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project.yaml
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project.yaml
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version: '3.0'
expectations:
population_size: 1000
actions:
create_dummy_data:
run: >
ehrql:v0
create-dummy-tables
analysis/dataset_definition.py output/dummydata
--
--day=0
outputs:
highly_sensitive:
openprompt_dummy: output/dummydata/open_prompt.csv
edit_dummy_data:
run: >
r:latest
analysis/00_dummy_data_editing/edit_automatic_dummy_data.R
needs: [create_dummy_data]
outputs:
highly_sensitive:
openprompt_dummy_edited: output/dummydata/dummy_edited/open_prompt.csv
scrape_all_data:
run: >
ehrql:v0
generate-dataset
analysis/scrape_data_response_dates.py
--output output/openprompt_all.csv
--dummy-tables output/dummydata/dummy_edited
needs: [edit_dummy_data]
outputs:
highly_sensitive:
openprompt_all: output/openprompt_all.csv
generate_openprompt_survey1:
run: >
ehrql:v0
generate-dataset
analysis/dataset_definition.py
--output output/openprompt_survey1.csv
--dummy-tables output/dummydata/dummy_edited
--
--day=0
--window=5
needs: [edit_dummy_data]
outputs:
highly_sensitive:
openprompt_survey1: output/openprompt_survey1.csv
generate_openprompt_survey2:
run: >
ehrql:v0
generate-dataset
analysis/dataset_definition.py
--output output/openprompt_survey2.csv
--dummy-tables output/dummydata/dummy_edited
--
--day=30
--window=5
needs: [edit_dummy_data]
outputs:
highly_sensitive:
openprompt_survey2: output/openprompt_survey2.csv
generate_openprompt_survey3:
run: >
ehrql:v0
generate-dataset
analysis/dataset_definition.py
--output output/openprompt_survey3.csv
--dummy-tables output/dummydata/dummy_edited
--
--day=60
--window=5
needs: [edit_dummy_data]
outputs:
highly_sensitive:
openprompt_survey3: output/openprompt_survey3.csv
generate_openprompt_survey4:
run: >
ehrql:v0
generate-dataset
analysis/dataset_definition.py
--output output/openprompt_survey4.csv
--dummy-tables output/dummydata/dummy_edited
--
--day=90
--window=5
needs: [edit_dummy_data]
outputs:
highly_sensitive:
openprompt_survey4: output/openprompt_survey4.csv
extract_linked_tpp_info:
run: >
ehrql:v0
generate-dataset
analysis/add_tpp_data.py
--output output/openprompt_linked_tpp.csv.gz
outputs:
highly_sensitive:
linked_tpp_data: output/openprompt_linked_tpp.csv.gz
extract_tpp_demographics:
run: >
ehrql:v0
generate-dataset
analysis/extract_tpp_demographics.py
--output output/opensafely_tpp_demographics.csv.gz
outputs:
highly_sensitive:
tpp_demog_data: output/opensafely_tpp_demographics.csv.gz
datacombine_and_figure1:
run: >
r:latest analysis/01_data_import/101_data_combine.R
needs: [scrape_all_data, generate_openprompt_survey1, generate_openprompt_survey2, generate_openprompt_survey3, generate_openprompt_survey4]
outputs:
highly_sensitive:
openprompt_combined: output/openprompt_raw.gz.parquet
moderately_sensitive:
openprompt_raw_skim: output/data_properties/op_raw_skim.txt
openprompt_raw_tab: output/data_properties/op_raw_tabulate.txt
openprompt_mapped_skim: output/data_properties/op_mapped_skim.txt
openprompt_mapped_tab: output/data_properties/op_mapped_tabulate.txt
raw_summ_base_s: output/data_properties/op_baseline_skim.txt
raw_summ_base_t: output/data_properties/op_baseline_tabulate.txt
raw_summ_survey1_s: output/data_properties/op_survey1_skim.txt
raw_summ_survey1_t: output/data_properties/op_survey1_tabulate.txt
raw_summ_survey2_s: output/data_properties/op_survey2_skim.txt
raw_summ_survey2_t: output/data_properties/op_survey2_tabulate.txt
raw_summ_survey3_s: output/data_properties/op_survey3_skim.txt
raw_summ_survey3_t: output/data_properties/op_survey3_tabulate.txt
raw_summ_survey4_s: output/data_properties/op_survey4_skim.txt
raw_summ_survey4_t: output/data_properties/op_survey4_tabulate.txt
check_days_after_baseline: output/data_properties/sample_day_lags.pdf
p1a_jpeg: output/plots/p1a_index_dates.jpeg
p1b_jpeg: output/plots/p1b_recorded_question_responses.jpeg
p1d_jpeg: output/plots/p1c_ltfu.jpeg
p1c_jpeg: output/plots/p1d_anyresponse_hist.jpeg
p1_jpeg: output/plots/p1_fup.jpeg
p1_pdf: output/plots/p1_fup.pdf
p1b_data: output/tables/fig1b_data.csv
p1c_data: output/tables/fig1c_data.csv
p1d_data: output/tables/fig1d_data.csv
import_linked_tpp:
run: >
r:latest analysis/01_data_import/102_import_linked_tpp.R
needs: [extract_linked_tpp_info]
outputs:
highly_sensitive:
linked_tpp_data_edited: output/openprompt_linked_tpp_edited.gz.parquet
moderately_sensitive:
openprompt_tpp_skim: output/data_properties/op_tpp_skim.txt
openprompt_tpp_tab: output/data_properties/op_tpp_tabulate.txt
export_table1_stats:
run: >
r:latest analysis/02_baseline_descriptive/201_table1stats.R
needs: [datacombine_and_figure1, import_linked_tpp]
outputs:
moderately_sensitive:
table1: output/tables/table1.html
table1_stats: output/tables/table1_stats.csv
# Then need to run analysis/02_baseline_descriptive/002-map-making.R to produce the Figure 2 for the paper
export_table2_fup_stats:
run: >
r:latest analysis/03_followup_responses/301_followup_table.R
needs: [datacombine_and_figure1]
outputs:
moderately_sensitive:
table2: output/tables/table2_followup.html
table2_stats: output/tables/table2_fup_stats.csv
# Then need to run analysis/03_followup_responses/302_followup_plots.R
export_data_agreement:
run: >
r:latest analysis/04_data_agreement/401_data_agreement.R
needs: [datacombine_and_figure1, import_linked_tpp]
outputs:
moderately_sensitive:
venndiagram_jpeg: output/plots/venn.jpeg
venndiagram_pdf: output/plots/venn.pdf
agreementdata: output/tables/table3_agreement.csv
export_data_representativeness:
run: >
r:latest analysis/05_representativeness/501_demographic_representativeness.R
needs: [datacombine_and_figure1, extract_tpp_demographics]
outputs:
moderately_sensitive:
table3_stats: output/tables/table3_rep_stats.csv
table3: output/tables/table3_represetativeness.html
# Then need to run analysis/05_representativeness/502_representativeness_plot.R to produce the Figure 4 for the paper