/over80s/all/any/covidadmitted/time*.svg
trendpng: output/over80s/all/any/covidadmitted/time*.png

model_over80s_all_pfizer_covidadmitted:
run: r:latest analysis/R/dose_1/model_msm.R over80s all pfizer covidadmitted
needs:
- design
- data_stset_over80s
- data_samples_over80s
outputs:
highly_sensitive:
models: output/over80s/all/pfizer/covidadmitted/model*.rds
data: output/over80s/all/pfizer/covidadmitted/data*.rds
moderately_sensitive:
weights: output/over80s/all/pfizer/covidadmitted/weights*

report_ipw_over80s_all_pfizer_covidadmitted:
run: r:latest analysis/R/dose_1/report_ipw.R over80s all pfizer covidadmitted
needs:
- design
- model_over80s_all_pfizer_covidadmitted
outputs:
highly_sensitive:
broom: output/over80s/all/pfizer/covidadmitted/broom*.rds
moderately_sensitive:
data: output/over80s/all/pfizer/covidadmitted/broom*.csv

report_msm_over80s_all_pfizer_covidadmitted:
run: r:latest analysis/R/dose_1/report_msm.R over80s all pfizer covidadmitted
needs:
- design
- model_over80s_all_pfizer_covidadmitted
outputs:
moderately_sensitive:
svg: output/over80s/all/pfizer/covidadmitted/VE_plot.svg
png: output/over80s/all/pfizer/covidadmitted/VE_plot.png
tables: output/over80s/all/pfizer/covidadmitted/estimates*.csv

report_incidence_over80s_all_pfizer_covidadmitted:
run: r:latest analysis/R/dose_1/report_incidence.R over80s all pfizer covidadmitted
needs:
- design
- model_over80s_all_pfizer_covidadmitted
outputs:
highly_sensitive:
data: output/over80s/all/pfizer/covidadmitted/data_incidence.rds
moderately_sensitive:
cmlsvg: output/over80s/all/pfizer/covidadmitted/cml_incidence*.svg
cmlpng: output/over80s/all/pfizer/covidadmitted/cml_incidence*.png
trendsvg: output/over80s/all/pfizer/covidadmitted/time*.svg
trendpng: output/over80s/all/pfizer/covidadmitted/time*.png

model_over80s_all_az_covidadmitted:
run: r:latest analysis/R/dose_1/model_msm.R over80s all az covidadmitted
needs:
- design
- data_stset_over80s
- data_samples_over80s
outputs:
highly_sensitive:
models: output/over80s/all/az/covidadmitted/model*.rds
data: output/over80s/all/az/covidadmitted/data*.rds
moderately_sensitive:
weights: output/over80s/all/az/covidadmitted/weights*

report_ipw_over80s_all_az_covidadmitted:
run: r:latest analysis/R/dose_1/report_ipw.R over80s all az covidadmitted
needs:
- design
- model_over80s_all_az_covidadmitted
outputs:
highly_sensitive:
broom: output/over80s/all/az/covidadmitted/broom*.rds
moderately_sensitive:
data: output/over80s/all/az/covidadmitted/broom*.csv

report_msm_over80s_all_az_covidadmitted:
run: r:latest analysis/R/dose_1/report_msm.R over80s all az covidadmitted
needs:
- design
- model_over80s_all_az_covidadmitted
outputs:
moderately_sensitive:
svg: output/over80s/all/az/covidadmitted/VE_plot.svg
png: output/over80s/all/az/covidadmitted/VE_plot.png
tables: output/over80s/all/az/covidadmitted/estimates*.csv

report_incidence_over80s_all_az_covidadmitted:
run: r:latest analysis/R/dose_1/report_incidence.R over80s all az covidadmitted
needs:
- design
- model_over80s_all_az_covidadmitted
outputs:
highly_sensitive:
data: output/over80s/all/az/covidadmitted/data_incidence.rds
moderately_sensitive:
cmlsvg: output/over80s/all/az/covidadmitted/cml_incidence*.svg
cmlpng: output/over80s/all/az/covidadmitted/cml_incidence*.png
trendsvg: output/over80s/all/az/covidadmitted/time*.svg
trendpng: output/over80s/all/az/covidadmitted/time*.png

model_over80s_all_any_coviddeath:
run: r:latest analysis/R/dose_1/model_msm.R over80s all any coviddeath
needs:
- design
- data_stset_over80s
- data_samples_over80s
outputs:
highly_sensitive:
models: output/over80s/all/any/coviddeath/model*.rds
data: output/over80s/all/any/coviddeath/data*.rds
moderately_sensitive:
weights: output/over80s/all/any/coviddeath/weights*

report_ipw_over80s_all_any_coviddeath:
run: r:latest analysis/R/dose_1/report_ipw.R over80s all any coviddeath
needs:
- design
- model_over80s_all_any_coviddeath
outputs:
highly_sensitive:
broom: output/over80s/all/any/coviddeath/broom*.rds
moderately_sensitive:
data: output/over80s/all/any/coviddeath/broom*.csv

report_msm_over80s_all_any_coviddeath:
run: r:latest analysis/R/dose_1/report_msm.R over80s all any coviddeath
needs:
- design
- model_over80s_all_any_coviddeath
outputs:
moderately_sensitive:
svg: output/over80s/all/any/coviddeath/VE_plot.svg
png: output/over80s/all/any/coviddeath/VE_plot.png
tables: output/over80s/all/any/coviddeath/estimates*.csv

report_incidence_over80s_all_any_coviddeath:
run: r:latest analysis/R/dose_1/report_incidence.R over80s all any coviddeath
needs:
- design
- model_over80s_all_any_coviddeath
outputs:
highly_sensitive:
data: output/over80s/all/any/coviddeath/data_incidence.rds
moderately_sensitive:
cmlsvg: output/over80s/all/any/coviddeath/cml_incidence*.svg
cmlpng: output/over80s/all/any/coviddeath/cml_incidence*.png
trendsvg: output/over80s/all/any/coviddeath/time*.svg
trendpng: output/over80s/all/any/coviddeath/time*.png

model_over80s_all_pfizer_coviddeath:
run: r:latest analysis/R/dose_1/model_msm.R over80s all pfizer coviddeath
needs:
- design
- data_stset_over80s
- data_samples_over80s
outputs:
highly_sensitive:
models: output/over80s/all/pfizer/coviddeath/model*.rds
data: output/over80s/all/pfizer/coviddeath/data*.rds
moderately_sensitive:
weights: output/over80s/all/pfizer/coviddeath/weights*

report_ipw_over80s_all_pfizer_coviddeath:
run: r:latest analysis/R/dose_1/report_ipw.R over80s all pfizer coviddeath
needs:
- design
- model_over80s_all_pfizer_coviddeath
outputs:
highly_sensitive:
broom: output/over80s/all/pfizer/coviddeath/broom*.rds
moderately_sensitive:
data: output/over80s/all/pfizer/coviddeath/broom*.csv

report_msm_over80s_all_pfizer_coviddeath:
run: r:latest analysis/R/dose_1/report_msm.R over80s all pfizer coviddeath
needs:
- design
- model_over80s_all_pfizer_coviddeath
outputs:
moderately_sensitive:
svg: output/over80s/all/pfizer/coviddeath/VE_plot.svg
png: output/over80s/all/pfizer/coviddeath/VE_plot.png
tables: output/over80s/all/pfizer/coviddeath/estimates*.csv

report_incidence_over80s_all_pfizer_coviddeath:
run: r:latest analysis/R/dose_1/report_incidence.R over80s all pfizer coviddeath
needs:
- design
- model_over80s_all_pfizer_coviddeath
outputs:
highly_sensitive:
data: output/over80s/all/pfizer/coviddeath/data_incidence.rds
moderately_sensitive:
cmlsvg: output/over80s/all/pfizer/coviddeath/cml_incidence*.svg
cmlpng: output/over80s/all/pfizer/coviddeath/cml_incidence*.png
trendsvg: output/over80s/all/pfizer/coviddeath/time*.svg
trendpng: output/over80s/all/pfizer/coviddeath/time*.png

model_over80s_all_az_coviddeath:
run: r:latest analysis/R/dose_1/model_msm.R over80s all az coviddeath
needs:
- design
- data_stset_over80s
- data_samples_over80s
outputs:
highly_sensitive:
models: output/over80s/all/az/coviddeath/model*.rds
data: output/over80s/all/az/coviddeath/data*.rds
moderately_sensitive:
weights: output/over80s/all/az/coviddeath/weights*

report_ipw_over80s_all_az_coviddeath:
run: r:latest analysis/R/dose_1/report_ipw.R over80s all az coviddeath
needs:
- design
- model_over80s_all_az_coviddeath
outputs:
highly_sensitive:
broom: output/over80s/all/az/coviddeath/broom*.rds
moderately_sensitive:
data: output/over80s/all/az/coviddeath/broom*.csv

report_msm_over80s_all_az_coviddeath:
run: r:latest analysis/R/dose_1/report_msm.R over80s all az coviddeath
needs:
- design
- model_over80s_all_az_coviddeath
outputs:
moderately_sensitive:
svg: output/over80s/all/az/coviddeath/VE_plot.svg
png: output/over80s/all/az/coviddeath/VE_plot.png
tables: output/over80s/all/az/coviddeath/estimates*.csv

report_incidence_over80s_all_az_coviddeath:
run: r:latest analysis/R/dose_1/report_incidence.R over80s all az coviddeath
needs:
- design
- model_over80s_all_az_coviddeath
outputs:
highly_sensitive:
data: output/over80s/all/az/coviddeath/data_incidence.rds
moderately_sensitive:
cmlsvg: output/over80s/all/az/coviddeath/cml_incidence*.svg
cmlpng: output/over80s/all/az/coviddeath/cml_incidence*.png
trendsvg: output/over80s/all/az/coviddeath/time*.svg
trendpng: output/over80s/all/az/coviddeath/time*.png

model_over80s_all_any_noncoviddeath:
run: r:latest analysis/R/dose_1/model_msm.R over80s all any noncoviddeath
needs:
- design
- data_stset_over80s
- data_samples_over80s
outputs:
highly_sensitive:
models: output/over80s/all/any/noncoviddeath/model*.rds
data: output/over80s/all/any/noncoviddeath/data*.rds
moderately_sensitive:
weights: output/over80s/all/any/noncoviddeath/weights*

report_ipw_over80s_all_any_noncoviddeath:
run: r:latest analysis/R/dose_1/report_ipw.R over80s all any noncoviddeath
needs:
- design
- model_over80s_all_any_noncoviddeath
outputs:
highly_sensitive:
broom: output/over80s/all/any/noncoviddeath/broom*.rds
moderately_sensitive:
data: output/over80s/all/any/noncoviddeath/broom*.csv

report_msm_over80s_all_any_noncoviddeath:
run: r:latest analysis/R/dose_1/report_msm.R over80s all any noncoviddeath
needs:
- design
- model_over80s_all_any_noncoviddeath
outputs:
moderately_sensitive:
svg: output/over80s/all/any/noncoviddeath/VE_plot.svg
png: output/over80s/all/any/noncoviddeath/VE_plot.png
tables: output/over80s/all/any/noncoviddeath/estimates*.csv

report_incidence_over80s_all_any_noncoviddeath:
run: r:latest analysis/R/dose_1/report_incidence.R over80s all any noncoviddeath
needs:
- design
- model_over80s_all_any_noncoviddeath
outputs:
highly_sensitive:
data: output/over80s/all/any/noncoviddeath/data_incidence.rds
moderately_sensitive:
cmlsvg: output/over80s/all/any/noncoviddeath/cml_incidence*.svg
cmlpng: output/over80s/all/any/noncoviddeath/cml_incidence*.png
trendsvg: output/over80s/all/any/noncoviddeath/time*.svg
trendpng: output/over80s/all/any/noncoviddeath/time*.png

model_over80s_all_pfizer_noncoviddeath:
run: r:latest analysis/R/dose_1/model_msm.R over80s all pfizer noncoviddeath
needs:
- design
- data_stset_over80s
- data_samples_over80s
outputs:
highly_sensitive:
models: output/over80s/all/pfizer/noncoviddeath/model*.rds
data: output/over80s/all/pfizer/noncoviddeath/data*.rds
moderately_sensitive:
weights: output/over80s/all/pfizer/noncoviddeath/weights*

report_ipw_over80s_all_pfizer_noncoviddeath:
run: r:latest analysis/R/dose_1/report_ipw.R over80s all pfizer noncoviddeath
needs:
- design
- model_over80s_all_pfizer_noncoviddeath
outputs:
highly_sensitive:
broom: output/over80s/all/pfizer/noncoviddeath/broom*.rds
moderately_sensitive:
data: output/over80s/all/pfizer/noncoviddeath/broom*.csv

report_msm_over80s_all_pfizer_noncoviddeath:
run: r:latest analysis/R/dose_1/report_msm.R over80s all pfizer noncoviddeath
needs:
- design
- model_over80s_all_pfizer_noncoviddeath
outputs:
moderately_sensitive:
svg: output/over80s/all/pfizer/noncoviddeath/VE_plot.svg
png: output/over80s/all/pfizer/noncoviddeath/VE_plot.png
tables: output/over80s/all/pfizer/noncoviddeath/estimates*.csv

report_incidence_over80s_all_pfizer_noncoviddeath:
run: r:latest analysis/R/dose_1/report_incidence.R over80s all pfizer noncoviddeath
needs:
- design
- model_over80s_all_pfizer_noncoviddeath
outputs:
highly_sensitive:
data: output/over80s/all/pfizer/noncoviddeath/data_incidence.rds
moderately_sensitive:
cmlsvg: output/over80s/all/pfizer/noncoviddeath/cml_incidence*.svg
cmlpng: output/over80s/all/pfizer/noncoviddeath/cml_incidence*.png
trendsvg: output/over80s/all/pfizer/noncoviddeath/time*.svg
trendpng: output/over80s/all/pfizer/noncoviddeath/time*.png

model_over80s_all_az_noncoviddeath:
run: r:latest analysis/R/dose_1/model_msm.R over80s all az noncoviddeath
needs:
- design
- data_stset_over80s
- data_samples_over80s
outputs:
highly_sensitive:
models: output/over80s/all/az/noncoviddeath/model*.rds
data: output/over80s/all/az/noncoviddeath/data*.rds
moderately_sensitive:
weights: output/over80s/all/az/noncoviddeath/weights*

report_ipw_over80s_all_az_noncoviddeath:
run: r:latest analysis/R/dose_1/report_ipw.R over80s all az noncoviddeath
needs:
- design
- model_over80s_all_az_noncoviddeath
outputs:
highly_sensitive:
broom: output/over80s/all/az/noncoviddeath/broom*.rds
moderately_sensitive:
data: output/over80s/all/az/noncoviddeath/broom*.csv

report_msm_over80s_all_az_noncoviddeath:
run: r:latest analysis/R/dose_1/report_msm.R over80s all az noncoviddeath
needs:
- design
- model_over80s_all_az_noncoviddeath
outputs:
moderately_sensitive:
svg: output/over80s/all/az/noncoviddeath/VE_plot.svg
png: output/over80s/all/az/noncoviddeath/VE_plot.png
tables: output/over80s/all/az/noncoviddeath/estimates*.csv

report_incidence_over80s_all_az_noncoviddeath:
run: r:latest analysis/R/dose_1/report_incidence.R over80s all az noncoviddeath
needs:
- design
- model_over80s_all_az_noncoviddeath
outputs:
highly_sensitive:
data: output/over80s/all/az/noncoviddeath/data_incidence.rds
moderately_sensitive:
cmlsvg: output/over80s/all/az/noncoviddeath/cml_incidence*.svg
cmlpng: output/over80s/all/az/noncoviddeath/cml_incidence*.png
trendsvg: output/over80s/all/az/noncoviddeath/time*.svg
trendpng: output/over80s/all/az/noncoviddeath/time*.png

model_over80s_all_any_death:
run: r:latest analysis/R/dose_1/model_msm.R over80s all any death
needs:
- design
- data_stset_over80s
- data_samples_over80s
outputs:
highly_sensitive:
models: output/over80s/all/any/death/model*.rds
data: output/over80s/all/any/death/data*.rds
moderately_sensitive:
weights: output/over80s/all/any/death/weights*

report_ipw_over80s_all_any_death:
run: r:latest analysis/R/dose_1/report_ipw.R over80s all any death
needs:
- design
- model_over80s_all_any_death
outputs:
highly_sensitive:
broom: output/over80s/all/any/death/broom*.rds
moderately_sensitive:
data: output/over80s/all/any/death/broom*.csv

report_msm_over80s_all_any_death:
run: r:latest analysis/R/dose_1/report_msm.R over80s all any death
needs:
- design
- model_over80s_all_any_death
outputs:
moderately_sensitive:
svg: output/over80s/all/any/death/VE_plot.svg
png: output/over80s/all/any/death/VE_plot.png
tables: output/over80s/all/any/death/estimates*.csv

report_incidence_over80s_all_any_death:
run: r:latest analysis/R/dose_1/report_incidence.R over80s all any death
needs:
- design
- model_over80s_all_any_death
outputs:
highly_sensitive:
data: output/over80s/all/any/death/data_incidence.rds
moderately_sensitive:
cmlsvg: output/over80s/all/any/death/cml_incidence*.svg
cmlpng: output/over80s/all/any/death/cml_incidence*.png
trendsvg: output/over80s/all/any/death/time*.svg
trendpng: output/over80s/all/any/death/time*.png

model_over80s_all_pfizer_death:
run: r:latest analysis/R/dose_1/model_msm.R over80s all pfizer death
needs:
- design
- data_stset_over80s
- data_samples_over80s
outputs:
highly_sensitive:
models: output/over80s/all/pfizer/death/model*.rds
data: output/over80s/all/pfizer/death/data*.rds
moderately_sensitive:
weights: output/over80s/all/pfizer/death/weights*

report_ipw_over80s_all_pfizer_death:
run: r:latest analysis/R/dose_1/report_ipw.R over80s all pfizer death
needs:
- design
- model_over80s_all_pfizer_death
outputs:
highly_sensitive:
broom: output/over80s/all/pfizer/death/broom*.rds
moderately_sensitive:
data: output/over80s/all/pfizer/death/broom*.csv

report_msm_over80s_all_pfizer_death:
run: r:latest analysis/R/dose_1/report_msm.R over80s all pfizer death
needs:
- design
- model_over80s_all_pfizer_death
outputs:
moderately_sensitive:
svg: output/over80s/all/pfizer/death/VE_plot.svg
png: output/over80s/all/pfizer/death/VE_plot.png
tables: output/over80s/all/pfizer/death/estimates*.csv

report_incidence_over80s_all_pfizer_death:
run: r:latest analysis/R/dose_1/report_incidence.R over80s all pfizer death
needs:
- design
- model_over80s_all_pfizer_death
outputs:
highly_sensitive:
data: output/over80s/all/pfizer/death/data_incidence.rds
moderately_sensitive:
cmlsvg: output/over80s/all/pfizer/death/cml_incidence*.svg
cmlpng: output/over80s/all/pfizer/death/cml_incidence*.png
trendsvg: output/over80s/all/pfizer/death/time*.svg
trendpng: output/over80s/all/pfizer/death/time*.png

model_over80s_all_az_death:
run: r:latest analysis/R/dose_1/model_msm.R over80s all az death
needs:
- design
- data_stset_over80s
- data_samples_over80s
outputs:
highly_sensitive:
models: output/over80s/all/az/death/model*.rds
data: output/over80s/all/az/death/data*.rds
moderately_sensitive:
weights: output/over80s/all/az/death/weights*

report_ipw_over80s_all_az_death:
run: r:latest analysis/R/dose_1/report_ipw.R over80s all az death
needs:
- design
- model_over80s_all_az_death
outputs:
highly_sensitive:
broom: output/over80s/all/az/death/broom*.rds
moderately_sensitive:
data: output/over80s/all/az/death/broom*.csv

report_msm_over80s_all_az_death:
run: r:latest analysis/R/dose_1/report_msm.R over80s all az death
needs:
- design
- model_over80s_all_az_death
outputs:
moderately_sensitive:
svg: output/over80s/all/az/death/VE_plot.svg
png: output/over80s/all/az/death/VE_plot.png
tables: output/over80s/all/az/death/estimates*.csv

report_incidence_over80s_all_az_death:
run: r:latest analysis/R/dose_1/report_incidence.R over80s all az death
needs:
- design
- model_over80s_all_az_death
outputs:
highly_sensitive:
data: output/over80s/all/az/death/data_incidence.rds
moderately_sensitive:
cmlsvg: output/over80s/all/az/death/cml_incidence*.svg
cmlpng: output/over80s/all/az/death/cml_incidence*.png
trendsvg: output/over80s/all/az/death/time*.svg
trendpng: output/over80s/all/az/death/time*.png

report_ipw_over80s_all:
run: r:latest analysis/R/dose_1/report_ipw_combined.R over80s all death
needs:
- design
- report_ipw_over80s_all_any_death
- report_ipw_over80s_all_pfizer_death
- report_ipw_over80s_all_az_death
outputs:
moderately_sensitive:
svg: output/over80s/all/combined/plot_vax1.svg
csv: output/over80s/all/combined/tab_vax1.csv
csv_wide: output/over80s/all/combined/tab_vax1_wide.csv

report_msm_over80s_all:
run: r:latest analysis/R/dose_1/report_msm_combined.R over80s all
needs:
- design
- report_msm_over80s_all_any_postest
- report_msm_over80s_all_any_covidadmitted
- report_msm_over80s_all_any_coviddeath
- report_msm_over80s_all_any_noncoviddeath
- report_msm_over80s_all_pfizer_postest
- report_msm_over80s_all_pfizer_covidadmitted
- report_msm_over80s_all_pfizer_coviddeath
- report_msm_over80s_all_pfizer_noncoviddeath
- report_msm_over80s_all_az_postest
- report_msm_over80s_all_az_covidadmitted
- report_msm_over80s_all_az_coviddeath
- report_msm_over80s_all_az_noncoviddeath
outputs:
moderately_sensitive:
svg: output/over80s/all/combined/VE*.svg
png: output/over80s/all/combined/VE*.png
csv: output/over80s/all/combined/*.csv

report_incidence_over80s_all:
run: r:latest analysis/R/dose_1/report_incidence_combined.R over80s all
needs:
- design
- report_incidence_over80s_all_any_postest
- report_incidence_over80s_all_any_covidadmitted
- report_incidence_over80s_all_any_coviddeath
- report_incidence_over80s_all_any_noncoviddeath
- report_incidence_over80s_all_pfizer_postest
- report_incidence_over80s_all_pfizer_covidadmitted
- report_incidence_over80s_all_pfizer_coviddeath
- report_incidence_over80s_all_pfizer_noncoviddeath
- report_incidence_over80s_all_az_postest
- report_incidence_over80s_all_az_covidadmitted
- report_incidence_over80s_all_az_coviddeath
- report_incidence_over80s_all_az_noncoviddeath
outputs:
moderately_sensitive:
svg: output/over80s/all/combined/cml_incidence*.svg
png: output/over80s/all/combined/cml_incidence*.png

## ####################################
## Immunosuppressed
## ####################################

model_over80s_any_immunosuppression_any_postest:
run: r:latest analysis/R/dose_1/model_msm.R over80s any_immunosuppression any
postest
needs:
- design
- data_stset_over80s
- data_samples_over80s
outputs:
highly_sensitive:
models: output/over80s/any_immunosuppression/any/postest/model*.rds
data: output/over80s/any_immunosuppression/any/postest/data*.rds
moderately_sensitive:
weights: output/over80s/any_immunosuppression/any/postest/weights*

report_ipw_over80s_any_immunosuppression_any_postest:
run: r:latest analysis/R/dose_1/report_ipw.R over80s any_immunosuppression any
postest
needs:
- design
- model_over80s_any_immunosuppression_any_postest
outputs:
highly_sensitive:
broom: output/over80s/any_immunosuppression/any/postest/broom*.rds
moderately_sensitive:
data: output/over80s/any_immunosuppression/any/postest/broom*.csv

report_msm_over80s_any_immunosuppression_any_postest:
run: r:latest analysis/R/dose_1/report_msm.R over80s any_immunosuppression any
postest
needs:
- design
- model_over80s_any_immunosuppression_any_postest
outputs:
moderately_sensitive:
svg: output/over80s/any_immunosuppression/any/postest/VE_plot.svg
png: output/over80s/any_immunosuppression/any/postest/VE_plot.png
tables: output/over80s/any_immunosuppression/any/postest/estimates*.csv

report_incidence_over80s_any_immunosuppression_any_postest:
run: r:latest analysis/R/dose_1/report_incidence.R over80s any_immunosuppression
any postest
needs:
- design
- model_over80s_any_immunosuppression_any_postest
outputs:
highly_sensitive:
data: output/over80s/any_immunosuppression/any/postest/data_incidence.rds
moderately_sensitive:
cmlsvg: output/over80s/any_immunosuppression/any/postest/cml_incidence*.svg
cmlpng: output/over80s/any_immunosuppression/any/postest/cml_incidence*.png
trendsvg: output/over80s/any_immunosuppression/any/postest/time*.svg
trendpng: output/over80s/any_immunosuppression/any/postest/time*.png

model_over80s_any_immunosuppression_pfizer_postest:
run: r:latest analysis/R/dose_1/model_msm.R over80s any_immunosuppression pfizer
postest
needs:
- design
- data_stset_over80s
- data_samples_over80s
outputs:
highly_sensitive:
models: output/over80s/any_immunosuppression/pfizer/postest/model*.rds
data: output/over80s/any_immunosuppression/pfizer/postest/data*.rds
moderately_sensitive:
weights: output/over80s/any_immunosuppression/pfizer/postest/weights*

report_ipw_over80s_any_immunosuppression_pfizer_postest:
run: r:latest analysis/R/dose_1/report_ipw.R over80s any_immunosuppression pfizer
postest
needs:
- design
- model_over80s_any_immunosuppression_pfizer_postest
outputs:
highly_sensitive:
broom: output/over80s/any_immunosuppression/pfizer/postest/broom*.rds
moderately_sensitive:
data: output/over80s/any_immunosuppression/pfizer/postest/broom*.csv

report_msm_over80s_any_immunosuppression_pfizer_postest:
run: r:latest analysis/R/dose_1/report_msm.R over80s any_immunosuppression pfizer
postest
needs:
- design
- model_over80s_any_immunosuppression_pfizer_postest
outputs:
moderately_sensitive:
svg: output/over80s/any_immunosuppression/pfizer/postest/VE_plot.svg
png: output/over80s/any_immunosuppression/pfizer/postest/VE_plot.png
tables: output/over80s/any_immunosuppression/pfizer/postest/estimates*.csv

report_incidence_over80s_any_immunosuppression_pfizer_postest:
run: r:latest analysis/R/dose_1/report_incidence.R over80s any_immunosuppression
pfizer postest
needs:
- design
- model_over80s_any_immunosuppression_pfizer_postest
outputs:
highly_sensitive:
data: output/over80s/any_immunosuppression/pfizer/postest/data_incidence.rds
moderately_sensitive:
cmlsvg: output/over80s/any_immunosuppression/pfizer/postest/cml_incidence*.svg
cmlpng: output/over80s/any_immunosuppression/pfizer/postest/cml_incidence*.png
trendsvg: output/over80s/any_immunosuppression/pfizer/postest/time*.svg
trendpng: output/over80s/any_immunosuppression/pfizer/postest/time*.png

model_over80s_any_immunosuppression_az_postest:
run: r:latest analysis/R/dose_1/model_msm.R over80s any_immunosuppression az postest
needs:
- design
- data_stset_over80s
- data_samples_over80s
outputs:
highly_sensitive:
models: output/over80s/any_immunosuppression/az/postest/model*.rds
data: output/over80s/any_immunosuppression/az/postest/data*.rds
moderately_sensitive:
weights: output/over80s/any_immunosuppression/az/postest/weights*

report_ipw_over80s_any_immunosuppression_az_postest:
run: r:latest analysis/R/dose_1/report_ipw.R over80s any_immunosuppression az
postest
needs:
- design
- model_over80s_any_immunosuppression_az_postest
outputs:
highly_sensitive:
broom: output/over80s/any_immunosuppression/az/postest/broom*.rds
moderately_sensitive:
data: output/over80s/any_immunosuppression/az/postest/broom*.csv

report_msm_over80s_any_immunosuppression_az_postest:
run: r:latest analysis/R/dose_1/report_msm.R over80s any_immunosuppression az
postest
needs:
- design
- model_over80s_any_immunosuppression_az_postest
outputs:
moderately_sensitive:
svg: output/over80s/any_immunosuppression/az/postest/VE_plot.svg
png: output/over80s/any_immunosuppression/az/postest/VE_plot.png
tables: output/over80s/any_immunosuppression/az/postest/estimates*.csv

report_incidence_over80s_any_immunosuppression_az_postest:
run: r:latest analysis/R/dose_1/report_incidence.R over80s any_immunosuppression
az postest
needs:
- design
- model_over80s_any_immunosuppression_az_postest
outputs:
highly_sensitive:
data: output/over80s/any_immunosuppression/az/postest/data_incidence.rds
moderately_sensitive:
cmlsvg: output/over80s/any_immunosuppression/az/postest/cml_incidence*.svg
cmlpng: output/over80s/any_immunosuppression/az/postest/cml_incidence*.png
trendsvg: output/over80s/any_immunosuppression/az/postest/time*.svg
trendpng: output/over80s/any_immunosuppression/az/postest/time*.png

model_over80s_any_immunosuppression_any_covidadmitted:
run: r:latest analysis/R/dose_1/model_msm.R over80s any_immunosuppression any
covidadmitted
needs:
- design
- data_stset_over80s
- data_samples_over80s
outputs:
highly_sensitive:
models: output/over80s/any_immunosuppression/any/covidadmitted/model*.rds
data: output/over80s/any_immunosuppression/any/covidadmitted/data*.rds
moderately_sensitive:
weights: output/over80s/any_immunosuppression/any/covidadmitted/weights*

report_ipw_over80s_any_immunosuppression_any_covidadmitted:
run: r:latest analysis/R/dose_1/report_ipw.R over80s any_immunosuppression any
covidadmitted
needs:
- design
- model_over80s_any_immunosuppression_any_covidadmitted
outputs:
highly_sensitive:
broom: output/over80s/any_immunosuppression/any/covidadmitted/broom*.rds
moderately_sensitive:
data: output/over80s/any_immunosuppression/any/covidadmitted/broom*.csv

report_msm_over80s_any_immunosuppression_any_covidadmitted:
run: r:latest analysis/R/dose_1/report_msm.R over80s any_immunosuppression any
covidadmitted
needs:
- design
- model_over80s_any_immunosuppression_any_covidadmitted
outputs:
moderately_sensitive:
svg: output/over80s/any_immunosuppression/any/covidadmitted/VE_plot.svg
png: output/over80s/any_immunosuppression/any/covidadmitted/VE_plot.png
tables: output/over80s/any_immunosuppression/any/covidadmitted/estimates*.csv

report_incidence_over80s_any_immunosuppression_any_covidadmitted:
run: r:latest analysis/R/dose_1/report_incidence.R over80s any_immunosuppression
any covidadmitted
needs:
- design
- model_over80s_any_immunosuppression_any_covidadmitted
outputs:
highly_sensitive:
data: output/over80s/any_immunosuppression/any/covidadmitted/data_incidence.rds
moderately_sensitive:
cmlsvg: output/over80s/any_immunosuppression/any/covidadmitted/cml_incidence*.svg
cmlpng: output/over80s/any_immunosuppression/any/covidadmitted/cml_incidence*.png
trendsvg: output/over80s/any_immunosuppression/any/covidadmitted/time*.svg
trendpng: output/over80s/any_immunosuppression/any/covidadmitted/time*.png

model_over80s_any_immunosuppression_pfizer_covidadmitted:
run: r:latest analysis/R/dose_1/model_msm.R over80s any_immunosuppression pfizer
covidadmitted
needs:
- design
- data_stset_over80s
- data_samples_over80s
outputs:
highly_sensitive:
models: output/over80s/any_immunosuppression/pfizer/covidadmitted/model*.rds
data: output/over80s/any_immunosuppression/pfizer/covidadmitted/data*.rds
moderately_sensitive:
weights: output/over80s/any_immunosuppression/pfizer/covidadmitted/weights*

report_ipw_over80s_any_immunosuppression_pfizer_covidadmitted:
run: r:latest analysis/R/dose_1/report_ipw.R over80s any_immunosuppression pfizer
covidadmitted
needs:
- design
- model_over80s_any_immunosuppression_pfizer_covidadmitted
outputs:
highly_sensitive:
broom: output/over80s/any_immunosuppression/pfizer/covidadmitted/broom*.rds
moderately_sensitive:
data: output/over80s/any_immunosuppression/pfizer/covidadmitted/broom*.csv

report_msm_over80s_any_immunosuppression_pfizer_covidadmitted:
run: r:latest analysis/R/dose_1/report_msm.R over80s any_immunosuppression pfizer
covidadmitted
needs:
- design
- model_over80s_any_immunosuppression_pfizer_covidadmitted
outputs:
moderately_sensitive:
svg: output/over80s/any_immunosuppression/pfizer/covidadmitted/VE_plot.svg
png: output/over80s/any_immunosuppression/pfizer/covidadmitted/VE_plot.png
tables: output/over80s/any_immunosuppression/pfizer/covidadmitted/estimates*.csv

report_incidence_over80s_any_immunosuppression_pfizer_covidadmitted:
run: r:latest analysis/R/dose_1/report_incidence.R over80s any_immunosuppression
pfizer covidadmitted
needs:
- design
- model_over80s_any_immunosuppression_pfizer_covidadmitted
outputs:
highly_sensitive:
data: output/over80s/any_immunosuppression/pfizer/covidadmitted/data_incidence.rds
moderately_sensitive:
cmlsvg: output/over80s/any_immunosuppression/pfizer/covidadmitted/cml_incidence*.svg
cmlpng: output/over80s/any_immunosuppression/pfizer/covidadmitted/cml_incidence*.png
trendsvg: output/over80s/any_immunosuppression/pfizer/covidadmitted/time*.svg
trendpng: output/over80s/any_immunosuppression/pfizer/covidadmitted/time*.png

model_over80s_any_immunosuppression_az_covidadmitted:
run: r:latest analysis/R/dose_1/model_msm.R over80s any_immunosuppression az covidadmitted
needs:
- design
- data_stset_over80s
- data_samples_over80s
outputs:
highly_sensitive:
models: output/over80s/any_immunosuppression/az/covidadmitted/model*.rds
data: output/over80s/any_immunosuppression/az/covidadmitted/data*.rds
moderately_sensitive:
weights: output/over80s/any_immunosuppression/az/covidadmitted/weights*

report_ipw_over80s_any_immunosuppression_az_covidadmitted:
run: r:latest analysis/R/dose_1/report_ipw.R over80s any_immunosuppression az
covidadmitted
needs:
- design
- model_over80s_any_immunosuppression_az_covidadmitted
outputs:
highly_sensitive:
broom: output/over80s/any_immunosuppression/az/covidadmitted/broom*.rds
moderately_sensitive:
data: output/over80s/any_immunosuppression/az/covidadmitted/broom*.csv

report_msm_over80s_any_immunosuppression_az_covidadmitted:
run: r:latest analysis/R/dose_1/report_msm.R over80s any_immunosuppression az
covidadmitted
needs:
- design
- model_over80s_any_immunosuppression_az_covidadmitted
outputs:
moderately_sensitive:
svg: output/over80s/any_immunosuppression/az/covidadmitted/VE_plot.svg
png: output/over80s/any_immunosuppression/az/covidadmitted/VE_plot.png
tables: output/over80s/any_immunosuppression/az/covidadmitted/estimates*.csv

report_incidence_over80s_any_immunosuppression_az_covidadmitted:
run: r:latest analysis/R/dose_1/report_incidence.R over80s any_immunosuppression
az covidadmitted
needs:
- design
- model_over80s_any_immunosuppression_az_covidadmitted
outputs:
highly_sensitive:
data: output/over80s/any_immunosuppression/az/covidadmitted/data_incidence.rds
moderately_sensitive:
cmlsvg: output/over80s/any_immunosuppression/az/covidadmitted/cml_incidence*.svg
cmlpng: output/over80s/any_immunosuppression/az/covidadmitted/cml_incidence*.png
trendsvg: output/over80s/any_immunosuppression/az/covidadmitted/time*.svg
trendpng: output/over80s/any_immunosuppression/az/covidadmitted/time*.png

model_over80s_any_immunosuppression_any_coviddeath:
run: r:latest analysis/R/dose_1/model_msm.R over80s any_immunosuppression any
coviddeath
needs:
- design
- data_stset_over80s
- data_samples_over80s
outputs:
highly_sensitive:
models: output/over80s/any_immunosuppression/any/coviddeath/model*.rds
data: output/over80s/any_immunosuppression/any/coviddeath/data*.rds
moderately_sensitive:
weights: output/over80s/any_immunosuppression/any/coviddeath/weights*

report_ipw_over80s_any_immunosuppression_any_coviddeath:
run: r:latest analysis/R/dose_1/report_ipw.R over80s any_immunosuppression any
coviddeath
needs:
- design
- model_over80s_any_immunosuppression_any_coviddeath
outputs:
highly_sensitive:
broom: output/over80s/any_immunosuppression/any/coviddeath/broom*.rds
moderately_sensitive:
data: output/over80s/any_immunosuppression/any/coviddeath/broom*.csv

report_msm_over80s_any_immunosuppression_any_coviddeath:
run: r:latest analysis/R/dose_1/report_msm.R over80s any_immunosuppression any
coviddeath
needs:
- design
- model_over80s_any_immunosuppression_any_coviddeath
outputs:
moderately_sensitive:
svg: output/over80s/any_immunosuppression/any/coviddeath/VE_plot.svg
png: output/over80s/any_immunosuppression/any/coviddeath/VE_plot.png
tables: output/over80s/any_immunosuppression/any/coviddeath/estimates*.csv

report_incidence_over80s_any_immunosuppression_any_coviddeath:
run: r:latest analysis/R/dose_1/report_incidence.R over80s any_immunosuppression
any coviddeath
needs:
- design
- model_over80s_any_immunosuppression_any_coviddeath
outputs:
highly_sensitive:
data: output/over80s/any_immunosuppression/any/coviddeath/data_incidence.rds
moderately_sensitive:
cmlsvg: output/over80s/any_immunosuppression/any/coviddeath/cml_incidence*.svg
cmlpng: output/over80s/any_immunosuppression/any/coviddeath/cml_incidence*.png
trendsvg: output/over80s/any_immunosuppression/any/coviddeath/time*.svg
trendpng: output/over80s/any_immunosuppression/any/coviddeath/time*.png

model_over80s_any_immunosuppression_pfizer_coviddeath:
run: r:latest analysis/R/dose_1/model_msm.R over80s any_immunosuppression pfizer
coviddeath
needs:
- design
- data_stset_over80s
- data_samples_over80s
outputs:
highly_sensitive:
models: output/over80s/any_immunosuppression/pfizer/coviddeath/model*.rds
data: output/over80s/any_immunosuppression/pfizer/coviddeath/data*.rds
moderately_sensitive:
weights: output/over80s/any_immunosuppression/pfizer/coviddeath/weights*

report_ipw_over80s_any_immunosuppression_pfizer_coviddeath:
run: r:latest analysis/R/dose_1/report_ipw.R over80s any_immunosuppression pfizer
coviddeath
needs:
- design
- model_over80s_any_immunosuppression_pfizer_coviddeath
outputs:
highly_sensitive:
broom: output/over80s/any_immunosuppression/pfizer/coviddeath/broom*.rds
moderately_sensitive:
data: output/over80s/any_immunosuppression/pfizer/coviddeath/broom*.csv

report_msm_over80s_any_immunosuppression_pfizer_coviddeath:
run: r:latest analysis/R/dose_1/report_msm.R over80s any_immunosuppression pfizer
coviddeath
needs:
- design
- model_over80s_any_immunosuppression_pfizer_coviddeath
outputs:
moderately_sensitive:
svg: output/over80s/any_immunosuppression/pfizer/coviddeath/VE_plot.svg
png: output/over80s/any_immunosuppression/pfizer/coviddeath/VE_plot.png
tables: output/over80s/any_immunosuppression/pfizer/coviddeath/estimates*.csv

report_incidence_over80s_any_immunosuppression_pfizer_coviddeath:
run: r:latest analysis/R/dose_1/report_incidence.R over80s any_immunosuppression
pfizer coviddeath
needs:
- design
- model_over80s_any_immunosuppression_pfizer_coviddeath
outputs:
highly_sensitive:
data: output/over80s/any_immunosuppression/pfizer/coviddeath/data_incidence.rds
moderately_sensitive:
cmlsvg: output/over80s/any_immunosuppression/pfizer/coviddeath/cml_incidence*.svg
cmlpng: output/over80s/any_immunosuppression/pfizer/coviddeath/cml_incidence*.png
trendsvg: output/over80s/any_immunosuppression/pfizer/coviddeath/time*.svg
trendpng: output/over80s/any_immunosuppression/pfizer/coviddeath/time*.png

model_over80s_any_immunosuppression_az_coviddeath:
run: r:latest analysis/R/dose_1/model_msm.R over80s any_immunosuppression az coviddeath
needs:
- design
- data_stset_over80s
- data_samples_over80s
outputs:
highly_sensitive:
models: output/over80s/any_immunosuppression/az/coviddeath/model*.rds
data: output/over80s/any_immunosuppression/az/coviddeath/data*.rds
moderately_sensitive:
weights: output/over80s/any_immunosuppression/az/coviddeath/weights*

report_ipw_over80s_any_immunosuppression_az_coviddeath:
run: r:latest analysis/R/dose_1/report_ipw.R over80s any_immunosuppression az
coviddeath
needs:
- design
- model_over80s_any_immunosuppression_az_coviddeath
outputs:
highly_sensitive:
broom: output/over80s/any_immunosuppression/az/coviddeath/broom*.rds
moderately_sensitive:
data: output/over80s/any_immunosuppression/az/coviddeath/broom*.csv

report_msm_over80s_any_immunosuppression_az_coviddeath:
run: r:latest analysis/R/dose_1/report_msm.R over80s any_immunosuppression az
coviddeath
needs:
- design
- model_over80s_any_immunosuppression_az_coviddeath
outputs:
moderately_sensitive:
svg: output/over80s/any_immunosuppression/az/coviddeath/VE_plot.svg
png: output/over80s/any_immunosuppression/az/coviddeath/VE_plot.png
tables: output/over80s/any_immunosuppression/az/coviddeath/estimates*.csv

report_incidence_over80s_any_immunosuppression_az_coviddeath:
run: r:latest analysis/R/dose_1/report_incidence.R over80s any_immunosuppression
az coviddeath
needs:
- design
- model_over80s_any_immunosuppression_az_coviddeath
outputs:
highly_sensitive:
data: output/over80s/any_immunosuppression/az/coviddeath/data_incidence.rds
moderately_sensitive:
cmlsvg: output/over80s/any_immunosuppression/az/coviddeath/cml_incidence*.svg
cmlpng: output/over80s/any_immunosuppression/az/coviddeath/cml_incidence*.png
trendsvg: output/over80s/any_immunosuppression/az/coviddeath/time*.svg
trendpng: output/over80s/any_immunosuppression/az/coviddeath/time*.png

model_over80s_any_immunosuppression_any_noncoviddeath:
run: r:latest analysis/R/dose_1/model_msm.R over80s any_immunosuppression any
noncoviddeath
needs:
- design
- data_stset_over80s
- data_samples_over80s
outputs:
highly_sensitive:
models: output/over80s/any_immunosuppression/any/noncoviddeath/model*.rds
data: output/over80s/any_immunosuppression/any/noncoviddeath/data*.rds
moderately_sensitive:
weights: output/over80s/any_immunosuppression/any/noncoviddeath/weights*

report_ipw_over80s_any_immunosuppression_any_noncoviddeath:
run: r:latest analysis/R/dose_1/report_ipw.R over80s any_immunosuppression any
noncoviddeath
needs:
- design
- model_over80s_any_immunosuppression_any_noncoviddeath
outputs:
highly_sensitive:
broom: output/over80s/any_immunosuppression/any/noncoviddeath/broom*.rds
moderately_sensitive:
data: output/over80s/any_immunosuppression/any/noncoviddeath/broom*.csv

report_msm_over80s_any_immunosuppression_any_noncoviddeath:
run: r:latest analysis/R/dose_1/report_msm.R over80s any_immunosuppression any
noncoviddeath
needs:
- design
- model_over80s_any_immunosuppression_any_noncoviddeath
outputs:
moderately_sensitive:
svg: output/over80s/any_immunosuppression/any/noncoviddeath/VE_plot.svg
png: output/over80s/any_immunosuppression/any/noncoviddeath/VE_plot.png
tables: output/over80s/any_immunosuppression/any/noncoviddeath/estimates*.csv

report_incidence_over80s_any_immunosuppression_any_noncoviddeath:
run: r:latest analysis/R/dose_1/report_incidence.R over80s any_immunosuppression
any noncoviddeath
needs:
- design
- model_over80s_any_immunosuppression_any_noncoviddeath
outputs:
highly_sensitive:
data: output/over80s/any_immunosuppression/any/noncoviddeath/data_incidence.rds
moderately_sensitive:
cmlsvg: output/over80s/any_immunosuppression/any/noncoviddeath/cml_incidence*.svg
cmlpng: output/over80s/any_immunosuppression/any/noncoviddeath/cml_incidence*.png
trendsvg: output/over80s/any_immunosuppression/any/noncoviddeath/time*.svg
trendpng: output/over80s/any_immunosuppression/any/noncoviddeath/time*.png

model_over80s_any_immunosuppression_pfizer_noncoviddeath:
run: r:latest analysis/R/dose_1/model_msm.R over80s any_immunosuppression pfizer
noncoviddeath
needs:
- design
- data_stset_over80s
- data_samples_over80s
outputs:
highly_sensitive:
models: output/over80s/any_immunosuppression/pfizer/noncoviddeath/model*.rds
data: output/over80s/any_immunosuppression/pfizer/noncoviddeath/data*.rds
moderately_sensitive:
weights: output/over80s/any_immunosuppression/pfizer/noncoviddeath/weights*

report_ipw_over80s_any_immunosuppression_pfizer_noncoviddeath:
run: r:latest analysis/R/dose_1/report_ipw.R over80s any_immunosuppression pfizer
noncoviddeath
needs:
- design
- model_over80s_any_immunosuppression_pfizer_noncoviddeath
outputs:
highly_sensitive:
broom: output/over80s/any_immunosuppression/pfizer/noncoviddeath/broom*.rds
moderately_sensitive:
data: output/over80s/any_immunosuppression/pfizer/noncoviddeath/broom*.csv

report_msm_over80s_any_immunosuppression_pfizer_noncoviddeath:
run: r:latest analysis/R/dose_1/report_msm.R over80s any_immunosuppression pfizer
noncoviddeath
needs:
- design
- model_over80s_any_immunosuppression_pfizer_noncoviddeath
outputs:
moderately_sensitive:
svg: output/over80s/any_immunosuppression/pfizer/noncoviddeath/VE_plot.svg
png: output/over80s/any_immunosuppression/pfizer/noncoviddeath/VE_plot.png
tables: output/over80s/any_immunosuppression/pfizer/noncoviddeath/estimates*.csv

report_incidence_over80s_any_immunosuppression_pfizer_noncoviddeath:
run: r:latest analysis/R/dose_1/report_incidence.R over80s any_immunosuppression
pfizer noncoviddeath
needs:
- design
- model_over80s_any_immunosuppression_pfizer_noncoviddeath
outputs:
highly_sensitive:
data: output/over80s/any_immunosuppression/pfizer/noncoviddeath/data_incidence.rds
moderately_sensitive:
cmlsvg: output/over80s/any_immunosuppression/pfizer/noncoviddeath/cml_incidence*.svg
cmlpng: output/over80s/any_immunosuppression/pfizer/noncoviddeath/cml_incidence*.png
trendsvg: output/over80s/any_immunosuppression/pfizer/noncoviddeath/time*.svg
trendpng: output/over80s/any_immunosuppression/pfizer/noncoviddeath/time*.png

model_over80s_any_immunosuppression_az_noncoviddeath:
run: r:latest analysis/R/dose_1/model_msm.R over80s any_immunosuppression az noncoviddeath
needs:
- design
- data_stset_over80s
- data_samples_over80s
outputs:
highly_sensitive:
models: output/over80s/any_immunosuppression/az/noncoviddeath/model*.rds
data: output/over80s/any_immunosuppression/az/noncoviddeath/data*.rds
moderately_sensitive:
weights: output/over80s/any_immunosuppression/az/noncoviddeath/weights*

report_ipw_over80s_any_immunosuppression_az_noncoviddeath:
run: r:latest analysis/R/dose_1/report_ipw.R over80s any_immunosuppression az
noncoviddeath
needs:
- design
- model_over80s_any_immunosuppression_az_noncoviddeath
outputs:
highly_sensitive:
broom: output/over80s/any_immunosuppression/az/noncoviddeath/broom*.rds
moderately_sensitive:
data: output/over80s/any_immunosuppression/az/noncoviddeath/broom*.csv

report_msm_over80s_any_immunosuppression_az_noncoviddeath:
run: r:latest analysis/R/dose_1/report_msm.R over80s any_immunosuppression az
noncoviddeath
needs:
- design
- model_over80s_any_immunosuppression_az_noncoviddeath
outputs:
moderately_sensitive:
svg: output/over80s/any_immunosuppression/az/noncoviddeath/VE_plot.svg
png: output/over80s/any_immunosuppression/az/noncoviddeath/VE_plot.png
tables: output/over80s/any_immunosuppression/az/noncoviddeath/estimates*.csv

report_incidence_over80s_any_immunosuppression_az_noncoviddeath:
run: r:latest analysis/R/dose_1/report_incidence.R over80s any_immunosuppression
az noncoviddeath
needs:
- design
- model_over80s_any_immunosuppression_az_noncoviddeath
outputs:
highly_sensitive:
data: output/over80s/any_immunosuppression/az/noncoviddeath/data_incidence.rds
moderately_sensitive:
cmlsvg: output/over80s/any_immunosuppression/az/noncoviddeath/cml_incidence*.svg
cmlpng: output/over80s/any_immunosuppression/az/noncoviddeath/cml_incidence*.png
trendsvg: output/over80s/any_immunosuppression/az/noncoviddeath/time*.svg
trendpng: output/over80s/any_immunosuppression/az/noncoviddeath/time*.png

model_over80s_any_immunosuppression_any_death:
run: r:latest analysis/R/dose_1/model_msm.R over80s any_immunosuppression any
death
needs:
- design
- data_stset_over80s
- data_samples_over80s
outputs:
highly_sensitive:
models: output/over80s/any_immunosuppression/any/death/model*.rds
data: output/over80s/any_immunosuppression/any/death/data*.rds
moderately_sensitive:
weights: output/over80s/any_immunosuppression/any/death/weights*

report_ipw_over80s_any_immunosuppression_any_death:
run: r:latest analysis/R/dose_1/report_ipw.R over80s any_immunosuppression any
death
needs:
- design
- model_over80s_any_immunosuppression_any_death
outputs:
highly_sensitive:
broom: output/over80s/any_immunosuppression/any/death/broom*.rds
moderately_sensitive:
data: output/over80s/any_immunosuppression/any/death/broom*.csv

report_msm_over80s_any_immunosuppression_any_death:
run: r:latest analysis/R/dose_1/report_msm.R over80s any_immunosuppression any
death
needs:
- design
- model_over80s_any_immunosuppression_any_death
outputs:
moderately_sensitive:
svg: output/over80s/any_immunosuppression/any/death/VE_plot.svg
png: output/over80s/any_immunosuppression/any/death/VE_plot.png
tables: output/over80s/any_immunosuppression/any/death/estimates*.csv

report_incidence_over80s_any_immunosuppression_any_death:
run: r:latest analysis/R/dose_1/report_incidence.R over80s any_immunosuppression
any death
needs:
- design
- model_over80s_any_immunosuppression_any_death
outputs:
highly_sensitive:
data: output/over80s/any_immunosuppression/any/death/data_incidence.rds
moderately_sensitive:
cmlsvg: output/over80s/any_immunosuppression/any/death/cml_incidence*.svg
cmlpng: output/over80s/any_immunosuppression/any/death/cml_incidence*.png
trendsvg: output/over80s/any_immunosuppression/any/death/time*.svg
trendpng: output/over80s/any_immunosuppression/any/death/time*.png

model_over80s_any_immunosuppression_pfizer_death:
run: r:latest analysis/R/dose_1/model_msm.R over80s any_immunosuppression pfizer
death
needs:
- design
- data_stset_over80s
- data_samples_over80s
outputs:
highly_sensitive:
models: output/over80s/any_immunosuppression/pfizer/death/model*.rds
data: output/over80s/any_immunosuppression/pfizer/death/data*.rds
moderately_sensitive:
weights: output/over80s/any_immunosuppression/pfizer/death/weights*

report_ipw_over80s_any_immunosuppression_pfizer_death:
run: r:latest analysis/R/dose_1/report_ipw.R over80s any_immunosuppression pfizer
death
needs:
- design
- model_over80s_any_immunosuppression_pfizer_death
outputs:
highly_sensitive:
broom: output/over80s/any_immunosuppression/pfizer/death/broom*.rds
moderately_sensitive:
data: output/over80s/any_immunosuppression/pfizer/death/broom*.csv

report_msm_over80s_any_immunosuppression_pfizer_death:
run: r:latest analysis/R/dose_1/report_msm.R over80s any_immunosuppression pfizer
death
needs:
- design
- model_over80s_any_immunosuppression_pfizer_death
outputs:
moderately_sensitive:
svg: output/over80s/any_immunosuppression/pfizer/death/VE_plot.svg
png: output/over80s/any_immunosuppression/pfizer/death/VE_plot.png
tables: output/over80s/any_immunosuppression/pfizer/death/estimates*.csv

report_incidence_over80s_any_immunosuppression_pfizer_death:
run: r:latest analysis/R/dose_1/report_incidence.R over80s any_immunosuppression
pfizer death
needs:
- design
- model_over80s_any_immunosuppression_pfizer_death
outputs:
highly_sensitive:
data: output/over80s/any_immunosuppression/pfizer/death/data_incidence.rds
moderately_sensitive:
cmlsvg: output/over80s/any_immunosuppression/pfizer/death/cml_incidence*.svg
cmlpng: output/over80s/any_immunosuppression/pfizer/death/cml_incidence*.png
trendsvg: output/over80s/any_immunosuppression/pfizer/death/time*.svg
trendpng: output/over80s/any_immunosuppression/pfizer/death/time*.png

model_over80s_any_immunosuppression_az_death:
run: r:latest analysis/R/dose_1/model_msm.R over80s any_immunosuppression az death
needs:
- design
- data_stset_over80s
- data_samples_over80s
outputs:
highly_sensitive:
models: output/over80s/any_immunosuppression/az/death/model*.rds
data: output/over80s/any_immunosuppression/az/death/data*.rds
moderately_sensitive:
weights: output/over80s/any_immunosuppression/az/death/weights*

report_ipw_over80s_any_immunosuppression_az_death:
run: r:latest analysis/R/dose_1/report_ipw.R over80s any_immunosuppression az
death
needs:
- design
- model_over80s_any_immunosuppression_az_death
outputs:
highly_sensitive:
broom: output/over80s/any_immunosuppression/az/death/broom*.rds
moderately_sensitive:
data: output/over80s/any_immunosuppression/az/death/broom*.csv

report_msm_over80s_any_immunosuppression_az_death:
run: r:latest analysis/R/dose_1/report_msm.R over80s any_immunosuppression az
death
needs:
- design
- model_over80s_any_immunosuppression_az_death
outputs:
moderately_sensitive:
svg: output/over80s/any_immunosuppression/az/death/VE_plot.svg
png: output/over80s/any_immunosuppression/az/death/VE_plot.png
tables: output/over80s/any_immunosuppression/az/death/estimates*.csv

report_incidence_over80s_any_immunosuppression_az_death:
run: r:latest analysis/R/dose_1/report_incidence.R over80s any_immunosuppression
az death
needs:
- design
- model_over80s_any_immunosuppression_az_death
outputs:
highly_sensitive:
data: output/over80s/any_immunosuppression/az/death/data_incidence.rds
moderately_sensitive:
cmlsvg: output/over80s/any_immunosuppression/az/death/cml_incidence*.svg
cmlpng: output/over80s/any_immunosuppression/az/death/cml_incidence*.png
trendsvg: output/over80s/any_immunosuppression/az/death/time*.svg
trendpng: output/over80s/any_immunosuppression/az/death/time*.png

report_ipw_over80s_any_immunosuppression:
run: r:latest analysis/R/dose_1/report_ipw_combined.R over80s any_immunosuppression
death
needs:
- design
- report_ipw_over80s_any_immunosuppression_any_death
- report_ipw_over80s_any_immunosuppression_pfizer_death
- report_ipw_over80s_any_immunosuppression_az_death
outputs:
moderately_sensitive:
svg: output/over80s/any_immunosuppression/combined/plot_vax1.svg
csv: output/over80s/any_immunosuppression/combined/tab_vax1.csv
csv_wide: output/over80s/any_immunosuppression/combined/tab_vax1_wide.csv

report_msm_over80s_any_immunosuppression:
run: r:latest analysis/R/dose_1/report_msm_combined.R over80s any_immunosuppression
needs:
- design
- report_msm_over80s_any_immunosuppression_any_postest
- report_msm_over80s_any_immunosuppression_any_covidadmitted
- report_msm_over80s_any_immunosuppression_any_coviddeath
- report_msm_over80s_any_immunosuppression_any_noncoviddeath
- report_msm_over80s_any_immunosuppression_pfizer_postest
- report_msm_over80s_any_immunosuppression_pfizer_covidadmitted
- report_msm_over80s_any_immunosuppression_pfizer_coviddeath
- report_msm_over80s_any_immunosuppression_pfizer_noncoviddeath
- report_msm_over80s_any_immunosuppression_az_postest
- report_msm_over80s_any_immunosuppression_az_covidadmitted
- report_msm_over80s_any_immunosuppression_az_coviddeath
- report_msm_over80s_any_immunosuppression_az_noncoviddeath
outputs:
moderately_sensitive:
svg: output/over80s/any_immunosuppression/combined/VE*.svg
png: output/over80s/any_immunosuppression/combined/VE*.png
csv: output/over80s/any_immunosuppression/combined/*.csv

report_incidence_over80s_any_immunosuppression:
run: r:latest analysis/R/dose_1/report_incidence_combined.R over80s any_immunosuppression
needs:
- design
- report_incidence_over80s_any_immunosuppression_any_postest
- report_incidence_over80s_any_immunosuppression_any_covidadmitted
- report_incidence_over80s_any_immunosuppression_any_coviddeath
- report_incidence_over80s_any_immunosuppression_any_noncoviddeath
- report_incidence_over80s_any_immunosuppression_pfizer_postest
- report_incidence_over80s_any_immunosuppression_pfizer_covidadmitted
- report_incidence_over80s_any_immunosuppression_pfizer_coviddeath
- report_incidence_over80s_any_immunosuppression_pfizer_noncoviddeath
- report_incidence_over80s_any_immunosuppression_az_postest
- report_incidence_over80s_any_immunosuppression_az_covidadmitted
- report_incidence_over80s_any_immunosuppression_az_coviddeath
- report_incidence_over80s_any_immunosuppression_az_noncoviddeath
outputs:
moderately_sensitive:
svg: output/over80s/any_immunosuppression/combined/cml_incidence*.svg
png: output/over80s/any_immunosuppression/combined/cml_incidence*.png

## ####################################
## in70s
## ####################################

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

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
datavaxlong: output/in70s/data/data_long_vax_dates.rds
datavaxwide: output/in70s/data/data_wide_vax_dates.rds

data_process_long_in70s:
run: r:latest analysis/R/data_process_long.R in70s
needs:
- data_process_in70s
outputs:
highly_sensitive:
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

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:
txt: 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:
cohort: output/in70s/data/data_cohort.rds
moderately_sensitive:
flow: output/in70s/data/flowchart.csv

data_stset_in70s:
run: r:latest analysis/R/data_stset.R in70s
needs:
- design
- data_selection_in70s
- data_process_long_in70s
outputs:
highly_sensitive:
fixed: output/in70s/data/data_fixed.rds
tte: output/in70s/data/data_tte.rds
pt: 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

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

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_tableirrold_in70s:
run: r:latest analysis/R/descr_tableirr.R in70s FALSE
needs:
- design
- data_selection_in70s
outputs:
moderately_sensitive:
html: output/in70s/descriptive/tables/table_irr_old.html
csv: output/in70s/descriptive/tables/table_irr_old.csv

descr_tableirr_in70s:
run: r:latest analysis/R/descr_tableirr_lite.R in70s FALSE
needs:
- design
- data_selection_in70s
outputs:
moderately_sensitive:
html: output/in70s/descriptive/tables/table_irr.html
csv: output/in70s/descriptive/tables/table_irr.csv

descr_tableirr_exclude_in70s:
run: r:latest analysis/R/descr_tableirr_lite.R in70s TRUE
needs:
- design
- data_selection_in70s
outputs:
moderately_sensitive:
html: output/in70s/descriptive/tables/table_irr_exclude_recentpostest.html
csv: output/in70s/descriptive/tables/table_irr_exclude_recentpostest.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

## ####################################
## all
## ####################################

model_in70s_all_any_postest:
run: r:latest analysis/R/dose_1/model_msm.R in70s all any postest
needs:
- design
- data_stset_in70s
- data_samples_in70s
outputs:
highly_sensitive:
models: output/in70s/all/any/postest/model*.rds
data: output/in70s/all/any/postest/data*.rds
moderately_sensitive:
weights: output/in70s/all/any/postest/weights*

report_ipw_in70s_all_any_postest:
run: r:latest analysis/R/dose_1/report_ipw.R in70s all any postest
needs:
- design
- model_in70s_all_any_postest
outputs:
highly_sensitive:
broom: output/in70s/all/any/postest/broom*.rds
moderately_sensitive:
data: output/in70s/all/any/postest/broom*.csv

report_msm_in70s_all_any_postest:
run: r:latest analysis/R/dose_1/report_msm.R in70s all any postest
needs:
- design
- model_in70s_all_any_postest
outputs:
moderately_sensitive:
svg: output/in70s/all/any/postest/VE_plot.svg
png: output/in70s/all/any/postest/VE_plot.png
tables: output/in70s/all/any/postest/estimates*.csv

report_incidence_in70s_all_any_postest:
run: r:latest analysis/R/dose_1/report_incidence.R in70s all any postest
needs:
- design
- model_in70s_all_any_postest
outputs:
highly_sensitive:
data: output/in70s/all/any/postest/data_incidence.rds
moderately_sensitive:
cmlsvg: output/in70s/all/any/postest/cml_incidence*.svg
cmlpng: output/in70s/all/any/postest/cml_incidence*.png
trendsvg: output/in70s/all/any/postest/time*.svg
trendpng: output/in70s/all/any/postest/time*.png

model_in70s_all_pfizer_postest:
run: r:latest analysis/R/dose_1/model_msm.R in70s all pfizer postest
needs:
- design
- data_stset_in70s
- data_samples_in70s
outputs:
highly_sensitive:
models: output/in70s/all/pfizer/postest/model*.rds
data: output/in70s/all/pfizer/postest/data*.rds
moderately_sensitive:
weights: output/in70s/all/pfizer/postest/weights*

report_ipw_in70s_all_pfizer_postest:
run: r:latest analysis/R/dose_1/report_ipw.R in70s all pfizer postest
needs:
- design
- model_in70s_all_pfizer_postest
outputs:
highly_sensitive:
broom: output/in70s/all/pfizer/postest/broom*.rds
moderately_sensitive:
data: output/in70s/all/pfizer/postest/broom*.csv

report_msm_in70s_all_pfizer_postest:
run: r:latest analysis/R/dose_1/report_msm.R in70s all pfizer postest
needs:
- design
- model_in70s_all_pfizer_postest
outputs:
moderately_sensitive:
svg: output/in70s/all/pfizer/postest/VE_plot.svg
png: output/in70s/all/pfizer/postest/VE_plot.png
tables: output/in70s/all/pfizer/postest/estimates*.csv

report_incidence_in70s_all_pfizer_postest:
run: r:latest analysis/R/dose_1/report_incidence.R in70s all pfizer postest
needs:
- design
- model_in70s_all_pfizer_postest
outputs:
highly_sensitive:
data: output/in70s/all/pfizer/postest/data_incidence.rds
moderately_sensitive:
cmlsvg: output/in70s/all/pfizer/postest/cml_incidence*.svg
cmlpng: output/in70s/all/pfizer/postest/cml_incidence*.png
trendsvg: output/in70s/all/pfizer/postest/time*.svg
trendpng: output/in70s/all/pfizer/postest/time*.png

model_in70s_all_az_postest:
run: r:latest analysis/R/dose_1/model_msm.R in70s all az postest
needs:
- design
- data_stset_in70s
- data_samples_in70s
outputs:
highly_sensitive:
models: output/in70s/all/az/postest/model*.rds
data: output/in70s/all/az/postest/data*.rds
moderately_sensitive:
weights: output/in70s/all/az/postest/weights*

report_ipw_in70s_all_az_postest:
run: r:latest analysis/R/dose_1/report_ipw.R in70s all az postest
needs:
- design
- model_in70s_all_az_postest
outputs:
highly_sensitive:
broom: output/in70s/all/az/postest/broom*.rds
moderately_sensitive:
data: output/in70s/all/az/postest/broom*.csv

report_msm_in70s_all_az_postest:
run: r:latest analysis/R/dose_1/report_msm.R in70s all az postest
needs:
- design
- model_in70s_all_az_postest
outputs:
moderately_sensitive:
svg: output/in70s/all/az/postest/VE_plot.svg
png: output/in70s/all/az/postest/VE_plot.png
tables: output/in70s/all/az/postest/estimates*.csv

report_incidence_in70s_all_az_postest:
run: r:latest analysis/R/dose_1/report_incidence.R in70s all az postest
needs:
- design
- model_in70s_all_az_postest
outputs:
highly_sensitive:
data: output/in70s/all/az/postest/data_incidence.rds
moderately_sensitive:
cmlsvg: output/in70s/all/az/postest/cml_incidence*.svg
cmlpng: output/in70s/all/az/postest/cml_incidence*.png
trendsvg: output/in70s/all/az/postest/time*.svg
trendpng: output/in70s/all/az/postest/time*.png

model_in70s_all_any_covidadmitted:
run: r:latest analysis/R/dose_1/model_msm.R in70s all any covidadmitted
needs:
- design
- data_stset_in70s
- data_samples_in70s
outputs:
highly_sensitive:
models: output/in70s/all/any/covidadmitted/model*.rds
data: output/in70s/all/any/covidadmitted/data*.rds
moderately_sensitive:
weights: output/in70s/all/any/covidadmitted/weights*

report_ipw_in70s_all_any_covidadmitted:
run: r:latest analysis/R/dose_1/report_ipw.R in70s all any covidadmitted
needs:
- design
- model_in70s_all_any_covidadmitted
outputs:
highly_sensitive:
broom: output/in70s/all/any/covidadmitted/broom*.rds
moderately_sensitive:
data: output/in70s/all/any/covidadmitted/broom*.csv

report_msm_in70s_all_any_covidadmitted:
run: r:latest analysis/R/dose_1/report_msm.R in70s all any covidadmitted
needs:
- design
- model_in70s_all_any_covidadmitted
outputs:
moderately_sensitive:
svg: output/in70s/all/any/covidadmitted/VE_plot.svg
png: output/in70s/all/any/covidadmitted/VE_plot.png
tables: output/in70s/all/any/covidadmitted/estimates*.csv

report_incidence_in70s_all_any_covidadmitted:
run: r:latest analysis/R/dose_1/report_incidence.R in70s all any covidadmitted
needs:
- design
- model_in70s_all_any_covidadmitted
outputs:
highly_sensitive:
data: output/in70s/all/any/covidadmitted/data_incidence.rds
moderately_sensitive:
cmlsvg: output/in70s/all/any/covidadmitted/cml_incidence*.svg
cmlpng: output/in70s/all/any/covidadmitted/cml_incidence*.png
trendsvg: output/in70s/all/any/covidadmitted/time*.svg
trendpng: output/in70s/all/any/covidadmitted/time*.png

model_in70s_all_pfizer_covidadmitted:
run: r:latest analysis/R/dose_1/model_msm.R in70s all pfizer covidadmitted
needs:
- design
- data_stset_in70s
- data_samples_in70s
outputs:
highly_sensitive:
models: output/in70s/all/pfizer/covidadmitted/model*.rds
data: output/in70s/all/pfizer/covidadmitted/data*.rds
moderately_sensitive:
weights: output/in70s/all/pfizer/covidadmitted/weights*

report_ipw_in70s_all_pfizer_covidadmitted:
run: r:latest analysis/R/dose_1/report_ipw.R in70s all pfizer covidadmitted
needs:
- design
- model_in70s_all_pfizer_covidadmitted
outputs:
highly_sensitive:
broom: output/in70s/all/pfizer/covidadmitted/broom*.rds
moderately_sensitive:
data: output/in70s/all/pfizer/covidadmitted/broom*.csv

report_msm_in70s_all_pfizer_covidadmitted:
run: r:latest analysis/R/dose_1/report_msm.R in70s all pfizer covidadmitted
needs:
- design
- model_in70s_all_pfizer_covidadmitted
outputs:
moderately_sensitive:
svg: output/in70s/all/pfizer/covidadmitted/VE_plot.svg
png: output/in70s/all/pfizer/covidadmitted/VE_plot.png
tables: output/in70s/all/pfizer/covidadmitted/estimates*.csv

report_incidence_in70s_all_pfizer_covidadmitted:
run: r:latest analysis/R/dose_1/report_incidence.R in70s all pfizer covidadmitted
needs:
- design
- model_in70s_all_pfizer_covidadmitted
outputs:
highly_sensitive:
data: output/in70s/all/pfizer/covidadmitted/data_incidence.rds
moderately_sensitive:
cmlsvg: output/in70s/all/pfizer/covidadmitted/cml_incidence*.svg
cmlpng: output/in70s/all/pfizer/covidadmitted/cml_incidence*.png
trendsvg: output/in70s/all/pfizer/covidadmitted/time*.svg
trendpng: output/in70s/all/pfizer/covidadmitted/time*.png

model_in70s_all_az_covidadmitted:
run: r:latest analysis/R/dose_1/model_msm.R in70s all az covidadmitted
needs:
- design
- data_stset_in70s
- data_samples_in70s
outputs:
highly_sensitive:
models: output/in70s/all/az/covidadmitted/model*.rds
data: output/in70s/all/az/covidadmitted/data*.rds
moderately_sensitive:
weights: output/in70s/all/az/covidadmitted/weights*

report_ipw_in70s_all_az_covidadmitted:
run: r:latest analysis/R/dose_1/report_ipw.R in70s all az covidadmitted
needs:
- design
- model_in70s_all_az_covidadmitted
outputs:
highly_sensitive:
broom: output/in70s/all/az/covidadmitted/broom*.rds
moderately_sensitive:
data: output/in70s/all/az/covidadmitted/broom*.csv

report_msm_in70s_all_az_covidadmitted:
run: r:latest analysis/R/dose_1/report_msm.R in70s all az covidadmitted
needs:
- design
- model_in70s_all_az_covidadmitted
outputs:
moderately_sensitive:
svg: output/in70s/all/az/covidadmitted/VE_plot.svg
png: output/in70s/all/az/covidadmitted/VE_plot.png
tables: output/in70s/all/az/covidadmitted/estimates*.csv

report_incidence_in70s_all_az_covidadmitted:
run: r:latest analysis/R/dose_1/report_incidence.R in70s all az covidadmitted
needs:
- design
- model_in70s_all_az_covidadmitted
outputs:
highly_sensitive:
data: output/in70s/all/az/covidadmitted/data_incidence.rds
moderately_sensitive:
cmlsvg: output/in70s/all/az/covidadmitted/cml_incidence*.svg
cmlpng: output/in70s/all/az/covidadmitted/cml_incidence*.png
trendsvg: output/in70s/all/az/covidadmitted/time*.svg
trendpng: output/in70s/all/az/covidadmitted/time*.png

model_in70s_all_any_coviddeath:
run: r:latest analysis/R/dose_1/model_msm.R in70s all any coviddeath
needs:
- design
- data_stset_in70s
- data_samples_in70s
outputs:
highly_sensitive:
models: output/in70s/all/any/coviddeath/model*.rds
data: output/in70s/all/any/coviddeath/data*.rds
moderately_sensitive:
weights: output/in70s/all/any/coviddeath/weights*

report_ipw_in70s_all_any_coviddeath:
run: r:latest analysis/R/dose_1/report_ipw.R in70s all any coviddeath
needs:
- design
- model_in70s_all_any_coviddeath
outputs:
highly_sensitive:
broom: output/in70s/all/any/coviddeath/broom*.rds
moderately_sensitive:
data: output/in70s/all/any/coviddeath/broom*.csv

report_msm_in70s_all_any_coviddeath:
run: r:latest analysis/R/dose_1/report_msm.R in70s all any coviddeath
needs:
- design
- model_in70s_all_any_coviddeath
outputs:
moderately_sensitive:
svg: output/in70s/all/any/coviddeath/VE_plot.svg
png: output/in70s/all/any/coviddeath/VE_plot.png
tables: output/in70s/all/any/coviddeath/estimates*.csv

report_incidence_in70s_all_any_coviddeath:
run: r:latest analysis/R/dose_1/report_incidence.R in70s all any coviddeath
needs:
- design
- model_in70s_all_any_coviddeath
outputs:
highly_sensitive:
data: output/in70s/all/any/coviddeath/data_incidence.rds
moderately_sensitive:
cmlsvg: output/in70s/all/any/coviddeath/cml_incidence*.svg
cmlpng: output/in70s/all/any/coviddeath/cml_incidence*.png
trendsvg: output/in70s/all/any/coviddeath/time*.svg
trendpng: output/in70s/all/any/coviddeath/time*.png

model_in70s_all_pfizer_coviddeath:
run: r:latest analysis/R/dose_1/model_msm.R in70s all pfizer coviddeath
needs:
- design
- data_stset_in70s
- data_samples_in70s
outputs:
highly_sensitive:
models: output/in70s/all/pfizer/coviddeath/model*.rds
data: output/in70s/all/pfizer/coviddeath/data*.rds
moderately_sensitive:
weights: output/in70s/all/pfizer/coviddeath/weights*

report_ipw_in70s_all_pfizer_coviddeath:
run: r:latest analysis/R/dose_1/report_ipw.R in70s all pfizer coviddeath
needs:
- design
- model_in70s_all_pfizer_coviddeath
outputs:
highly_sensitive:
broom: output/in70s/all/pfizer/coviddeath/broom*.rds
moderately_sensitive:
data: output/in70s/all/pfizer/coviddeath/broom*.csv

report_msm_in70s_all_pfizer_coviddeath:
run: r:latest analysis/R/dose_1/report_msm.R in70s all pfizer coviddeath
needs:
- design
- model_in70s_all_pfizer_coviddeath
outputs:
moderately_sensitive:
svg: output/in70s/all/pfizer/coviddeath/VE_plot.svg
png: output/in70s/all/pfizer/coviddeath/VE_plot.png
tables: output/in70s/all/pfizer/coviddeath/estimates*.csv

report_incidence_in70s_all_pfizer_coviddeath:
run: r:latest analysis/R/dose_1/report_incidence.R in70s all pfizer coviddeath
needs:
- design
- model_in70s_all_pfizer_coviddeath
outputs:
highly_sensitive:
data: output/in70s/all/pfizer/coviddeath/data_incidence.rds
moderately_sensitive:
cmlsvg: output/in70s/all/pfizer/coviddeath/cml_incidence*.svg
cmlpng: output/in70s/all/pfizer/coviddeath/cml_incidence*.png
trendsvg: output/in70s/all/pfizer/coviddeath/time*.svg
trendpng: output/in70s/all/pfizer/coviddeath/time*.png

model_in70s_all_az_coviddeath:
run: r:latest analysis/R/dose_1/model_msm.R in70s all az coviddeath
needs:
- design
- data_stset_in70s
- data_samples_in70s
outputs:
highly_sensitive:
models: output/in70s/all/az/coviddeath/model*.rds
data: output/in70s/all/az/coviddeath/data*.rds
moderately_sensitive:
weights: output/in70s/all/az/coviddeath/weights*

report_ipw_in70s_all_az_coviddeath:
run: r:latest analysis/R/dose_1/report_ipw.R in70s all az coviddeath
needs:
- design
- model_in70s_all_az_coviddeath
outputs:
highly_sensitive:
broom: output/in70s/all/az/coviddeath/broom*.rds
moderately_sensitive:
data: output/in70s/all/az/coviddeath/broom*.csv

report_msm_in70s_all_az_coviddeath:
run: r:latest analysis/R/dose_1/report_msm.R in70s all az coviddeath
needs:
- design
- model_in70s_all_az_coviddeath
outputs:
moderately_sensitive:
svg: output/in70s/all/az/coviddeath/VE_plot.svg
png: output/in70s/all/az/coviddeath/VE_plot.png
tables: output/in70s/all/az/coviddeath/estimates*.csv

report_incidence_in70s_all_az_coviddeath:
run: r:latest analysis/R/dose_1/report_incidence.R in70s all az coviddeath
needs:
- design
- model_in70s_all_az_coviddeath
outputs:
highly_sensitive:
data: output/in70s/all/az/coviddeath/data_incidence.rds
moderately_sensitive:
cmlsvg: output/in70s/all/az/coviddeath/cml_incidence*.svg
cmlpng: output/in70s/all/az/coviddeath/cml_incidence*.png
trendsvg: output/in70s/all/az/coviddeath/time*.svg
trendpng: output/in70s/all/az/coviddeath/time*.png

model_in70s_all_any_noncoviddeath:
run: r:latest analysis/R/dose_1/model_msm.R in70s all any noncoviddeath
needs:
- design
- data_stset_in70s
- data_samples_in70s
outputs:
highly_sensitive:
models: output/in70s/all/any/noncoviddeath/model*.rds
data: output/in70s/all/any/noncoviddeath/data*.rds
moderately_sensitive:
weights: output/in70s/all/any/noncoviddeath/weights*

report_ipw_in70s_all_any_noncoviddeath:
run: r:latest analysis/R/dose_1/report_ipw.R in70s all any noncoviddeath
needs:
- design
- model_in70s_all_any_noncoviddeath
outputs:
highly_sensitive:
broom: output/in70s/all/any/noncoviddeath/broom*.rds
moderately_sensitive:
data: output/in70s/all/any/noncoviddeath/broom*.csv

report_msm_in70s_all_any_noncoviddeath:
run: r:latest analysis/R/dose_1/report_msm.R in70s all any noncoviddeath
needs:
- design
- model_in70s_all_any_noncoviddeath
outputs:
moderately_sensitive:
svg: output/in70s/all/any/noncoviddeath/VE_plot.svg
png: output/in70s/all/any/noncoviddeath/VE_plot.png
tables: output/in70s/all/any/noncoviddeath/estimates*.csv

report_incidence_in70s_all_any_noncoviddeath:
run: r:latest analysis/R/dose_1/report_incidence.R in70s all any noncoviddeath
needs:
- design
- model_in70s_all_any_noncoviddeath
outputs:
highly_sensitive:
data: output/in70s/all/any/noncoviddeath/data_incidence.rds
moderately_sensitive:
cmlsvg: output/in70s/all/any/noncoviddeath/cml_incidence*.svg
cmlpng: output/in70s/all/any/noncoviddeath/cml_incidence*.png
trendsvg: output/in70s/all/any/noncoviddeath/time*.svg
trendpng: output/in70s/all/any/noncoviddeath/time*.png

model_in70s_all_pfizer_noncoviddeath:
run: r:latest analysis/R/dose_1/model_msm.R in70s all pfizer noncoviddeath
needs:
- design
- data_stset_in70s
- data_samples_in70s
outputs:
highly_sensitive:
models: output/in70s/all/pfizer/noncoviddeath/model*.rds
data: output/in70s/all/pfizer/noncoviddeath/data*.rds
moderately_sensitive:
weights: output/in70s/all/pfizer/noncoviddeath/weights*

report_ipw_in70s_all_pfizer_noncoviddeath:
run: r:latest analysis/R/dose_1/report_ipw.R in70s all pfizer noncoviddeath
needs:
- design
- model_in70s_all_pfizer_noncoviddeath
outputs:
highly_sensitive:
broom: output/in70s/all/pfizer/noncoviddeath/broom*.rds
moderately_sensitive:
data: output/in70s/all/pfizer/noncoviddeath/broom*.csv

report_msm_in70s_all_pfizer_noncoviddeath:
run: r:latest analysis/R/dose_1/report_msm.R in70s all pfizer noncoviddeath
needs:
- design
- model_in70s_all_pfizer_noncoviddeath
outputs:
moderately_sensitive:
svg: output/in70s/all/pfizer/noncoviddeath/VE_plot.svg
png: output/in70s/all/pfizer/noncoviddeath/VE_plot.png
tables: output/in70s/all/pfizer/noncoviddeath/estimates*.csv

report_incidence_in70s_all_pfizer_noncoviddeath:
run: r:latest analysis/R/dose_1/report_incidence.R in70s all pfizer noncoviddeath
needs:
- design
- model_in70s_all_pfizer_noncoviddeath
outputs:
highly_sensitive:
data: output/in70s/all/pfizer/noncoviddeath/data_incidence.rds
moderately_sensitive:
cmlsvg: output/in70s/all/pfizer/noncoviddeath/cml_incidence*.svg
cmlpng: output/in70s/all/pfizer/noncoviddeath/cml_incidence*.png
trendsvg: output/in70s/all/pfizer/noncoviddeath/time*.svg
trendpng: output/in70s/all/pfizer/noncoviddeath/time*.png

model_in70s_all_az_noncoviddeath:
run: r:latest analysis/R/dose_1/model_msm.R in70s all az noncoviddeath
needs:
- design
- data_stset_in70s
- data_samples_in70s
outputs:
highly_sensitive:
models: output/in70s/all/az/noncoviddeath/model*.rds
data: output/in70s/all/az/noncoviddeath/data*.rds
moderately_sensitive:
weights: output/in70s/all/az/noncoviddeath/weights*

report_ipw_in70s_all_az_noncoviddeath:
run: r:latest analysis/R/dose_1/report_ipw.R in70s all az noncoviddeath
needs:
- design
- model_in70s_all_az_noncoviddeath
outputs:
highly_sensitive:
broom: output/in70s/all/az/noncoviddeath/broom*.rds
moderately_sensitive:
data: output/in70s/all/az/noncoviddeath/broom*.csv

report_msm_in70s_all_az_noncoviddeath:
run: r:latest analysis/R/dose_1/report_msm.R in70s all az noncoviddeath
needs:
- design
- model_in70s_all_az_noncoviddeath
outputs:
moderately_sensitive:
svg: output/in70s/all/az/noncoviddeath/VE_plot.svg
png: output/in70s/all/az/noncoviddeath/VE_plot.png
tables: output/in70s/all/az/noncoviddeath/estimates*.csv

report_incidence_in70s_all_az_noncoviddeath:
run: r:latest analysis/R/dose_1/report_incidence.R in70s all az noncoviddeath
needs:
- design
- model_in70s_all_az_noncoviddeath
outputs:
highly_sensitive:
data: output/in70s/all/az/noncoviddeath/data_incidence.rds
moderately_sensitive:
cmlsvg: output/in70s/all/az/noncoviddeath/cml_incidence*.svg
cmlpng: output/in70s/all/az/noncoviddeath/cml_incidence*.png
trendsvg: output/in70s/all/az/noncoviddeath/time*.svg
trendpng: output/in70s/all/az/noncoviddeath/time*.png

model_in70s_all_any_death:
run: r:latest analysis/R/dose_1/model_msm.R in70s all any death
needs:
- design
- data_stset_in70s
- data_samples_in70s
outputs:
highly_sensitive:
models: output/in70s/all/any/death/model*.rds
data: output/in70s/all/any/death/data*.rds
moderately_sensitive:
weights: output/in70s/all/any/death/weights*

report_ipw_in70s_all_any_death:
run: r:latest analysis/R/dose_1/report_ipw.R in70s all any death
needs:
- design
- model_in70s_all_any_death
outputs:
highly_sensitive:
broom: output/in70s/all/any/death/broom*.rds
moderately_sensitive:
data: output/in70s/all/any/death/broom*.csv

report_msm_in70s_all_any_death:
run: r:latest analysis/R/dose_1/report_msm.R in70s all any death
needs:
- design
- model_in70s_all_any_death
outputs:
moderately_sensitive:
svg: output/in70s/all/any/death/VE_plot.svg
png: output/in70s/all/any/death/VE_plot.png
tables: output/in70s/all/any/death/estimates*.csv

report_incidence_in70s_all_any_death:
run: r:latest analysis/R/dose_1/report_incidence.R in70s all any death
needs:
- design
- model_in70s_all_any_death
outputs:
highly_sensitive:
data: output/in70s/all/any/death/data_incidence.rds
moderately_sensitive:
cmlsvg: output/in70s/all/any/death/cml_incidence*.svg
cmlpng: output/in70s/all/any/death/cml_incidence*.png
trendsvg: output/in70s/all/any/death/time*.svg
trendpng: output/in70s/all/any/death/time*.png

model_in70s_all_pfizer_death:
run: r:latest analysis/R/dose_1/model_msm.R in70s all pfizer death
needs:
- design
- data_stset_in70s
- data_samples_in70s
outputs:
highly_sensitive:
models: output/in70s/all/pfizer/death/model*.rds
data: output/in70s/all/pfizer/death/data*.rds
moderately_sensitive:
weights: output/in70s/all/pfizer/death/weights*

report_ipw_in70s_all_pfizer_death:
run: r:latest analysis/R/dose_1/report_ipw.R in70s all pfizer death
needs:
- design
- model_in70s_all_pfizer_death
outputs:
highly_sensitive:
broom: output/in70s/all/pfizer/death/broom*.rds
moderately_sensitive:
data: output/in70s/all/pfizer/death/broom*.csv

report_msm_in70s_all_pfizer_death:
run: r:latest analysis/R/dose_1/report_msm.R in70s all pfizer death
needs:
- design
- model_in70s_all_pfizer_death
outputs:
moderately_sensitive:
svg: output/in70s/all/pfizer/death/VE_plot.svg
png: output/in70s/all/pfizer/death/VE_plot.png
tables: output/in70s/all/pfizer/death/estimates*.csv

report_incidence_in70s_all_pfizer_death:
run: r:latest analysis/R/dose_1/report_incidence.R in70s all pfizer death
needs:
- design
- model_in70s_all_pfizer_death
outputs:
highly_sensitive:
data: output/in70s/all/pfizer/death/data_incidence.rds
moderately_sensitive:
cmlsvg: output/in70s/all/pfizer/death/cml_incidence*.svg
cmlpng: output/in70s/all/pfizer/death/cml_incidence*.png
trendsvg: output/in70s/all/pfizer/death/time*.svg
trendpng: output/in70s/all/pfizer/death/time*.png

model_in70s_all_az_death:
run: r:latest analysis/R/dose_1/model_msm.R in70s all az death
needs:
- design
- data_stset_in70s
- data_samples_in70s
outputs:
highly_sensitive:
models: output/in70s/all/az/death/model*.rds
data: output/in70s/all/az/death/data*.rds
moderately_sensitive:
weights: output/in70s/all/az/death/weights*

report_ipw_in70s_all_az_death:
run: r:latest analysis/R/dose_1/report_ipw.R in70s all az death
needs:
- design
- model_in70s_all_az_death
outputs:
highly_sensitive:
broom: output/in70s/all/az/death/broom*.rds
moderately_sensitive:
data: output/in70s/all/az/death/broom*.csv

report_msm_in70s_all_az_death:
run: r:latest analysis/R/dose_1/report_msm.R in70s all az death
needs:
- design
- model_in70s_all_az_death
outputs:
moderately_sensitive:
svg: output/in70s/all/az/death/VE_plot.svg
png: output/in70s/all/az/death/VE_plot.png
tables: output/in70s/all/az/death/estimates*.csv

report_incidence_in70s_all_az_death:
run: r:latest analysis/R/dose_1/report_incidence.R in70s all az death
needs:
- design
- model_in70s_all_az_death
outputs:
highly_sensitive:
data: output/in70s/all/az/death/data_incidence.rds
moderately_sensitive:
cmlsvg: output/in70s/all/az/death/cml_incidence*.svg
cmlpng: output/in70s/all/az/death/cml_incidence*.png
trendsvg: output/in70s/all/az/death/time*.svg
trendpng: output/in70s/all/az/death/time*.png

report_ipw_in70s_all:
run: r:latest analysis/R/dose_1/report_ipw_combined.R in70s all death
needs:
- design
- report_ipw_in70s_all_any_death
- report_ipw_in70s_all_pfizer_death
- report_ipw_in70s_all_az_death
outputs:
moderately_sensitive:
svg: output/in70s/all/combined/plot_vax1.svg
csv: output/in70s/all/combined/tab_vax1.csv
csv_wide: output/in70s/all/combined/tab_vax1_wide.csv

report_msm_in70s_all:
run: r:latest analysis/R/dose_1/report_msm_combined.R in70s all
needs:
- design
- report_msm_in70s_all_any_postest
- report_msm_in70s_all_any_covidadmitted
- report_msm_in70s_all_any_coviddeath
- report_msm_in70s_all_any_noncoviddeath
- report_msm_in70s_all_pfizer_postest
- report_msm_in70s_all_pfizer_covidadmitted
- report_msm_in70s_all_pfizer_coviddeath
- report_msm_in70s_all_pfizer_noncoviddeath
- report_msm_in70s_all_az_postest
- report_msm_in70s_all_az_covidadmitted
- report_msm_in70s_all_az_coviddeath
- report_msm_in70s_all_az_noncoviddeath
outputs:
moderately_sensitive:
svg: output/in70s/all/combined/VE*.svg
png: output/in70s/all/combined/VE*.png
csv: output/in70s/all/combined/*.csv

report_incidence_in70s_all:
run: r:latest analysis/R/dose_1/report_incidence_combined.R in70s all
needs:
- design
- report_incidence_in70s_all_any_postest
- report_incidence_in70s_all_any_covidadmitted
- report_incidence_in70s_all_any_coviddeath
- report_incidence_in70s_all_any_noncoviddeath
- report_incidence_in70s_all_pfizer_postest
- report_incidence_in70s_all_pfizer_covidadmitted
- report_incidence_in70s_all_pfizer_coviddeath
- report_incidence_in70s_all_pfizer_noncoviddeath
- report_incidence_in70s_all_az_postest
- report_incidence_in70s_all_az_covidadmitted
- report_incidence_in70s_all_az_coviddeath
- report_incidence_in70s_all_az_noncoviddeath
outputs:
moderately_sensitive:
svg: output/in70s/all/combined/cml_incidence*.svg
png: output/in70s/all/combined/cml_incidence*.png

Jobs

ID Status Action
uf6obdj7ol2wt4bd succeeded model_in70s_all_any_death View
pbvxhdhkniz4rwfb succeeded report_ipw_in70s_all_any_death View
6cp5jqgyn3tpr27f succeeded report_msm_in70s_all_any_death View
7ixdoqgztfsvwjoy succeeded report_incidence_in70s_all_any_death View