This page shows the technical details of what happened when authorised researcher Miriam Samuel requested one or more actions to be run against real patient data in the 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.
Jobs
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Pipeline
Show project.yaml
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
generate_study_population_dm1:
run: cohortextractor:latest generate_cohort --study-definition study_definition_dm_meds --output-dir=output/data --index-date-range "2015-03-01"
outputs:
highly_sensitive:
cohort: output/data/input_dm_meds_2015-03-01.csv
generate_study_population_dm2:
run: cohortextractor:latest generate_cohort --study-definition study_definition_dm_meds --output-dir=output/data --index-date-range "2016-03-01"
outputs:
highly_sensitive:
cohort: output/data/input_dm_meds_2016-03-01.csv
generate_study_population_dm3:
run: cohortextractor:latest generate_cohort --study-definition study_definition_dm_meds --output-dir=output/data --index-date-range "2017-03-01"
outputs:
highly_sensitive:
cohort: output/data/input_dm_meds_2017-03-01.csv
generate_study_population_dm4:
run: cohortextractor:latest generate_cohort --study-definition study_definition_dm_meds --output-dir=output/data --index-date-range "2018-03-01"
outputs:
highly_sensitive:
cohort: output/data/input_dm_meds_2018-03-01.csv
generate_study_population_dm5:
run: cohortextractor:latest generate_cohort --study-definition study_definition_dm_meds --output-dir=output/data --index-date-range "2019-03-01"
outputs:
highly_sensitive:
cohort: output/data/input_dm_meds_2019-03-01.csv
generate_study_population_dm6:
run: cohortextractor:latest generate_cohort --study-definition study_definition_dm_meds --output-dir=output/data --index-date-range "2020-03-01"
outputs:
highly_sensitive:
cohort: output/data/input_dm_meds_2020-03-01.csv
generate_study_population_dm7:
run: cohortextractor:latest generate_cohort --study-definition study_definition_dm_meds --output-dir=output/data --index-date-range "2021-03-01"
outputs:
highly_sensitive:
cohort: output/data/input_dm_meds_2021-03-01.csv
### Develop yearly BMI data sets to de-duplicate data and calculate median BMI each year. Feather format to reduce data quantity.
join_meds:
run: r:latest analysis/add_medication.R --output-dir=output/data --output-format feather
needs: [join_ethnicity, generate_study_population_dm1, generate_study_population_dm2, generate_study_population_dm3, generate_study_population_dm4, generate_study_population_dm5, generate_study_population_dm6, generate_study_population_dm7]
outputs:
highly_sensitive:
cohort1: output/data/complete_meds_2015.feather
cohort2: output/data/complete_meds_2016.feather
cohort3: output/data/complete_meds_2017.feather
cohort4: output/data/complete_meds_2018.feather
cohort5: output/data/complete_meds_2019.feather
cohort6: output/data/complete_meds_2020.feather
cohort7: output/data/complete_meds_2021.feather
generate_BMI_2015_data:
run: r:latest analysis/BMI_2015.R --output-dir=output/data --output-format feather
needs: [join_meds]
outputs:
highly_sensitive:
cohort1: output/data/BMI_complete_median_2015.feather
cohort2: output/data/BMI_complete_long_2015.feather
moderately_sensitive:
table1: output/data/BMI_data_checks_2015.csv
generate_BMI_2016_data:
run: r:latest analysis/BMI_2016.R --output-dir=output/data --output-format feather
needs: [join_meds]
outputs:
highly_sensitive:
cohort1: output/data/BMI_complete_median_2016.feather
cohort2: output/data/BMI_complete_long_2016.feather
moderately_sensitive:
table1: output/data/BMI_data_checks_2016.csv
generate_BMI_2017_data:
run: r:latest analysis/BMI_2017.R --output-dir=output/data --output-format feather
needs: [join_meds]
outputs:
highly_sensitive:
cohort1: output/data/BMI_complete_median_2017.feather
cohort2: output/data/BMI_complete_long_2017.feather
moderately_sensitive:
table1: output/data/BMI_data_checks_2017.csv
generate_BMI_2019_data:
run: r:latest analysis/BMI_2019.R --output-dir=output/data --output-format feather
needs: [join_meds]
outputs:
highly_sensitive:
cohort1: output/data/BMI_complete_median_2019.feather
cohort2: output/data/BMI_complete_long_2019.feather
moderately_sensitive:
table1: output/data/BMI_data_checks_2019.csv
generate_BMI_2021_data:
run: r:latest analysis/BMI_2021.R --output-dir=output/data --output-format feather
needs: [join_meds]
outputs:
highly_sensitive:
cohort1: output/data/BMI_complete_median_2021.feather
cohort2: output/data/BMI_complete_long_2021.feather
moderately_sensitive:
table1: output/data/BMI_data_checks_2021.csv
generate_BMI_2018_data:
run: r:latest analysis/BMI_2018.R --output-dir=output/data --output-format feather
needs: [join_meds]
outputs:
highly_sensitive:
cohort1: output/data/BMI_complete_median_2018.feather
cohort2: output/data/BMI_complete_long_2018.feather
moderately_sensitive:
table1: output/data/BMI_data_checks_2018.csv
generate_BMI_2020_data:
run: r:latest analysis/BMI_2020.R --output-dir=output/data --output-format feather
needs: [join_meds]
outputs:
highly_sensitive:
cohort1: output/data/BMI_complete_median_2020.feather
cohort2: output/data/BMI_complete_long_2020.feather
moderately_sensitive:
table1: output/data/BMI_data_checks_2020.csv
# 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
generate_complete_long_BMI_data:
run: r:latest analysis/BMI_complete_long.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/all_bmi_long.feather
generate_BMI_trajectories_data1:
run: r:latest analysis/BMI_change_1.R --output-dir=output/data --output-format feather
needs: [generate_complete_long_BMI_data]
outputs:
highly_sensitive:
cohort1: output/data/BMI_demog.feather
cohort2: output/data/BMI_all_long_sample.feather
generate_BMI_trajectories_data2:
run: r:latest analysis/BMI_change_2.R --output-dir=output/data --output-format feather
needs: [generate_BMI_trajectories_data1]
outputs:
highly_sensitive:
cohort1: output/data/BMI_trajectories.feather
generate_BMI_trajectories_data3:
run: r:latest analysis/BMI_change_3.R --output-dir=output/data --output-format feather
needs: [generate_BMI_trajectories_data2, generate_BMI_trajectories_data1]
outputs:
highly_sensitive:
cohort1: output/data/BMI_trajectories_final.feather
BMI_trajectories_demographics_correction:
run: r:latest analysis/BMI_change_demographic_correction.R --output-dir=output/data --output-format feather
needs: [generate_BMI_trajectories_data3, generate_complete_long_BMI_data]
outputs:
highly_sensitive:
cohort1: output/data/BMI_trajectories_final_demog.feather
moderately_sensitive:
table1: output/data/BMI_traj_demog.html
########################################
## POPULATION DEMOGRAPHICS
#######################################
demographics_analysis_pop:
run: r:latest analysis/pop_demographics/pop_demographics_total_pop.R --output-dir=output/data
needs: [generate_complete_median_BMI_data]
outputs:
moderately_sensitive:
table1: output/data/demographics_study_population.csv
demographics_had_bmi:
run: r:latest analysis/pop_demographics/pop_demographics_had_bmi.R --output-dir=output/data
needs: [generate_complete_median_BMI_data]
outputs:
moderately_sensitive:
table1: output/data/demographics_had_bmi.csv
demographics_t2dm:
run: r:latest analysis/pop_demographics/pop_demographics_t2dm.R --output-dir=output/data
needs: [generate_complete_median_BMI_data]
outputs:
moderately_sensitive:
table1: output/data/demographics_study_population_t2dm.csv
table2: output/data/demographics_had_bmi_t2dm.csv
demographics_t1dm:
run: r:latest analysis/pop_demographics/pop_demographics_t1dm.R --output-dir=output/data
needs: [generate_complete_median_BMI_data]
outputs:
moderately_sensitive:
table1: output/data/demographics_study_population_t1dm.csv
table2: output/data/demographics_had_bmi_t1dm.csv
demographics_hypertension:
run: r:latest analysis/pop_demographics/pop_demographics_hypertension.R --output-dir=output/data
needs: [generate_complete_median_BMI_data]
outputs:
moderately_sensitive:
table1: output/data/demographics_study_population_hypertension.csv
table2: output/data/demographics_had_bmi_hypertension.csv
demographics_bmi_change_all:
run: r:latest analysis/pop_demographics/pop_demographics_bmi_change_all.R --output-dir=output/data
needs: [bmi_change_category_proportion_plots]
outputs:
moderately_sensitive:
table1: output/data/demographics_bmi_change_analysis_all.csv
demographics_bmi_change_lowbmiexc:
run: r:latest analysis/pop_demographics/pop_demographics_bmi_change_lowbmiexc.R --output-dir=output/data
needs: [bmi_change_category_proportion_plots]
outputs:
moderately_sensitive:
table1: output/data/demographics_bmi_change_analysis_lowbmiexc.csv
demographics_bmi_change_t2dm:
run: r:latest analysis/pop_demographics/pop_demographics_bmi_change_t2dm.R --output-dir=output/data
needs: [bmi_change_category_proportion_plots]
outputs:
moderately_sensitive:
table1: output/data/demographics_bmi_change_analysis_all_t2dm.csv
table2: output/data/demographics_bmi_change_analysis_lowbmiexc_t2dm.csv
demographics_bmi_change_t1dm:
run: r:latest analysis/pop_demographics/pop_demographics_bmi_change_t1dm.R --output-dir=output/data
needs: [bmi_change_category_proportion_plots]
outputs:
moderately_sensitive:
table1: output/data/demographics_bmi_change_analysis_all_t1dm.csv
table2: output/data/demographics_bmi_change_analysis_lowbmiexc_t1dm.csv
demographics_bmi_change_hypertension:
run: r:latest analysis/pop_demographics/pop_demographics_bmi_change_hypertension.R --output-dir=output/data
needs: [bmi_change_category_proportion_plots]
outputs:
moderately_sensitive:
table1: output/data/demographics_bmi_change_analysis_all_hypertension.csv
table2: output/data/demographics_bmi_change_analysis_lowbmiexc_hypertension.csv
#########################################################
## TOP DECILE: BMI_ CHANGE
##########################################################
topdecile_bmi_change_univariate:
run: r:latest analysis/bmi_trajectory/top_decile_change/top_decile_change_univariate.R --output-dir=output/data
needs: [bmi_trajectory_change_summary]
outputs:
moderately_sensitive:
table1: output/data/change_90th_univariate_lowbmiexc.csv
table2: output/data/change_deciles_lowbmiexc.csv
table3: output/data/change_90th_counts_lowbmiexc.csv
topdecile_bmi_change_counts_correction:
run: r:latest analysis/bmi_trajectory/top_decile_change/top_decile_change_counts.R --output-dir=output/data
needs: [bmi_trajectory_change_summary]
outputs:
moderately_sensitive:
table1: output/data/change_90th_counts_lowbmiexc_corrected.csv
topdecile_bmi_change_age_adjusted:
run: r:latest analysis/bmi_trajectory/top_decile_change/top_decile_change_age_adjusted.R --output-dir=output/data
needs: [bmi_trajectory_change_summary]
outputs:
moderately_sensitive:
table1: output/data/change_90th_age_adjusted_lowbmiexc.csv
table2: output/data/change_90th_wald_age.csv
topdecile_bmi_change_sex_adjusted:
run: r:latest analysis/bmi_trajectory/top_decile_change/top_decile_change_sex_adjusted.R --output-dir=output/data
needs: [bmi_trajectory_change_summary]
outputs:
moderately_sensitive:
table1: output/data/change_90th_sex_adjusted_lowbmiexc.csv
table2: output/data/change_90th_wald_sex.csv
topdecile_bmi_change_age_sex_adjusted:
run: r:latest analysis/bmi_trajectory/top_decile_change/top_decile_change_age_sex_adjusted.R --output-dir=output/data
needs: [bmi_trajectory_change_summary]
outputs:
moderately_sensitive:
table1: output/data/change_90th_age_sex_adjusted_lowbmiexc.csv
table2: output/data/change_90th_wald_age_sex.csv
## hypertension
topdecile_bmi_change_hypertension:
run: r:latest analysis/bmi_trajectory/top_decile_change/top_decile_change_hypertension.R --output-dir=output/data
needs: [bmi_trajectory_change_summary]
outputs:
moderately_sensitive:
table1: output/data/change_90th_univariate_lowbmiexc_hypertension.csv
table2: output/data/change_deciles_lowbmiexc_hypertension.csv
table3: output/data/change_90th_counts_lowbmiexc_hypertension.csv
table4: output/data/change_90th_age_adj_lowbmiexc_hypertension.csv
table5: output/data/change_90th_sex_adj_lowbmiexc_hypertension.csv
table6: output/data/change_90th_agesex_adj_lowbmiexc_hypertension.csv
topdecile_bmi_change_T1DM:
run: r:latest analysis/bmi_trajectory/top_decile_change/top_decile_change_T1DM.R --output-dir=output/data
needs: [bmi_trajectory_change_summary]
outputs:
moderately_sensitive:
table1: output/data/change_90th_univariate_lowbmiexc_T1DM.csv
table2: output/data/change_deciles_lowbmiexc_T1DM.csv
table3: output/data/change_90th_counts_lowbmiexc_T1DM.csv
table4: output/data/change_90th_age_adj_lowbmiexc_T1DM.csv
table5: output/data/change_90th_sex_adj_lowbmiexc_T1DM.csv
table6: output/data/change_90th_agesex_adj_lowbmiexc_T1DM.csv
topdecile_bmi_change_T2DM:
run: r:latest analysis/bmi_trajectory/top_decile_change/top_decile_change_T2DM.R --output-dir=output/data
needs: [bmi_trajectory_change_summary]
outputs:
moderately_sensitive:
table1: output/data/change_90th_univariate_lowbmiexc_T2DM.csv
table2: output/data/change_deciles_lowbmiexc_T2DM.csv
table3: output/data/change_90th_counts_lowbmiexc_T2DM.csv
table4: output/data/change_90th_age_adj_lowbmiexc_T2DM.csv
table5: output/data/change_90th_sex_adj_lowbmiexc_T2DM.csv
table6: output/data/change_90th_agesex_adj_lowbmiexc_T2DM.csv
##################################################################
### >> 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_complete_median_BMI_data]
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_complete_median_BMI_data]
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_complete_median_BMI_data]
outputs:
moderately_sensitive:
table1: output/data/proportion_had_bmi_2021.csv
## Look at odds of having BMI across the years
had_bmi_2019_2021_models1:
run: r:latest analysis/had_bmi_check/had_bmi_all_years_models.R --output-dir=output/data
needs: [generate_complete_median_BMI_data]
outputs:
moderately_sensitive:
table1: output/data/had_bmi_2019_21_models_1.csv
had_bmi_2019_2021_models1_counts:
run: r:latest analysis/had_bmi_check/had_bmi_all_years_models_counts.R --output-dir=output/data
needs: [generate_complete_median_BMI_data]
outputs:
moderately_sensitive:
table1: output/data/had_bmi_2019_21_models_1_counts.csv
table2: output/data/had_bmi_2019_21_models_1_demographics.csv
had_bmi_2019_2021_models1_counts_round:
run: r:latest analysis/had_bmi_check/had_bmi_models_counts_round.R --output-dir=output/data
needs: [had_bmi_2019_2021_models1_counts]
outputs:
moderately_sensitive:
table1: output/data/had_bmi_2019_21_models_1_demographics_round.csv
had_bmi_2019_2021_models_comorbidities:
run: r:latest analysis/had_bmi_check/had_bmi_all_years_comorbidities_models.R --output-dir=output/data
needs: [generate_complete_median_BMI_data]
outputs:
moderately_sensitive:
table1: output/data/had_bmi_2019_21_comorbidity_models.csv
table2: output/data/had_bmi_2019_21_comorbidity_models_counts.csv
had_bmi_2019_2021_proportions:
run: r:latest analysis/had_bmi_check/had_bmi_all_years_prop_chi.R --output-dir=output/data
needs: [generate_complete_median_BMI_data]
outputs:
moderately_sensitive:
table1: output/data/proportion_had_bmi_2019_2021.csv
table2: output/data/proportion_had_bmi_2019_2021_chisquare.csv
## check the output from the cohort extractor 'had_bmi'
had_bmi_proportion_2019_check:
run: r:latest analysis/had_bmi_check/had_bmi_check_2019.R --output-dir=output/data
needs: [generate_complete_median_BMI_data]
outputs:
moderately_sensitive:
table1: output/data/proportion_had_bmi_check_2019.csv
table2: output/data/had_bmi_numbers_check.csv
#########################################################
## PROPORTION OBESE ANALYSIS
generate_obese_proportion_2019:
run: r:latest analysis/obese_proportions_2019.R --output-dir=output/data
needs: [generate_complete_median_BMI_data]
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_complete_median_BMI_data]
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_complete_median_BMI_data]
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
## tables of median BMI and range
generate_median_bmi_range_2015:
run: r:latest analysis/median_range_bmi/median_range_2015.R --output-dir=output/data
needs: [generate_complete_median_BMI_data]
outputs:
moderately_sensitive:
table1: output/data/median_range_bmi_2015.csv
generate_median_bmi_range_2016:
run: r:latest analysis/median_range_bmi/median_range_2016.R --output-dir=output/data
needs: [generate_complete_median_BMI_data]
outputs:
moderately_sensitive:
table1: output/data/median_range_bmi_2016.csv
generate_median_bmi_range_2017:
run: r:latest analysis/median_range_bmi/median_range_2017.R --output-dir=output/data
needs: [generate_complete_median_BMI_data]
outputs:
moderately_sensitive:
table1: output/data/median_range_bmi_2017.csv
generate_median_bmi_range_2018:
run: r:latest analysis/median_range_bmi/median_range_2018.R --output-dir=output/data
needs: [generate_complete_median_BMI_data]
outputs:
moderately_sensitive:
table1: output/data/median_range_bmi_2018.csv
generate_median_bmi_range_2019:
run: r:latest analysis/median_range_bmi/median_range_2019.R --output-dir=output/data
needs: [generate_complete_median_BMI_data]
outputs:
moderately_sensitive:
table1: output/data/median_range_bmi_2019.csv
generate_median_bmi_range_2020:
run: r:latest analysis/median_range_bmi/median_range_2020.R --output-dir=output/data
needs: [generate_complete_median_BMI_data]
outputs:
moderately_sensitive:
table1: output/data/median_range_bmi_2020.csv
generate_median_bmi_range_2021:
run: r:latest analysis/median_range_bmi/median_range_2021.R --output-dir=output/data
needs: [generate_complete_median_BMI_data]
outputs:
moderately_sensitive:
table1: output/data/median_range_bmi_2021.csv
combine_median_range_BMI:
run: r:latest analysis/median_range_bmi/combine_median_range_BMI.R --output-dir=output/data
needs: [generate_median_bmi_range_2021, generate_median_bmi_range_2020, generate_median_bmi_range_2019, generate_median_bmi_range_2018, generate_median_bmi_range_2017, generate_median_bmi_range_2016, generate_median_bmi_range_2015]
outputs:
moderately_sensitive:
table1: output/data/median_range_bmi_2015_2021.csv
## Proportion Obese
proportion_obese_2015:
run: r:latest analysis/proportion_obese/proportion_obese_2015.R --output-dir=output/data
needs: [generate_complete_median_BMI_data]
outputs:
moderately_sensitive:
table1: output/data/obese_2015.csv
proportion_obese_2016:
run: r:latest analysis/proportion_obese/proportion_obese_2016.R --output-dir=output/data
needs: [generate_complete_median_BMI_data]
outputs:
moderately_sensitive:
table1: output/data/obese_2016.csv
proportion_obese_2017:
run: r:latest analysis/proportion_obese/proportion_obese_2017.R --output-dir=output/data
needs: [generate_complete_median_BMI_data]
outputs:
moderately_sensitive:
table1: output/data/obese_2017.csv
proportion_obese_2018:
run: r:latest analysis/proportion_obese/proportion_obese_2018.R --output-dir=output/data
needs: [generate_complete_median_BMI_data]
outputs:
moderately_sensitive:
table1: output/data/obese_2018.csv
proportion_obese_2019:
run: r:latest analysis/proportion_obese/proportion_obese_2019.R --output-dir=output/data
needs: [generate_complete_median_BMI_data]
outputs:
moderately_sensitive:
table1: output/data/obese_2019.csv
proportion_obese_2020:
run: r:latest analysis/proportion_obese/proportion_obese_2020.R --output-dir=output/data
needs: [generate_complete_median_BMI_data]
outputs:
moderately_sensitive:
table1: output/data/obese_2020.csv
proportion_obese_2021:
run: r:latest analysis/proportion_obese/proportion_obese_2021.R --output-dir=output/data
needs: [generate_complete_median_BMI_data]
outputs:
moderately_sensitive:
table1: output/data/obese_2021.csv
## Proportion Obese
proportion_weight_categories_2015:
run: r:latest analysis/proportion_weight_categories/proportion_weight_categories_2015.R --output-dir=output/data
needs: [generate_complete_median_BMI_data]
outputs:
moderately_sensitive:
table1: output/data/weight_categories_2015.csv
proportion_weight_categories_2016:
run: r:latest analysis/proportion_weight_categories/proportion_weight_categories_2016.R --output-dir=output/data
needs: [generate_complete_median_BMI_data]
outputs:
moderately_sensitive:
table1: output/data/weight_categories_2016.csv
proportion_weight_categories_2017:
run: r:latest analysis/proportion_weight_categories/proportion_weight_categories_2017.R --output-dir=output/data
needs: [generate_complete_median_BMI_data]
outputs:
moderately_sensitive:
table1: output/data/weight_categories_2017.csv
proportion_weight_categories_2018:
run: r:latest analysis/proportion_weight_categories/proportion_weight_categories_2018.R --output-dir=output/data
needs: [generate_complete_median_BMI_data]
outputs:
moderately_sensitive:
table1: output/data/weight_categories_2018.csv
proportion_weight_categories_2019:
run: r:latest analysis/proportion_weight_categories/proportion_weight_categories_2019.R --output-dir=output/data
needs: [generate_complete_median_BMI_data]
outputs:
moderately_sensitive:
table1: output/data/weight_categories_2019.csv
proportion_weight_categories_2020:
run: r:latest analysis/proportion_weight_categories/proportion_weight_categories_2020.R --output-dir=output/data
needs: [generate_complete_median_BMI_data]
outputs:
moderately_sensitive:
table1: output/data/weight_categories_2020.csv
proportion_weight_categories_2021:
run: r:latest analysis/proportion_weight_categories/proportion_weight_categories_2021.R --output-dir=output/data
needs: [generate_complete_median_BMI_data]
outputs:
moderately_sensitive:
table1: output/data/weight_categories_2021.csv
proportion_obese_2019_2021:
run: r:latest analysis/proportion_weight_categories/proportion_obese_models.R --output-dir=output/data
needs: [generate_complete_median_BMI_data]
outputs:
moderately_sensitive:
table1: output/data/obese_2019_21_models_1.csv
proportion_obese_2019_2021_comorbidities:
run: r:latest analysis/proportion_weight_categories/proportion_obese_comorbidities_models.R --output-dir=output/data
needs: [generate_complete_median_BMI_data]
outputs:
moderately_sensitive:
table1: output/data/obese_2019_21_comorbidity_models.csv
########## BMI_trajectory_data
proportion_complete_bmi_trajectory:
run: r:latest analysis/proportion_complete_BMI_trajectory.R --output-dir=output/data
needs: [BMI_trajectories_demographics_correction]
outputs:
moderately_sensitive:
table1: output/data/complete_bmi_trajectories_proportions.csv
bmi_change_plots:
run: r:latest analysis/BMI_change_plot.R --output-dir=output/data
needs: [BMI_trajectories_demographics_correction]
outputs:
moderately_sensitive:
table1: output/data/short_bmi_change_summary.csv
chart1: output/bmi_change_plot.png
chart2: output/bmi_change_plot_age.png
chart3: output/bmi_change_plot_counts.png
chart4: output/bmi_change_plot_age_precovid_counts.png
chart5: output/bmi_change_plot_age_postcovid_counts.png
bmi_change_extremes:
run: r:latest analysis/BMI_change_check_extremes.R --output-dir=output/data
needs: [BMI_trajectories_demographics_correction]
outputs:
moderately_sensitive:
table1: output/data/short_bmi_change_extremes.csv
bmi_timeinterval_check:
run: r:latest analysis/check_timeintervals_BMI_change.R --output-dir=output/data
needs: [generate_BMI_trajectories_data3]
outputs:
moderately_sensitive:
table1: output/data/bmi_timeinterval_check.csv
table2: output/data/time1_error.csv
pandemic_bmi_changes:
run: r:latest analysis/BMI_change_pandemic.R --output-dir=output/data
needs: [BMI_trajectories_demographics_correction]
outputs:
moderately_sensitive:
table1: output/data/prepandemic_bmi_change_per_year.csv
table2: output/data/postpandemic_bmi_change_per_year.csv
pandemic_bmi_trajectory_plots:
run: r:latest analysis/BMI_change_postcovid_plots.R --output-dir=output/data
needs: [BMI_trajectories_demographics_correction]
outputs:
highly_sensitive:
table1: output/data/BMI_trajectory_data.feather
table2: output/data/BMI_trajectory_data_filtered.feather
moderately_sensitive:
chart1: output/precovid_stable_bmi.png
chart2: output/precovid_slow_inc_bmi.png
chart3: output/precovid_mod_inc_bmi.png
chart4: output/precovid_rapid_inc_bmi.png
## violin plots to see distribution before filtering
postcovid_BMI_change_plots:
run: r:latest analysis/bmi_change_postcovid_distribution_plots.R --output-dir=output/data
needs: [pandemic_bmi_trajectory_plots]
outputs:
moderately_sensitive:
chart1: output/SMI_postcovid_trajectory.png
chart2: output/region_postcovid_trajectory.png
chart3: output/precovid_traj_postcovid_trajectory.png
chart4: output/bmi_postcovid_trajectory.png
chart5: output/LD_postcovid_trajectory.png
chart6: output/imd_postcovid_trajectory.png
chart7: output/hypertension_postcovid_trajectory.png
chart8: output/ethnic_postcovid_trajectory.png
chart9: output/diabetes2_postcovid_trajectory.png
chart10: output/diabetes1_postcovid_trajectory.png
chart11: output/depression_postcovid_trajectory.png
chart12: output/age_postcovid_trajectory.png
## stacked column charts showing proportion in different BMI change categories
bmi_change_category_proportion_plots:
run: r:latest analysis/BMI_change_category_prop_plots.R --output-dir=output/data
needs: [BMI_trajectories_demographics_correction]
outputs:
highly_sensitive:
table1: output/data/BMI_trajectory_data_long.feather
moderately_sensitive:
chart1: output/category_bmi_change_depression.png
chart2: output/category_bmi_change_ethnicity.png
chart3: output/category_bmi_change_learning_diff.png
chart4: output/category_bmi_change_region.png
chart5: output/category_bmi_change_sex.png
chart6: output/category_bmi_change_serious_mental.png
chart7: output/category_bmi_change_t1dm.png
chart8: output/category_bmi_change_t2dm.png
chart9: output/category_bmi_change_imd.png
chart10: output/category_bmi_change_hypertension.png
## description proportions in each change group
bmi_change_groups_description:
run: r:latest analysis/bmi_trajectory/BMI_change_category_description.R --output-dir=output/data
needs: [bmi_change_category_proportion_plots]
outputs:
moderately_sensitive:
table1: output/data/precovid_bmichange_description.csv
table2: output/data/postcovid_bmichange_description.csv
## logistic regression predictors of rapid bmi change in pre and post covid period
bmi_change_univariate:
run: r:latest analysis/BMI_change_rapid_univariate.R --output-dir=output/data
needs: [bmi_change_category_proportion_plots]
outputs:
moderately_sensitive:
table1: output/data/rapid_bmi_change_univariate.csv
table2: output/data/rapid_bmi_change_popcharac.csv
bmi_change_age_adjusted:
run: r:latest analysis/BMI_change_rapid_age_model.R --output-dir=output/data
needs: [bmi_change_category_proportion_plots]
outputs:
moderately_sensitive:
table1: output/data/rapid_bmi_change_age_adjusted.csv
## Predictors of rapid bmi change with cancer and low pre pandemic weight removed.
bmi_change_univariate_lowbmiexcluded:
run: r:latest analysis/BMI_change_rapid_lowbmi_excluded_univariate.R --output-dir=output/data
needs: [bmi_change_category_proportion_plots]
outputs:
moderately_sensitive:
table1: output/data/rapid_bmi_change_cancerandlowbmi_removed_univariate.csv
table2: output/data/rapid_bmi_change_cancerandlowbmi_removed_popcharac.csv
bmi_change_age_adjusted_lowbmiexcluded:
run: r:latest analysis/BMI_change_rapid_lowbmi_excluded_age_models.R --output-dir=output/data
needs: [bmi_change_category_proportion_plots]
outputs:
moderately_sensitive:
table1: output/data/rapid_bmi_change_cancerandlowbmi_removed_age_adjusted.csv
### RAPID CHANGE BMI - ADJUSTED MODELS
bmi_rapid_change_sex_adjusted_lowbmiexcluded:
run: r:latest analysis/bmi_trajectory/rapid_bmi_change/rapid_change_cancerlowbmiexc_sex_adj.R --output-dir=output/data
needs: [bmi_change_category_proportion_plots]
outputs:
moderately_sensitive:
table1: output/data/rapid_bmi_change_cancerandlowbmi_removed_sex_adjusted.csv
bmi_rapid_change_imd_adjusted_lowbmiexcluded:
run: r:latest analysis/bmi_trajectory/rapid_bmi_change/rapid_change_cancerlowbmiexc_imd_adj.R --output-dir=output/data
needs: [bmi_change_category_proportion_plots]
outputs:
moderately_sensitive:
table1: output/data/rapid_bmi_change_cancerandlowbmi_removed_imd_adjusted.csv
bmi_rapid_change_ethnic_adjusted_lowbmiexcluded:
run: r:latest analysis/bmi_trajectory/rapid_bmi_change/rapid_change_cancerlowbmiexc_ethnic_adj.R --output-dir=output/data
needs: [bmi_change_category_proportion_plots]
outputs:
moderately_sensitive:
table1: output/data/rapid_bmi_change_cancerandlowbmi_removed_ethnic_adjusted.csv
bmi_rapid_change_sexage_adjusted_lowbmiexcluded:
run: r:latest analysis/bmi_trajectory/rapid_bmi_change/rapid_change_cancerlowbmiec_sexage_adj.R --output-dir=output/data
needs: [bmi_change_category_proportion_plots]
outputs:
moderately_sensitive:
table1: output/data/rapid_bmi_change_cancerandlowbmi_removed_sexage_adjusted.csv
bmi_rapid_change_imdsexage_adjusted_lowbmiexcluded:
run: r:latest analysis/bmi_trajectory/rapid_bmi_change/rapid_change_cancerlowbmiexc_imdsexage_adj.R --output-dir=output/data
needs: [bmi_change_category_proportion_plots]
outputs:
moderately_sensitive:
table1: output/data/rapid_bmi_change_cancerandlowbmi_removed_imdsexage_adjusted.csv
bmi_rapid_change_imdsexageethnic_adjusted_lowbmiexcluded:
run: r:latest analysis/bmi_trajectory/rapid_bmi_change/rapid_change_cancerlowbmiexc_imdsexageethnic_adj.R --output-dir=output/data
needs: [bmi_change_category_proportion_plots]
outputs:
moderately_sensitive:
table1: output/data/rapid_bmi_change_cancerandlowbmi_removed_imdsexageethnic_adjusted.csv
## Top decile weight gain all
## TOP decile weight gain
bmi_gain_top_decile_univariate.R:
run: r:latest analysis/bmi_trajectory/top_decile/top_decile_weightgain_univariate.R --output-dir=output/data
needs: [bmi_change_category_proportion_plots]
outputs:
moderately_sensitive:
table1: output/data/weightgain_90th_popcharac.csv
table2: output/data/weightgain_90th_univariate.csv
table3: output/data/yearly_bmi_change_deciles.csv
bmi_gain_top_decile_age:
run: r:latest analysis/bmi_trajectory/top_decile/top_decile_weightgain_age_adj.R --output-dir=output/data
needs: [bmi_change_category_proportion_plots]
outputs:
moderately_sensitive:
table1: output/data/weightgain_90th_age_adj.csv
bmi_gain_top_decile_sex:
run: r:latest analysis/bmi_trajectory/top_decile/top_decile_weightgain_sex_adj.R --output-dir=output/data
needs: [bmi_change_category_proportion_plots]
outputs:
moderately_sensitive:
table1: output/data/weightgain_90th_sex_adj.csv
bmi_gain_top_decile_imd:
run: r:latest analysis/bmi_trajectory/top_decile/top_decile_weightgain_imd_adj.R --output-dir=output/data
needs: [bmi_change_category_proportion_plots]
outputs:
moderately_sensitive:
table1: output/data/weightgain_90th_imd_adj.csv
bmi_gain_top_decile_eth:
run: r:latest analysis/bmi_trajectory/top_decile/top_decile_weightgain_ethnicity_adj.R --output-dir=output/data
needs: [bmi_change_category_proportion_plots]
outputs:
moderately_sensitive:
table1: output/data/weightgain_90th_ethnicity_adj.csv
bmi_gain_top_decile_agesex:
run: r:latest analysis/bmi_trajectory/top_decile/top_decile_weightgain_agesex.R --output-dir=output/data
needs: [bmi_change_category_proportion_plots]
outputs:
moderately_sensitive:
table1: output/data/weightgain_90th_agesex_adj.csv
## top decile lowbmi excluded
bmi_gain_top_decile_lowbmiexc_univariate:
run: r:latest analysis/bmi_trajectory/top_decile/top_decile_weightgain_lowbmiexc_univariate.R --output-dir=output/data
needs: [bmi_change_category_proportion_plots]
outputs:
highly_sensitive:
table1: output/data/weightgain_lowbmiexc_90th_data.csv
moderately_sensitive:
table1: output/data/weightgain_lowbmiexc_90th_popcharac.csv
table2: output/data/weightgain_lowbmiexc_90th_univariate.csv
table3: output/data/yearly_lowbmiexc_bmi_change_deciles.csv
bmi_gain_top_decile_lowbmiexc_age:
run: r:latest analysis/bmi_trajectory/top_decile/top_decile_weightgain_lowbmiexc_age.R --output-dir=output/data
needs: [bmi_gain_top_decile_lowbmiexc_univariate]
outputs:
moderately_sensitive:
table1: output/data/weightgain_lowbmiexc_90th_age_adj.csv
bmi_gain_top_decile_lowbmiexc_sex:
run: r:latest analysis/bmi_trajectory/top_decile/top_decile_weightgain_lowbmiexc_sex.R --output-dir=output/data
needs: [bmi_gain_top_decile_lowbmiexc_univariate]
outputs:
moderately_sensitive:
table1: output/data/weightgain_lowbmiexc_90th_sex_adj.csv
bmi_gain_top_decile_lowbmiexc_agesex:
run: r:latest analysis/bmi_trajectory/top_decile/top_decile_weightgain_lowbmiexc_agesex.R --output-dir=output/data
needs: [bmi_gain_top_decile_lowbmiexc_univariate]
outputs:
moderately_sensitive:
table1: output/data/weightgain_lowbmiexc_90th_agesex_adj.csv
## change in BMI trajectory pre and post covid
bmi_trajectory_change_summary:
run: r:latest analysis/BMI_change_diff_trajectories_summary.R --output-dir=output/data
needs: [BMI_trajectories_demographics_correction]
outputs:
highly_sensitive:
cohort1: output/data/BMI_trajectory_models_data.feather
moderately_sensitive:
table1: output/data/mean_bmi_traj_change.csv
chart1: output/change_bmi_trajectories.png
chart2: output/change_bmi_trajectories_counts.png
bmi_positive_trajectory_change_proportion:
run: r:latest analysis/bmi_trajectory/bmi_trajectory_positive_change_prop.R --output-dir=output/data
needs: [bmi_trajectory_change_summary]
outputs:
moderately_sensitive:
table1: output/data/bmi_trajectory_positive_change_proportions.csv
bmi_positive_trajectory_change_chi:
run: r:latest analysis/bmi_trajectory/bmi_trajectory_positive_change_chi.R --output-dir=output/data
needs: [bmi_trajectory_change_summary]
outputs:
moderately_sensitive:
table1: output/data/bmi_trajectory_positive_change_chi.csv
bmi_trajectory_change_summary_DWMP:
run: r:latest analysis/BMI_change_diff_traj_summ_DWMP_groups.R --output-dir=output/data
needs: [bmi_trajectory_change_summary]
outputs:
moderately_sensitive:
table1: output/data/mean_bmi_traj_change_hypertension.csv
table2: output/data/mean_bmi_traj_change_t2dm.csv
table3: output/data/mean_bmi_traj_change_t1dm.csv
bmi_trajectory_change_summary_mentalhealth_2:
run: r:latest analysis/bmi_trajectory/trajectory_change/BMI_change_traj_summ_mentalhealthLD_groups.R --output-dir=output/data
needs: [bmi_trajectory_change_summary]
outputs:
moderately_sensitive:
table1: output/data/mean_bmi_traj_change_depression.csv
table2: output/data/mean_bmi_traj_change_learning_disability.csv
table3: output/data/mean_bmi_traj_change_psychosis_schiz_bipolar.csv
bmi_trajectory_change_model_univariate:
run: r:latest analysis/BMI_change_diff_trajectories_univariate.R --output-dir=output/data
needs: [bmi_trajectory_change_summary]
outputs:
moderately_sensitive:
table1: output/data/univariate_bmi_trajectory_change.csv
table2: output/data/univariate_bmi_trajectory_change_hypertension.csv
table3: output/data/univariate_bmi_trajectory_change_T1DM.csv
table4: output/data/univariate_bmi_trajectory_change_T2DM.csv
bmi_trajectory_change_model_age:
run: r:latest analysis/BMI_change_diff_trajectories_age_model.R --output-dir=output/data
needs: [bmi_trajectory_change_summary]
outputs:
moderately_sensitive:
table1: output/data/age_adjusted_bmi_trajectory_change.csv
table2: output/data/age_adjusted_bmi_trajectory_change_hypertension.csv
table3: output/data/age_adjusted_bmi_trajectory_change_T1DM.csv
table4: output/data/age_adjusted_bmi_trajectory_change_T2DM.csv
redact_bmi_trajectory_change_T1DM:
run: r:latest analysis/redact_bmi_trajectory_change_T1DM.R --output-dir=output/data
needs: [bmi_trajectory_change_summary_DWMP, bmi_trajectory_change_model_univariate, bmi_trajectory_change_model_age]
outputs:
moderately_sensitive:
table1: output/data/mean_bmi_traj_change_t1dm_redacted.csv
table2: output/data/univariate_bmi_traj_change_t1dm_redacted.csv
table3: output/data/age_adj_bmi_traj_change_t1dm_redacted.csv
bmi_trajectory_change_pop_with_depression:
run: r:latest analysis/bmi_trajectory/trajectory_change/BMI_traj_change_lowbmi_exc_depression_models.R --output-dir=output/data
needs: [bmi_trajectory_change_summary]
outputs:
moderately_sensitive:
table1: output/data/depression_lowbmi_excluded_bmi_trajectory_change_univariate.csv
table2: output/data/depression_lowbmi_excluded_bmi_trajectory_change_sex_adj.csv
table3: output/data/depression_lowbmi_excluded_bmi_trajectory_change_age_adj.csv
table4: output/data/depression_lowbmi_excluded_bmi_trajectory_change_ethnicity_adj.csv
table5: output/data/depression_lowbmi_excluded_bmi_trajectory_change_imd_adj.csv
table6: output/data/depression_lowbmi_excluded_bmi_trajectory_change_sexage_adj.csv
table7: output/data/depression_lowbmi_excluded_bmi_trajectory_change_sexageimd_adj.csv
table8: output/data/depression_lowbmi_excluded_bmi_trajectory_change_sexageeth_adj.csv
table9: output/data/depression_lowbmi_excluded_bmi_trajectory_change_sexageethimd_adj.csv
bmi_trajectory_change_pop_with_learning_diff:
run: r:latest analysis/bmi_trajectory/trajectory_change/BMI_traj_change_lowbmi_exc_learning_diff_models.R --output-dir=output/data
needs: [bmi_trajectory_change_summary]
outputs:
moderately_sensitive:
table1: output/data/learning_diff_lowbmi_excluded_bmi_trajectory_change_univariate.csv
table2: output/data/learning_diff_lowbmi_excluded_bmi_trajectory_change_sex_adj.csv
table3: output/data/learning_diff_lowbmi_excluded_bmi_trajectory_change_age_adj.csv
table4: output/data/learning_diff_lowbmi_excluded_bmi_trajectory_change_ethnicity_adj.csv
table5: output/data/learning_diff_lowbmi_excluded_bmi_trajectory_change_imd_adj.csv
table6: output/data/learning_diff_lowbmi_excluded_bmi_trajectory_change_sexage_adj.csv
table7: output/data/learning_diff_lowbmi_excluded_bmi_trajectory_change_sexageimd_adj.csv
table8: output/data/learning_diff_lowbmi_excluded_bmi_trajectory_change_sexageeth_adj.csv
table9: output/data/learning_diff_lowbmi_excluded_bmi_trajectory_change_sexageethimd_adj.csv
bmi_trajectory_change_pop_with_SMI:
run: r:latest analysis/bmi_trajectory/trajectory_change/BMI_traj_change_lowbmi_exc_SMI_models.R --output-dir=output/data
needs: [bmi_trajectory_change_summary]
outputs:
moderately_sensitive:
table1: output/data/SMI_lowbmi_excluded_bmi_trajectory_change_univariate.csv
table2: output/data/SMI_lowbmi_excluded_bmi_trajectory_change_sex_adj.csv
table3: output/data/SMI_lowbmi_excluded_bmi_trajectory_change_age_adj.csv
table4: output/data/SMI_lowbmi_excluded_bmi_trajectory_change_ethnicity_adj.csv
table5: output/data/SMI_lowbmi_excluded_bmi_trajectory_change_imd_adj.csv
table6: output/data/SMI_lowbmi_excluded_bmi_trajectory_change_sexage_adj.csv
table7: output/data/SMI_lowbmi_excluded_bmi_trajectory_change_sexageimd_adj.csv
table8: output/data/SMI_lowbmi_excluded_bmi_trajectory_change_sexageeth_adj.csv
table9: output/data/SMI_lowbmi_excluded_bmi_trajectory_change_sexageethimd_adj.csv
bmi_trajectory_change_pop_with_SMI_redact:
run: r:latest analysis/bmi_trajectory/trajectory_change/redact_SMI_traj_change.R --output-dir=output/data
needs: [bmi_trajectory_change_pop_with_SMI, bmi_trajectory_change_summary_mentalhealth_2]
outputs:
moderately_sensitive:
table1: output/data/SMI_lowbmi_excluded_bmi_trajectory_change_univariate_redact.csv
table2: output/data/SMI_lowbmi_excluded_bmi_trajectory_change_sex_adj_redact.csv
table3: output/data/SMI_lowbmi_excluded_bmi_trajectory_change_age_adj_redact.csv
table4: output/data/SMI_lowbmi_excluded_bmi_trajectory_change_ethnicity_adj_redact.csv
table5: output/data/SMI_lowbmi_excluded_bmi_trajectory_change_imd_adj_redact.csv
table6: output/data/SMI_lowbmi_excluded_bmi_trajectory_change_sexage_adj_redact.csv
table7: output/data/SMI_lowbmi_excluded_bmi_trajectory_change_sexageimd_adj_redact.csv
table8: output/data/SMI_lowbmi_excluded_bmi_trajectory_change_sexageeth_adj_redact.csv
table9: output/data/SMI_lowbmi_excluded_bmi_trajectory_change_sexageethimd_adj_redact.csv
table10: output/data/mean_bmi_traj_change_psychosis_schiz_bipolar_redact.csv
bmi_trajectory_change_precovid_change_lowbmiexc:
run: r:latest analysis/bmi_trajectory/trajectory_change/BMI_traj_change_precovid_change_lowbmiexc.R --output-dir=output/data
needs: [bmi_trajectory_change_summary]
outputs:
moderately_sensitive:
table1: output/data/mean_traj_change_by_precovid_change_lowbmiexc.csv
table2: output/data/models_traj_change_by_precovid_change_lowbmiexc.csv
bmi_trajectory_change_precovid_change:
run: r:latest analysis/bmi_trajectory/trajectory_change/BMI_traj_change_precovid_change.R --output-dir=output/data
needs: [bmi_trajectory_change_summary]
outputs:
moderately_sensitive:
table1: output/data/mean_traj_change_by_precovid_change.csv
table2: output/data/models_traj_change_by_precovid_change.csv
## trajectory change calculations - with prepandemic underweight and cancer excluded
bmi_trajectory_change_summary_lowbmi_excluded:
run: r:latest analysis/BMI_change_diff_traj_summ_cancerandlowbmi_removed.R --output-dir=output/data
needs: [bmi_trajectory_change_summary]
outputs:
moderately_sensitive:
table1: output/data/mean_bmi_traj_change_cancerandlowbmi_removed_hypertension.csv
table2: output/data/mean_bmi_traj_change_cancerandlowbmi_removed_t2dm.csv
table3: output/data/mean_bmi_traj_change_cancerandlowbmi_removed_t1dm.csv
table4: output/data/mean_bmi_traj_change_cancerandlowbmi_removed.csv
bmi_trajectory_change_lowbmi_excluded_univariate:
run: r:latest analysis/BMI_trajectory_change_lowbmi_excluded_univariate.R --output-dir=output/data
needs: [bmi_trajectory_change_summary]
outputs:
moderately_sensitive:
table1: output/data/univariate_lowbmi_excluded_bmi_trajectory_change.csv
table2: output/data/univariate_lowbmi_excluded_bmi_trajectory_change_hypertension.csv
table3: output/data/univariate_lowbmi_excluded_bmi_trajectory_change_T1DM.csv
table4: output/data/univariate_lowbmi_excluded_bmi_trajectory_change_T2DM.csv
bmi_trajectory_change_lowbmi_excluded_age_adjusted:
run: r:latest analysis/BMI_trajectory_change_lowbmi_excluded_age_adjusted.R --output-dir=output/data
needs: [bmi_trajectory_change_summary]
outputs:
moderately_sensitive:
table1: output/data/age_adjusted_lowbmi_excluded_bmi_trajectory_change.csv
table2: output/data/age_adjusted_lowbmi_excluded_bmi_trajectory_change_hypertension.csv
table3: output/data/age_adjusted_lowbmi_excluded_bmi_trajectory_change_T1DM.csv
table4: output/data/age_adjusted_lowbmi_excluded_bmi_trajectory_change_T2DM.csv
## adjusted models
bmi_trajectory_change_lowbmi_excluded_sex_adjusted:
run: r:latest analysis/bmi_trajectory/trajectory_change/BMI_trajectory_change_lowbmi_excluded_sex_adjusted.R --output-dir=output/data
needs: [bmi_trajectory_change_summary]
outputs:
moderately_sensitive:
table1: output/data/sex_adjusted_lowbmi_excluded_bmi_trajectory_change.csv
table2: output/data/sex_adjusted_lowbmi_excluded_bmi_trajectory_change_hypertension.csv
table3: output/data/sex_adjusted_lowbmi_excluded_bmi_trajectory_change_T1DM.csv
table4: output/data/sex_adjusted_lowbmi_excluded_bmi_trajectory_change_T2DM.csv
bmi_trajectory_change_lowbmi_excluded_imd_adjusted:
run: r:latest analysis/bmi_trajectory/trajectory_change/BMI_trajectory_change_lowbmi_excluded_imd_adjusted.R --output-dir=output/data
needs: [bmi_trajectory_change_summary]
outputs:
moderately_sensitive:
table1: output/data/imd_adjusted_lowbmi_excluded_bmi_trajectory_change.csv
table2: output/data/imd_adjusted_lowbmi_excluded_bmi_trajectory_change_hypertension.csv
table3: output/data/imd_adjusted_lowbmi_excluded_bmi_trajectory_change_T1DM.csv
table4: output/data/imd_adjusted_lowbmi_excluded_bmi_trajectory_change_T2DM.csv
bmi_trajectory_change_lowbmi_excluded_ethnic_adjusted:
run: r:latest analysis/bmi_trajectory/trajectory_change/BMI_trajectory_change_lowbmi_excluded_ethnic_adjusted.R --output-dir=output/data
needs: [bmi_trajectory_change_summary]
outputs:
moderately_sensitive:
table1: output/data/ethnic_adjusted_lowbmi_excluded_bmi_trajectory_change.csv
table2: output/data/ethnic_adjusted_lowbmi_excluded_bmi_trajectory_change_hypertension.csv
table3: output/data/ethnic_adjusted_lowbmi_excluded_bmi_trajectory_change_T1DM.csv
table4: output/data/ethnic_adjusted_lowbmi_excluded_bmi_trajectory_change_T2DM.csv
bmi_trajectory_change_lowbmi_excluded_sexage_adjusted:
run: r:latest analysis/bmi_trajectory/trajectory_change/BMI_trajectory_change_lowbmi_excluded_sexage_adjusted.R --output-dir=output/data
needs: [bmi_trajectory_change_summary]
outputs:
moderately_sensitive:
table1: output/data/sexage_adjusted_lowbmi_excluded_bmi_trajectory_change.csv
table2: output/data/sexage_adjusted_lowbmi_excluded_bmi_trajectory_change_hypertension.csv
table3: output/data/sexage_adjusted_lowbmi_excluded_bmi_trajectory_change_T1DM.csv
table4: output/data/sexage_adjusted_lowbmi_excluded_bmi_trajectory_change_T2DM.csv
bmi_trajectory_change_lowbmi_excluded_sexageimd_adjusted:
run: r:latest analysis/bmi_trajectory/trajectory_change/BMI_trajectory_change_lowbmi_excluded_sexageimd_adjusted.R --output-dir=output/data
needs: [bmi_trajectory_change_summary]
outputs:
moderately_sensitive:
table1: output/data/sexageimd_adjusted_lowbmi_excluded_bmi_trajectory_change.csv
table2: output/data/sexageimd_adjusted_lowbmi_excluded_bmi_trajectory_change_hypertension.csv
table3: output/data/sexageimd_adjusted_lowbmi_excluded_bmi_trajectory_change_T1DM.csv
table4: output/data/sexageimd_adjusted_lowbmi_excluded_bmi_trajectory_change_T2DM.csv
bmi_trajectory_change_lowbmi_excluded_sexageethnic_adjusted:
run: r:latest analysis/bmi_trajectory/trajectory_change/BMI_trajectory_change_lowbmi_excluded_sexageethnic_adjusted.R --output-dir=output/data
needs: [bmi_trajectory_change_summary]
outputs:
moderately_sensitive:
table1: output/data/sexageethnic_adjusted_lowbmi_excluded_bmi_trajectory_change.csv
table2: output/data/sexageethnic_adjusted_lowbmi_excluded_bmi_trajectory_change_hypertension.csv
table3: output/data/sexageethnic_adjusted_lowbmi_excluded_bmi_trajectory_change_T1DM.csv
table4: output/data/sexageethnic_adjusted_lowbmi_excluded_bmi_trajectory_change_T2DM.csv
bmi_trajectory_change_lowbmi_excluded_sexageimdethnic_adjusted:
run: r:latest analysis/bmi_trajectory/trajectory_change/BMI_trajectory_change_lowbmi_excluded_sexageimdethnic_adjusted.R --output-dir=output/data
needs: [bmi_trajectory_change_summary]
outputs:
moderately_sensitive:
table1: output/data/sexageimdethnic_adjusted_lowbmi_excluded_bmi_trajectory_change.csv
table2: output/data/sexageimdethnic_adjusted_lowbmi_excluded_bmi_trajectory_change_hypertension.csv
table3: output/data/sexageimdethnic_adjusted_lowbmi_excluded_bmi_trajectory_change_T1DM.csv
table4: output/data/sexageimdethnic_adjusted_lowbmi_excluded_bmi_trajectory_change_T2DM.csv
bmi_trajectory_change_lowbmi_excluded_T1DM_redact:
run: r:latest analysis/bmi_trajectory/trajectory_change/redact_T1DM_traj_change.R --output-dir=output/data
needs: [bmi_trajectory_change_lowbmi_excluded_sexageimdethnic_adjusted, bmi_trajectory_change_lowbmi_excluded_sexageethnic_adjusted, bmi_trajectory_change_lowbmi_excluded_sexageimd_adjusted, bmi_trajectory_change_lowbmi_excluded_sexage_adjusted, bmi_trajectory_change_lowbmi_excluded_ethnic_adjusted, bmi_trajectory_change_lowbmi_excluded_imd_adjusted, bmi_trajectory_change_lowbmi_excluded_sex_adjusted, bmi_trajectory_change_lowbmi_excluded_age_adjusted, bmi_trajectory_change_lowbmi_excluded_univariate, bmi_trajectory_change_summary_lowbmi_excluded ]
outputs:
moderately_sensitive:
table1: output/data/mean_bmi_traj_change_cancerandlowbmi_removed_T1DM_redact.csv
table2: output/data/univariate_lowbmi_excluded_bmi_trajectory_change_T1DM_redact.csv
table3: output/data/ethnic_adjusted_lowbmi_excluded_bmi_trajectory_change_T1DM_redact.csv
table4: output/data/sex_adjusted_lowbmi_excluded_bmi_trajectory_change_T1DM_redact.csv
table5: output/data/sexageimdethnic_adjusted_lowbmi_excluded_bmi_trajectory_change_T1DM_redact.csv
table6: output/data/sexageethnic_adjusted_lowbmi_excluded_bmi_trajectory_change_T1DM_redact.csv
table7: output/data/sexageimd_adjusted_lowbmi_excluded_bmi_trajectory_change_T1DM_redact.csv
table8: output/data/sexage_adjusted_lowbmi_excluded_bmi_trajectory_change_T1DM_redact.csv
table9: output/data/imd_adjusted_lowbmi_excluded_bmi_trajectory_change_T1DM_redact.csv
table10: output/data/age_adjusted_lowbmi_excluded_bmi_trajectory_change_T1DM_redact.csv
bmi_trajectory_change_lowbmi_excluded_complete_data_proportions:
run: r:latest analysis/bmi_trajectory/trajectory_change/BMI_traj_change_complete_case_counts.R --output-dir=output/data
needs: [bmi_change_category_proportion_plots]
outputs:
moderately_sensitive:
table1: output/data/complete_traj_data_proportions.csv
bmi_trajectory_change_lowbmi_excluded_complete_data_chi:
run: r:latest analysis/bmi_trajectory/trajectory_change/BMI_traj_change_complete_cases_chi.R --output-dir=output/data
needs: [bmi_change_category_proportion_plots]
outputs:
moderately_sensitive:
table1: output/data/complete_traj_data_prop_chi.csv
## box plots with filtered data (excluding extreme changes
bmi_change_boxplots:
run: r:latest analysis/bmi_change_boxplots.R --output-dir=output/data
needs: [BMI_trajectories_demographics_correction]
outputs:
moderately_sensitive:
chart1: output/covid_bmi_change_cardiac.png
chart2: output/covid_bmi_change_depression.png
chart3: output/covid_bmi_change_ethnicity.png
chart4: output/covid_bmi_change_learning_diff.png
chart5: output/covid_bmi_change_region.png
chart6: output/covid_bmi_change_sex.png
chart7: output/covid_bmi_change_serious_mental.png
chart8: output/covid_bmi_change_t1dm.png
chart9: output/covid_bmi_change_t2dm.png
chart10: output/covid_bmi_change_imd.png
chart11: output/covid_bmi_change_hypertension.png
## Tables of BMI change categories
bmi_change_category_tables:
run: r:latest analysis/BMI_change_trajectories_table.R --output-dir=output/data
needs: [bmi_change_category_proportion_plots]
outputs:
moderately_sensitive:
table1: output/data/postcovid_bmi_trajectories.csv
table2: output/data/precovid_bmi_trajectories.csv
### Transition between BMI categories
generate_bmi_category_data:
run: r:latest analysis/BMI_cat_change_data.R --output-dir=output/data
needs: [generate_complete_median_BMI_data]
outputs:
highly_sensitive:
table1: output/data/BMI_category_transition.feather
## univariate models of transition between categories
bmi_category_transitions:
run: r:latest analysis/BMI_category_transitions_univariate.R --output-dir=output/data
needs: [generate_bmi_category_data]
outputs:
moderately_sensitive:
table1: output/data/bmi_category_transitions.csv
table2: output/data/healthy_transition_weightgain_univariate.csv
table3: output/data/healthy_transition_weightgain_2017_univariate.csv
table4: output/data/healthy_transition_weightgain_2019_univariate.csv
table5: output/data/overweight_transition_weightgain_univariate.csv
table6: output/data/overweight_transition_weightgain_2017_univariate.csv
table7: output/data/overweight_transition_weightgain_2019_univariate.csv
table8: output/data/overweight_transition_weightloss_univariate.csv
table9: output/data/overweight_transition_weightloss_2017_univariate.csv
table10: output/data/overweight_transition_weightloss_2019_univariate.csv
table11: output/data/obese_transition_weightloss_univariate.csv
table12: output/data/obese_transition_weightloss_2017_univariate.csv
table13: output/data/obese_transition_weightloss_2019_univariate.csv
## age adjusted models of transition between categories
bmi_category_transitions_age_adjusted:
run: r:latest analysis/BMI_category_transitions_age_adj.R --output-dir=output/data
needs: [generate_bmi_category_data]
outputs:
moderately_sensitive:
table1: output/data/bmi_category_transitions_round.csv
table2: output/data/healthy_transition_weightgain_age_adj.csv
table3: output/data/healthy_transition_weightgain_2017_age_adj.csv
table4: output/data/healthy_transition_weightgain_2019_age_adj.csv
table5: output/data/overweight_transition_weightgain_age_adj.csv
table6: output/data/overweight_transition_weightgain_2017_age_adj.csv
table7: output/data/overweight_transition_weightgain_2019_age_adj.csv
table8: output/data/overweight_transition_weightloss_age_adj.csv
table9: output/data/overweight_transition_weightloss_2017_age_adj.csv
table10: output/data/overweight_transition_weightloss_2019_age_adj.csv
table11: output/data/obese_transition_weightloss_age_adj.csv
table12: output/data/obese_transition_weightloss_2017_age_adj.csv
table13: output/data/obese_transition_weightloss_2019_age_adj.csv
bmi_category_transitions_admin:
run: r:latest analysis/admin_round_bmi_category_transitions.R --output-dir=output/data
needs: [bmi_category_transitions_age_adjusted]
outputs:
moderately_sensitive:
table1: output/data/bmi_category_transitions_round_2.csv
bmi_category_transitions_counts:
run: r:latest analysis/BMI_category_transitions_counts.R --output-dir=output/data
needs: [generate_bmi_category_data]
outputs:
moderately_sensitive:
table1: output/data/healthy_transition_weightgain_counts.csv
table2: output/data/overweight_transition_weightgain_counts.csv
table3: output/data/overweight_transition_weightloss_counts.csv
table4: output/data/obese_transition_weightloss_counts.csv
###########################
###########################
## DWMP Eligible
generate_DWMP_proportion:
run: r:latest analysis/DWMP_proportion.R --output-dir=output/data
needs: [generate_complete_median_BMI_data]
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_complete_median_BMI_data]
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_complete_median_BMI_data]
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_complete_median_BMI_data]
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
DWMP_2017_2021_counts:
run: r:latest analysis/DWMP_counts.R --output-dir=output/data
needs: [generate_complete_median_BMI_data]
outputs:
moderately_sensitive:
table1: output/data/DWMP_counts_total_pop.csv
table2: output/data/DWMP_counts_all_eligible.csv
table3: output/data/DWMP_counts_hypertension.csv
table4: output/data/DWMP_counts_T1DM.csv
table5: output/data/DWMP_counts_T2DM.csv
DWMP_2017_2021_models:
run: r:latest analysis/DWMP_counts_models.R --output-dir=output/data
needs: [generate_complete_median_BMI_data]
outputs:
moderately_sensitive:
table1: output/data/univariate_DWMP_hypertension.csv
table2: output/data/univariate_DWMP_T2DM.csv
table3: output/data/univariate_DWMP_T1DM.csv
table4: output/data/age_adjusted_DWMP_hypertension.csv
table5: output/data/age_adjusted_DWMP_T2DM.csv
table6: output/data/age_adjusted_DWMP_T1DM.csv
## TOTAL ELIGIBLE USING ALL BMI DATA FROM LAST 5 YEARS
DWMP_eligible_5yr_data:
run: r:latest analysis/DWMP_eligibility/DWMP_eligible.R --output-dir=output/data
needs: [generate_complete_median_BMI_data]
outputs:
moderately_sensitive:
table1: output/data/DWMP_eligible_5yr_data_all.csv
table2: output/data/DWMP_eligible_5yr_data_hypertension.csv
table3: output/data/DWMP_eligible_5yr_data_T1DM.csv
table4: output/data/DWMP_eligible_5yr_data_T2DM.csv
table5: output/data/DWMP_eligible_5yr_data_years.csv
DWMP_eligible_5yr_data_2019:
run: r:latest analysis/DWMP_eligibility/DWMP_eligible_2019.R --output-dir=output/data
needs: [generate_complete_median_BMI_data]
outputs:
moderately_sensitive:
table1: output/data/DWMP_eligible_5yr_data_all_2019.csv
table2: output/data/DWMP_eligible_5yr_data_hypertension_2019.csv
table3: output/data/DWMP_eligible_5yr_data_T1DM_2019.csv
table4: output/data/DWMP_eligible_5yr_data_T2DM_2019.csv
table5: output/data/DWMP_eligible_5yr_data_years_2019.csv
obese_eligible_5yr_data:
run: r:latest analysis/DWMP_eligibility/Obese_5yr.R --output-dir=output/data
needs: [generate_complete_median_BMI_data]
outputs:
moderately_sensitive:
table1: output/data/obese_5yr_data_all.csv
table2: output/data/obese_5yr_data_hypertension.csv
table3: output/data/obese_5yr_data_T1DM.csv
table4: output/data/obese_5yr_data_T2DM.csv
table5: output/data/obese_5yr_data_years.csv
obese_eligible_5yr_data_2019:
run: r:latest analysis/DWMP_eligibility/Obese_5yr_2019.R --output-dir=output/data
needs: [generate_complete_median_BMI_data]
outputs:
moderately_sensitive:
table1: output/data/obese_5yr_data_all_2019.csv
table2: output/data/obese_5yr_data_hypertension_2019.csv
table3: output/data/obese_5yr_data_T1DM_2019.csv
table4: output/data/obese_5yr_data_T2DM_2019.csv
table5: output/data/obese_5yr_data_years_2019.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: [generate_complete_median_BMI_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: [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: [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_2019.R --output-dir=output/data --output-format feather
needs: [join_meds]
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_meds]
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
T2DM_hba1c_proportions_2019:
run: r:latest analysis/hba1c_had_proportion_2019_t2dm.R --output-dir=output/data --output-format feather
needs: [generate_hba1c_2018_2019_data]
outputs:
moderately_sensitive:
table1: output/data/T2DM_proportion_hba1c_2019.csv
T2DM_hba1c_proportions_2020:
run: r:latest analysis/hba1c_had_proportion_2020_t2dm.R --output-dir=output/data --output-format feather
needs: [generate_hba1c_2018_2019_data, generate_hba1c_2020_2021_data]
outputs:
moderately_sensitive:
table1: output/data/T2DM_proportion_hba1c_2020.csv
T2DM_hba1c_proportions_2021:
run: r:latest analysis/hba1c_had_proportion_2021_t2dm.R --output-dir=output/data --output-format feather
needs: [generate_hba1c_2018_2019_data, generate_hba1c_2020_2021_data]
outputs:
moderately_sensitive:
table1: output/data/T2DM_proportion_hba1c_2021.csv
check_hba1c:
run: r:latest analysis/check_hba1c.R --output-dir=output/data --output-format feather
needs: [generate_study_population_1]
outputs:
moderately_sensitive:
table1: output/data/check_hba1c.csv
merge_tables:
run: r:latest analysis/combine_proportions.R --output-dir=output/data --output-format feather
needs: [generate_median_bmi_range_2019, generate_median_bmi_range_2020, generate_median_bmi_range_2021, generate_DWMP_proportion, generate_DWMP_hypertension_proportion, generate_DWMP_t2dm_proportion, generate_DWMP_t1dm_proportion, generate_had_bmi_proportion_2019, generate_had_bmi_proportion_2020, generate_had_bmi_proportion_2021, generate_obese_proportion_2019, generate_obese_proportion_2020, generate_obese_proportion_2021, generate_had_sbp_proportion_2019, generate_had_sbp_proportion_2020, generate_had_sbp_proportion_2021]
outputs:
moderately_sensitive:
table1: output/data/had_bmi_all.csv
table2: output/data/proportion_obese_all.csv
table3: output/data/had_sbp_all.csv
table4: output/data/DWMP_all.csv
table5: output/data/DWMP_hypertension_all.csv
table6: output/data/DWMP_T2DM_all.csv
table7: output/data/DWMP_T1DM_all.csv
table8: output/data/BMI_median_range_all.csv
round_tables:
run: r:latest analysis/admin_round_redact_table.R --output-dir=output/data --output-format feather
needs: [bmi_change_univariate, bmi_change_category_tables, bmi_trajectory_change_summary]
outputs:
moderately_sensitive:
table1: output/data/rapid_bmi_change_popcharac_round.csv
table2: output/data/precovid_bmi_trajectories.round.csv
table3: output/data/postcovid_bmi_trajectories.round.csv
table4: output/data/mean_bmi_traj_change_round.csv
round_tables_2:
run: r:latest analysis/admin_round_2.R --output-dir=output/data --output-format feather
needs: [BMI_trajectories_demographics_correction]
outputs:
moderately_sensitive:
table1: output/data/complete_bmi_trajectory_data.csv
###########
## SENSITIVITY ANALYSIS
###########
## Prepare for MICS
MICE_data_1:
run: r:latest analysis/sensitivity_analyses/MICE_data_prep1.R --output-dir=output/data --output-format feather
needs: [BMI_trajectories_demographics_correction]
outputs:
highly_sensitive:
table1: output/data/imputation_data_long.csv
MICE_data_2:
run: r:latest analysis/sensitivity_analyses/MICE_data_prep2.R --output-dir=output/data --output-format feather
needs: [MICE_data_1]
outputs:
highly_sensitive:
table1: output/data/imputation_dataframe.csv
table2: output/data/imputation_DF_for_impute.csv
table3: output/data/imputation_sample_missing.csv
MICE_sample_data:
run: r:latest analysis/sensitivity_analyses/MICE_sample_pop_demog.R --output-dir=output/data --output-format feather
needs: [MICE_data_2]
outputs:
moderately_sensitive:
table1: output/data/imputation_sample_pop_demographics.csv
table2: output/data/imputation_sample_missing_data.csv
MICE_model_check:
run: r:latest analysis/sensitivity_analyses/MICE_model_check.R --output-dir=output/data --output-format feather
needs: [MICE_data_1]
outputs:
highly_sensitive:
table1: output/data/imputation_dataframe_check.csv
table2: output/data/imputation_DF_for_impute_check.csv
MICE_models_age:
run: r:latest analysis/sensitivity_analyses/MICE_models_age_adj.R --output-dir=output/data --output-format feather
needs: [MICE_data_2]
outputs:
moderately_sensitive:
table1: output/data/imputation_age_adj.csv
MICE_models_sex:
run: r:latest analysis/sensitivity_analyses/MICE_models_sex.R --output-dir=output/data --output-format feather
needs: [MICE_data_2]
outputs:
moderately_sensitive:
table1: output/data/imputation_sex_adj.csv
MICE_models_age_sex:
run: r:latest analysis/sensitivity_analyses/MICE_models_age_sex.R --output-dir=output/data --output-format feather
needs: [MICE_data_2]
outputs:
moderately_sensitive:
table1: output/data/imputation_age_sex_adj.csv
MICE_data_3:
run: r:latest analysis/sensitivity_analyses/MICE_data_prep3.R --output-dir=output/data --output-format feather
needs: [MICE_data_2, MICE_sample_data]
outputs:
moderately_sensitive:
table1: output/data/imputation_univariate.csv
table2: output/data/imputation_sample_pop_demographic_round.csv
Timeline
-
Created:
-
Started:
-
Finished:
-
Runtime:
These timestamps are generated and stored using the UTC timezone on the backend.
Job information
- Status
-
Succeeded
- Backend
- TPP
- Workspace
- bmi_and_hba1c
- Requested by
- Miriam Samuel
- Branch
- main
- Force run dependencies
- No
- Git commit hash
- 4ccfda3
- Requested actions
-
-
bmi_gain_top_decile_lowbmiexc_univariate -
bmi_gain_top_decile_lowbmiexc_age -
bmi_gain_top_decile_lowbmiexc_sex -
bmi_gain_top_decile_lowbmiexc_agesex -
bmi_positive_trajectory_change_proportion -
bmi_positive_trajectory_change_chi -
bmi_trajectory_change_precovid_change_lowbmiexc -
bmi_trajectory_change_precovid_change -
bmi_trajectory_change_lowbmi_excluded_complete_data_chi -
DWMP_eligible_5yr_data_2019 -
obese_eligible_5yr_data_2019
-