generated from opensafely/research-template
/
project.yaml
434 lines (338 loc) · 16.6 KB
/
project.yaml
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version: '3.0'
expectations:
population_size: 50000
actions:
### 1. Extract the cohort
## use the Measure function to allow data for different time periods to be extracted in the same study population: --index-date-range ""yyyy-mm-dd"" --output-format feather
generate_study_population_1:
run: cohortextractor:latest generate_cohort --study-definition study_definition_all --output-dir=output/data --index-date-range "2015-03-01" --output-format feather
outputs:
highly_sensitive:
cohort: output/data/input_all_2015-03-01.feather
generate_study_population_2:
run: cohortextractor:latest generate_cohort --study-definition study_definition_all --output-dir=output/data --index-date-range "2016-03-01" --output-format feather
outputs:
highly_sensitive:
cohort: output/data/input_all_2016-03-01.feather
generate_study_population_3:
run: cohortextractor:latest generate_cohort --study-definition study_definition_all --output-dir=output/data --index-date-range "2017-03-01" --output-format feather
outputs:
highly_sensitive:
cohort: output/data/input_all_2017-03-01.feather
generate_study_population_4:
run: cohortextractor:latest generate_cohort --study-definition study_definition_all --output-dir=output/data --index-date-range "2018-03-01" --output-format feather
outputs:
highly_sensitive:
cohort: output/data/input_all_2018-03-01.feather
generate_study_population_5:
run: cohortextractor:latest generate_cohort --study-definition study_definition_all --output-dir=output/data --index-date-range "2019-03-01" --output-format feather
outputs:
highly_sensitive:
cohort: output/data/input_all_2019-03-01.feather
generate_study_population_6:
run: cohortextractor:latest generate_cohort --study-definition study_definition_all --output-dir=output/data --index-date-range "2020-03-01" --output-format feather
outputs:
highly_sensitive:
cohort: output/data/input_all_2020-03-01.feather
generate_study_population_7:
run: cohortextractor:latest generate_cohort --study-definition study_definition_all --output-dir=output/data --index-date-range "2021-03-01" --output-format feather
outputs:
highly_sensitive:
cohort: output/data/input_all_2021-03-01.feather
generate_study_population_ethnicity:
run: cohortextractor:latest generate_cohort --study-definition study_definition_ethnicity --output-dir=output/data --output-format=feather
outputs:
highly_sensitive:
cohort: output/data/input_ethnicity.feather
join_ethnicity:
run: python:latest python analysis/join_ethnicity.py --output-dir=output/data --output-format feather
needs: [generate_study_population_1, generate_study_population_2, generate_study_population_3, generate_study_population_4, generate_study_population_5, generate_study_population_6, generate_study_population_7, generate_study_population_ethnicity]
outputs:
highly_sensitive:
cohort: output/data/input*.feather
### Develop yearly BMI data sets to de-duplicate data and calculate median BMI each year. Feather format to reduce data quantity.
generate_BMI_2015_data:
run: r:latest analysis/BMI_2015.R --output-dir=output/data --output-format feather
needs: [join_ethnicity]
outputs:
highly_sensitive:
cohort1: output/data/BMI_complete_median_2015.feather
cohort2: output/data/BMI_complete_long_2015.feather
generate_BMI_2016_data:
run: r:latest analysis/BMI_2016.R --output-dir=output/data --output-format feather
needs: [join_ethnicity]
outputs:
highly_sensitive:
cohort1: output/data/BMI_complete_median_2016.feather
cohort2: output/data/BMI_complete_long_2016.feather
generate_BMI_2017_data:
run: r:latest analysis/BMI_2017.R --output-dir=output/data --output-format feather
needs: [join_ethnicity]
outputs:
highly_sensitive:
cohort1: output/data/BMI_complete_median_2017.feather
cohort2: output/data/BMI_complete_long_2017.feather
generate_BMI_2019_data:
run: r:latest analysis/BMI_2019.R --output-dir=output/data --output-format feather
needs: [join_ethnicity]
outputs:
highly_sensitive:
cohort1: output/data/BMI_complete_median_2019.feather
cohort2: output/data/BMI_complete_long_2019.feather
generate_BMI_2021_data:
run: r:latest analysis/BMI_2021.R --output-dir=output/data --output-format feather
needs: [join_ethnicity]
outputs:
highly_sensitive:
cohort1: output/data/BMI_complete_median_2021.feather
cohort2: output/data/BMI_complete_long_2021.feather
generate_BMI_2018_data:
run: r:latest analysis/BMI_2018.R --output-dir=output/data --output-format feather
needs: [join_ethnicity]
outputs:
highly_sensitive:
cohort1: output/data/BMI_complete_median_2018.feather
cohort2: output/data/BMI_complete_long_2018.feather
generate_BMI_2020_data:
run: r:latest analysis/BMI_2020.R --output-dir=output/data --output-format feather
needs: [join_ethnicity]
outputs:
highly_sensitive:
cohort1: output/data/BMI_complete_median_2020.feather
cohort2: output/data/BMI_complete_long_2020.feather
# Append yearly data sets to produce a complete data set for analysis of change in trends
generate_complete_median_BMI_data:
run: r:latest analysis/BMI_median_combine_datasets.R --output-dir=output/data --output-format feather
needs: [generate_BMI_2015_data, generate_BMI_2016_data, generate_BMI_2017_data, generate_BMI_2018_data, generate_BMI_2019_data, generate_BMI_2020_data, generate_BMI_2021_data ]
outputs:
highly_sensitive:
cohort1: output/data/BMI_complete_median.feather
##################################################################
## IMD reference chart: issue with IMD codes in some of derived data sets
generate_imd:
run: r:latest analysis/IMD_reference_script.R --output-dir=output/data --output-format feather
needs: [generate_study_population_1, generate_study_population_2, generate_study_population_3, generate_study_population_4, generate_study_population_5, generate_study_population_6, generate_study_population_7]
outputs:
highly_sensitive:
cohort1: output/data/patient_imd.feather
#############################################################################################
### >> CREATE DATA SET WITH BMI AND WHOLE POPULATION DATA TO ASSESS ODDS OF HAVING BMI TEST
##############################################################################################
generate_whole_pop_2019:
run: r:latest analysis/create_BMI_all_2019.R --output-dir=output/data --output-format feather
needs: [join_ethnicity, generate_BMI_2019_data]
outputs:
highly_sensitive:
cohort1: output/data/BMI_all_2019.feather
generate_whole_pop_2020:
run: r:latest analysis/create_BMI_all_2020.R --output-dir=output/data --output-format feather
needs: [join_ethnicity, generate_BMI_2020_data, generate_complete_median_BMI_data]
outputs:
highly_sensitive:
cohort1: output/data/BMI_all_2020.feather
generate_whole_pop_2021:
run: r:latest analysis/create_BMI_all_2021.R --output-dir=output/data --output-format feather
needs: [join_ethnicity, generate_BMI_2021_data, generate_complete_median_BMI_data]
outputs:
highly_sensitive:
cohort1: output/data/BMI_all_2021.feather
##################################################################
### >> HAD_BMI ANALYSIS
######################################################################
# who had_bmi measured:
generate_had_bmi_proportion_2019:
run: r:latest analysis/had_bmi_proportions_2019.R --output-dir=output/data
needs: [generate_whole_pop_2019]
outputs:
moderately_sensitive:
table1: output/data/proportion_had_bmi_2019.csv
generate_had_bmi_proportion_2020:
run: r:latest analysis/had_bmi_proportions_2020.R --output-dir=output/data
needs: [generate_whole_pop_2020]
outputs:
moderately_sensitive:
table1: output/data/proportion_had_bmi_2020.csv
generate_had_bmi_proportion_2021:
run: r:latest analysis/had_bmi_proportions_2021.R --output-dir=output/data
needs: [generate_whole_pop_2021]
outputs:
moderately_sensitive:
table1: output/data/proportion_had_bmi_2021.csv
#########################################################
## PROPORTION OBESE ANALYSIS
generate_obese_proportion_2019:
run: r:latest analysis/obese_proportions_2019.R --output-dir=output/data
needs: [generate_whole_pop_2019]
outputs:
moderately_sensitive:
table1: output/data/proportion_obese_2019.csv
generate_obese_proportion_2020:
run: r:latest analysis/obese_proportions_2020.R --output-dir=output/data
needs: [generate_whole_pop_2020]
outputs:
moderately_sensitive:
table1: output/data/proportion_obese_2020.csv
generate_obese_proportion_2021:
run: r:latest analysis/obese_proportions_2021.R --output-dir=output/data
needs: [generate_whole_pop_2021]
outputs:
moderately_sensitive:
table1: output/data/proportion_obese_2021.csv
######################################################################################
# >> Median BMI Analysis
#######################################################################################
# generate summary stats of median BMI by exposures
generate_median_summary_stats:
run: r:latest analysis/BMI_median_summary_stats.R --output-dir=output/data
needs: [generate_complete_median_BMI_data]
outputs:
moderately_sensitive:
table1: output/data/median_bmi_summary_table_demographic.csv
table2: output/data/median_bmi_summary_table_covariates.csv
# generate summary stats of median BMI by exposures
generate_median_bmi_plots_2019:
run: r:latest analysis/median_bmi_plots.R --output-dir=output/data
needs: [generate_whole_pop_2019]
outputs:
moderately_sensitive:
chart1: output/median_bmi_all_2019.png
chart2: output/median_bmi_age_T2DM_2019.png
chart3: output/median_bmi_age_hypertension_2019.png
generate_median_bmi_plots_2020:
run: r:latest analysis/median_bmi_plots_2020.R --output-dir=output/data
needs: [generate_whole_pop_2020]
outputs:
moderately_sensitive:
chart1: output/median_bmi_all_2020.png
chart2: output/median_bmi_age_T2DM_2020.png
chart3: output/median_bmi_age_hypertension_2020.png
generate_median_bmi_plots_2021:
run: r:latest analysis/median_bmi_plots_2021.R --output-dir=output/data
needs: [generate_whole_pop_2021]
outputs:
moderately_sensitive:
chart1: output/median_bmi_all_2021.png
chart2: output/median_bmi_age_T2DM_2021.png
chart3: output/median_bmi_age_hypertension_2021.png
## tables of median BMI and range
generate_median_bmi_range_2019:
run: r:latest analysis/median_range_2019.R --output-dir=output/data
needs: [generate_whole_pop_2019]
outputs:
moderately_sensitive:
table1: output/data/median_range_bmi_2019.csv
generate_median_bmi_range_2020:
run: r:latest analysis/median_range_2020.R --output-dir=output/data
needs: [generate_whole_pop_2020]
outputs:
moderately_sensitive:
table1: output/data/median_range_bmi_2020.csv
generate_median_bmi_range_2021:
run: r:latest analysis/median_range_2021.R --output-dir=output/data
needs: [generate_whole_pop_2021]
outputs:
moderately_sensitive:
table1: output/data/median_range_bmi_2021.csv
## Trajectory analysis
generate_bmi_complete_long:
run: r:latest analysis/BMI_complete_long.R --output-dir=output/data --output-format feather
needs: [generate_imd, generate_BMI_2015_data, generate_BMI_2016_data, generate_BMI_2017_data, generate_BMI_2018_data, generate_BMI_2019_data, generate_BMI_2020_data, generate_BMI_2021_data ]
outputs:
highly_sensitive:
table1: output/data/all_bmi_long.feather
###########################
## DWMP Eligible
generate_DWMP_proportion:
run: r:latest analysis/DWMP_proportion.R --output-dir=output/data
needs: [generate_whole_pop_2019,generate_whole_pop_2021, generate_whole_pop_2020]
outputs:
moderately_sensitive:
table1: output/data/proportion_DWMP_eligible_2019.csv
table2: output/data/proportion_DWMP_eligible_2020.csv
table3: output/data/proportion_DWMP_eligible_2021.csv
generate_DWMP_hypertension_proportion:
run: r:latest analysis/DWMP_proportion_hypertension.R --output-dir=output/data
needs: [generate_whole_pop_2019,generate_whole_pop_2021, generate_whole_pop_2020]
outputs:
moderately_sensitive:
table1: output/data/proportion_DWMP_hypertension_2019.csv
table2: output/data/proportion_DWMP_hypertension_2020.csv
table3: output/data/proportion_DWMP_hypertension_2021.csv
generate_DWMP_t2dm_proportion:
run: r:latest analysis/DWMP_proportion_t2dm.R --output-dir=output/data
needs: [generate_whole_pop_2019,generate_whole_pop_2021, generate_whole_pop_2020]
outputs:
moderately_sensitive:
table1: output/data/proportion_DWMP_T2DM_2019.csv
table2: output/data/proportion_DWMP_T2DM_2020.csv
table3: output/data/proportion_DWMP_T2DM_2021.csv
generate_DWMP_t1dm_proportion:
run: r:latest analysis/DWMP_proportion_t1dm.R --output-dir=output/data
needs: [generate_whole_pop_2019,generate_whole_pop_2021, generate_whole_pop_2020]
outputs:
moderately_sensitive:
table1: output/data/proportion_DWMP_T1DM_2019.csv
table2: output/data/proportion_DWMP_T1DM_2020.csv
table3: output/data/proportion_DWMP_T1DM_2021.csv
##################################################################
### >> HAD_SBP ANALYSIS
######################################################################
# who had_bmi measured:
generate_had_sbp_proportion_2019:
run: r:latest analysis/had_sbp_proportions_2019.R --output-dir=output/data
needs: [join_ethnicity, generate_BMI_2019_data]
outputs:
moderately_sensitive:
table1: output/data/proportion_had_sbp_2019.csv
generate_had_sbp_proportion_2020:
run: r:latest analysis/had_sbp_proportions_2020.R --output-dir=output/data
needs: [join_ethnicity, generate_BMI_2020_data, generate_complete_median_BMI_data]
outputs:
moderately_sensitive:
table1: output/data/proportion_had_sbp_2020.csv
generate_had_sbp_proportion_2021:
run: r:latest analysis/had_sbp_proportions_2021.R --output-dir=output/data
needs: [join_ethnicity, generate_BMI_2021_data, generate_complete_median_BMI_data]
outputs:
moderately_sensitive:
table1: output/data/proportion_had_sbp_2021.csv
############################################################
## Hba1c
##############################################################
generate_hba1c_2018_2019_data:
run: r:latest analysis/hba1c_2018_19.R --output-dir=output/data --output-format feather
needs: [join_ethnicity]
outputs:
highly_sensitive:
cohort1: output/data/hba1c_2019_summary.feather
cohort2: output/data/hba1c_2018_summary.feather
cohort3: output/data/hba1c_2019_long.feather
cohort4: output/data/hba1c_2018_long.feather
cohort5: output/data/precovid_hba1c_control.feather
generate_hba1c_2020_2021_data:
run: r:latest analysis/hba1c_2020_2021.R --output-dir=output/data --output-format feather
needs: [join_ethnicity]
outputs:
highly_sensitive:
cohort1: output/data/hba1c_2020_summary.feather
cohort2: output/data/hba1c_2021_summary.feather
cohort3: output/data/hba1c_2021_long.feather
cohort4: output/data/hba1c_2020_long.feather
generate_hba1c_2019_proportion:
run: r:latest analysis/had_hba1c_2019.R --output-dir=output/data --output-format feather
needs: [generate_hba1c_2018_2019_data]
outputs:
moderately_sensitive:
table1: output/data/proportion_had_hba1c_2019.csv
generate_hba1c_proportions_2019:
run: r:latest analysis/had_hba1c_2019_proportions.R --output-dir=output/data --output-format feather
needs: [generate_hba1c_2018_2019_data]
outputs:
moderately_sensitive:
table1: output/data/proportion_hba1c_2019.csv
check_hba1c:
run: r:latest analysis/check_hba1c.R --output-dir=output/data --output-format feather
needs: [generate_hba1c_2018_2019_data]
outputs:
moderately_sensitive:
table1: output/data/check_hba1c.csv