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project.yaml
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version: '3.0'
# Ignore this`expectation` block. It is required but not used, and will be removed in future versions.
expectations:
population_size: 1000
actions:
study_dates:
run: r:latest analysis/metadates.R
outputs:
highly_sensitive:
study_dates_json: output/study_dates.json
generate_dataset_dm_algo:
run: ehrql:v1 generate-dataset analysis/dataset_definition_dm_algo.py --output output/dataset_dm_algo.arrow
needs:
- study_dates
outputs:
highly_sensitive:
dataset: output/dataset_dm_algo.arrow
data_process_dm_algo:
run: r:latest analysis/data_process_dm_algo.R
needs:
- generate_dataset_dm_algo
outputs:
highly_sensitive:
rds: output/data/data_processed_dm_algo.rds
generate_dataset:
run: ehrql:v1 generate-dataset analysis/dataset_definition_landmark.py --output output/dataset.arrow
needs:
- study_dates
outputs:
highly_sensitive:
dataset: output/dataset.arrow
data_process:
run: r:latest analysis/data_process.R
needs:
- generate_dataset
- data_process_dm_algo
outputs:
highly_sensitive:
rds: output/data/data_processed.rds
feather: output/data/data_plots.feather
moderately_sensitive:
csv: output/data_properties/*.csv
km_estimates_metfin:
run: r:latest analysis/km.R
--df_input=output/data/data_plots.feather
--dir_output=output/metfin
--exposure=exp_bin_metfin_anytime
--origin_date=elig_date_t2dm
--event_date=exp_date_metfin_anytime
--censor_date=out_date_covid19_severe
--max_fup=1095
--plot=FALSE
needs:
- data_process
outputs:
moderately_sensitive:
output: output/metfin/*.csv
km_estimates_metfin_mono:
run: r:latest analysis/km.R
--df_input=output/data/data_plots.feather
--dir_output=output/metfin_mono
--exposure=exp_bin_metfin_mono_anytime
--origin_date=elig_date_t2dm
--event_date=exp_date_metfin_mono_anytime
--censor_date=out_date_covid19_severe
--max_fup=1095
--plot=FALSE
needs:
- data_process
outputs:
moderately_sensitive:
output: output/metfin_mono/*.csv
km_estimates_dpp4_mono:
run: r:latest analysis/km.R
--df_input=output/data/data_plots.feather
--dir_output=output/dpp4_mono
--exposure=exp_bin_dpp4_mono_anytime
--origin_date=elig_date_t2dm
--event_date=exp_date_dpp4_mono_anytime
--censor_date=out_date_covid19_severe
--max_fup=1095
--plot=FALSE
needs:
- data_process
outputs:
moderately_sensitive:
output: output/dpp4_mono/*.csv
km_estimates_tzd_mono:
run: r:latest analysis/km.R
--df_input=output/data/data_plots.feather
--dir_output=output/tzd_mono
--exposure=exp_bin_tzd_mono_anytime
--origin_date=elig_date_t2dm
--event_date=exp_date_tzd_mono_anytime
--censor_date=out_date_covid19_severe
--max_fup=1095
--plot=FALSE
needs:
- data_process
outputs:
moderately_sensitive:
output: output/tzd_mono/*.csv
km_estimates_sglt2_mono:
run: r:latest analysis/km.R
--df_input=output/data/data_plots.feather
--dir_output=output/sglt2_mono
--exposure=exp_bin_sglt2_mono_anytime
--origin_date=elig_date_t2dm
--event_date=exp_date_sglt2_mono_anytime
--censor_date=out_date_covid19_severe
--max_fup=1095
--plot=FALSE
needs:
- data_process
outputs:
moderately_sensitive:
output: output/sglt2_mono/*.csv
km_estimates_sulfo_mono:
run: r:latest analysis/km.R
--df_input=output/data/data_plots.feather
--dir_output=output/sulfo_mono
--exposure=exp_bin_sulfo_mono_anytime
--origin_date=elig_date_t2dm
--event_date=exp_date_sulfo_mono_anytime
--censor_date=out_date_covid19_severe
--max_fup=1095
--plot=FALSE
needs:
- data_process
outputs:
moderately_sensitive:
output: output/sulfo_mono/*.csv
km_estimates_glp1_mono:
run: r:latest analysis/km.R
--df_input=output/data/data_plots.feather
--dir_output=output/glp1_mono
--exposure=exp_bin_glp1_mono_anytime
--origin_date=elig_date_t2dm
--event_date=exp_date_glp1_mono_anytime
--censor_date=out_date_covid19_severe
--max_fup=1095
--plot=FALSE
needs:
- data_process
outputs:
moderately_sensitive:
output: output/glp1_mono/*.csv
km_estimates_megli_mono:
run: r:latest analysis/km.R
--df_input=output/data/data_plots.feather
--dir_output=output/megli_mono
--exposure=exp_bin_megli_mono_anytime
--origin_date=elig_date_t2dm
--event_date=exp_date_megli_mono_anytime
--censor_date=out_date_covid19_severe
--max_fup=1095
--plot=FALSE
needs:
- data_process
outputs:
moderately_sensitive:
output: output/megli_mono/*.csv
km_estimates_agi_mono:
run: r:latest analysis/km.R
--df_input=output/data/data_plots.feather
--dir_output=output/agi_mono
--exposure=exp_bin_agi_mono_anytime
--origin_date=elig_date_t2dm
--event_date=exp_date_agi_mono_anytime
--censor_date=out_date_covid19_severe
--max_fup=1095
--plot=FALSE
needs:
- data_process
outputs:
moderately_sensitive:
output: output/agi_mono/*.csv
km_estimates_insulin_mono:
run: r:latest analysis/km.R
--df_input=output/data/data_plots.feather
--dir_output=output/insulin_mono
--exposure=exp_bin_insulin_mono_anytime
--origin_date=elig_date_t2dm
--event_date=exp_date_insulin_mono_anytime
--censor_date=out_date_covid19_severe
--max_fup=1095
--plot=FALSE
needs:
- data_process
outputs:
moderately_sensitive:
output: output/insulin_mono/*.csv
plot_km_estimates:
run: r:latest analysis/km_plot.R
needs:
- km_estimates_metfin
- km_estimates_metfin_mono
- km_estimates_dpp4_mono
- km_estimates_tzd_mono
- km_estimates_sglt2_mono
- km_estimates_sulfo_mono
- km_estimates_glp1_mono
- km_estimates_megli_mono
- km_estimates_agi_mono
- km_estimates_insulin_mono
outputs:
moderately_sensitive:
plot: output/data_properties/*.png
# km_estimates_metfin:
# run: kaplan-meier-function:v0.0.2
# --df_input=output/data/data_plots.feather
# --dir_output=output/km_estimates_metfin.feather ### double-check!!!
# --exposure=exp_bin_metfin_anytime
# --origin_date=elig_date_t2dm
# --event_date=exp_date_metfin_anytime
# --censor_date=out_date_covid19_severe
# --plot=TRUE
# needs:
# - data_process
# outputs:
# highly_sensitive:
# output: output/km_estimates_metfin.feather