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project.yaml
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project.yaml
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version: '3.0'
expectations:
population_size: 100000
actions:
# generate_notebook:
# run: jupyter:latest jupyter nbconvert /workspace/notebooks/population_characteristics.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400
#
# needs: [generate_delivery_cohort]
# outputs:
# moderately_sensitive:
# notebook: output/population_characteristics.html
get_packages:
run: r:latest analysis/R/export_package_names.R
outputs:
moderately_sensitive:
cohort: output/available_packages.csv
## Descriptive info on vaccinated patients
extract_vaccinated:
run: cohortextractor:latest generate_cohort --study-definition study_definition_vaccinated
outputs:
highly_sensitive:
cohort: output/input_vaccinated.csv
data_process_vaccinated:
run: r:latest analysis/R/data_process_vaccinated.R
needs: [extract_vaccinated]
outputs:
highly_sensitive:
cohort: output/data/data_vaccinated.rds
vaxdates: output/data/data_vaccinated_vax_dates.rds
data_properties_vaccinated:
run: r:latest analysis/R/data_properties.R output/data/data_vaccinated.rds output/data_properties
needs: [data_process_vaccinated]
outputs:
moderately_sensitive:
summary: output/data_properties/data_vaccinated*.txt
data_summarise_vaccinated:
run: r:latest analysis/R/data_summarise.R
needs: [data_process_vaccinated]
outputs:
moderately_sensitive:
summary1: output/variable_summary/categorical.txt
summary2: output/variable_summary/numeric.txt
summary3: output/variable_summary/date.txt
summarytables: output/variable_summary/tables/categorical_*.csv
summarystats: output/summary_stats.json
vaccine_tables:
run: r:latest analysis/R/vaccine_type.R
needs: [data_process_vaccinated]
outputs:
moderately_sensitive:
tables: output/vaccine_type/tables/vaccine_type_*.csv
tte_tables:
run: r:latest analysis/R/tte_tables.R
needs: [data_process_vaccinated]
outputs:
moderately_sensitive:
tables: output/tte/tables/event_rates_*.csv
tte_plots:
run: r:latest analysis/R/tte_plots.R
needs: [data_process_vaccinated]
outputs:
moderately_sensitive:
plots: output/tte/figures/plot_*.svg
# data for whole cohort
extract_all:
run: cohortextractor:latest generate_cohort --study-definition study_definition_all
outputs:
highly_sensitive:
cohort: output/input_all.csv
data_process_all:
run: r:latest analysis/R/data_process_all.R
needs: [extract_all]
outputs:
highly_sensitive:
data1: output/data/data_all.rds
data2: output/data/data_long_vax_dates.rds
data3: output/data/data_long_admission_dates.rds
data_properties_all:
run: r:latest analysis/R/data_properties.R output/data/data_all.rds output/data_properties
needs: [data_process_all]
outputs:
moderately_sensitive:
datasummary: output/data_properties/data_all*.txt
## VE models in over 80s
data_cohorts:
run: r:latest analysis/R/data_define_cohorts.R
needs: [data_process_all]
outputs:
highly_sensitive:
data: output/modeldata/data_cohorts.rds
moderately_sensitive:
metadata: output/modeldata/metadata_cohorts.rds
data_stset_over80s:
run: r:latest analysis/R/data_stset.R over80s
needs: [data_cohorts, data_process_all]
outputs:
highly_sensitive:
data: output/modeldata/data_*over80s.rds
data_properties_over80s:
run: r:latest analysis/R/data_properties.R output/modeldata/data_wide_over80s.rds output/data_properties
needs: [data_stset_over80s]
outputs:
moderately_sensitive:
datasummary: output/data_properties/data_wide_over80s*.txt
summary_postests_over80s:
run: r:latest analysis/R/plot_outcomes_per_day.R over80s
needs: [data_cohorts, data_stset_over80s]
outputs:
moderately_sensitive:
datasummary: output/models/msm/over80s/positive_test*.svg
models_msm_over80s:
run: r:latest analysis/R/models_msms.R over80s
needs: [data_cohorts, data_stset_over80s]
outputs:
highly_sensitive:
models: output/models/msm/over80s/model*.rds
data: output/models/msm/over80s/data_weights.rds
moderately_sensitive:
weights: output/models/msm/over80s/weights.txt
reportmodels_msm_over80s:
run: r:latest analysis/R/reportmodels_msms.R over80s
needs: [data_cohorts, models_msm_over80s]
outputs:
moderately_sensitive:
forest: output/models/msm/over80s/forest*.svg
trend: output/models/msm/over80s/secular_trends*.svg
eventrate: output/models/msm/over80s/event_rate.svg
tables: output/models/msm/over80s/*.csv
# data_stset_under65s:
# run: r:latest analysis/R/data_stset.R under65s
# needs: [data_cohorts, data_process_all]
# outputs:
# highly_sensitive:
# data: output/modeldata/data_*under65s.rds
#
# data_properties_under65s:
# run: r:latest analysis/R/data_properties.R output/modeldata/data_wide_under65s.rds output/data_properties
# needs: [data_stset_under65s]
# outputs:
# moderately_sensitive:
# datasummary: output/data_properties/data_wide_under65s*.txt
#
# models_msm_under65s:
# run: r:latest analysis/R/models_msms.R under65s
# needs: [data_cohorts, data_stset_under65s]
# outputs:
# moderately_sensitive:
# weights: output/models/msm/under65s/weights.txt
# forest: output/models/msm/under65s/forest*.svg
# trend: output/models/msm/under65s/secular_trends*.svg
# tables: output/models/msm/under65s/*.csv
# models_cox_over80s:
# run: r:latest analysis/R/models_cox_over80s.R
# needs: [data_stset_over80s]
# outputs:
# moderately_sensitive:
# zph: output/models/cox/over80s/zph*.png
# forest: output/models/cox/over80s/forest*.svg
# tables: output/models/cox/over80s/*.csv
# run_ve:
# run: cohortextractor:latest --version
# needs: [extract_all, data_process_all, data_properties_all, data_tte_over80s, models_cox_over80s]
# outputs:
# moderately_sensitive:
# whatever: output/.gitignore