generated from opensafely/research-template
/
project.yaml
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/
project.yaml
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version: '3.0'
expectations:
population_size: 1000
actions:
generate_ethnicity:
run: cohortextractor:latest generate_cohort --study-definition study_definition_ethnicity --output-format=feather
outputs:
highly_sensitive:
cohort: output/input_ethnicity.feather
# generate_study_population:
# run: cohortextractor:latest generate_cohort --study-definition study_definition
# outputs:
# highly_sensitive:
# cohort: output/input.csv
#
generate_rates_1:
run: cohortextractor:latest generate_cohort --study-definition study_definition_rates --index-date-range "2023-05-01 to 2024-08-01 by month" --skip-existing --output-dir=output --output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/measures/inpu*.csv.gz
generate_rates_2:
run: cohortextractor:latest generate_cohort --study-definition study_definition_rates --index-date-range "2023-09-01 to 2024-03-01 by month" --skip-existing --output-dir=output --output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/measures/inp*.csv.gz
join_ethnicity:
run: python:latest python analysis/join_ethnicity_csvgz.py
needs:
[
generate_rates_1,
generate_rates_2,
generate_ethnicity,
]
outputs:
highly_sensitive:
cohort: output/measures/in*.csv.gz
generate_measures:
run: cohortextractor:latest generate_measures --study-definition study_definition_rates --skip-existing --output-dir=output/measures
needs:
[join_ethnicity]
outputs:
moderately_sensitive:
measure_csv1a: output/measures/measure_self_harmAE*_rate.csv
measure_csv1b: output/measures/measure_self_harmAEbyRegion*_rate.csv
measure_csv1c: output/measures/measure_self_harmAEbyIMD*_rate.csv
measure_csv1d: output/measures/measure_self_harmAEbyEthnicity*_rate.csv
measure_csv1e: output/measures/measure_self_harmAEbyAge*_rate.csv
measure_csv1f: output/measures/measure_self_harmHo*_rate.csv
measure_csv1g: output/measures/measure_self_harmHobyRegion*_rate.csv
measure_csv1h: output/measures/measure_self_harmHobyIMD*_rate.csv
measure_csv1i: output/measures/measure_self_harmHobyEthnicity*_rate.csv
measure_csv1j: output/measures/measure_self_harmHobyAge*_rate.csv
# measure_csv1k: output/measures/measure_self_harmDe*_rate.csv
# measure_csv1l: output/measures/measure_self_harmDebyRegion*_rate.csv
# measure_csv1m: output/measures/measure_self_harmDebyIMD*_rate.csv
# measure_csv1n: output/measures/measure_self_harmDebyEthnicity*_rate.csv
# measure_csv1o: output/measures/measure_self_harmDebyAge*_rate.csv
measure_csv2a: output/measures/measure_emot_distAE*_rate.csv
measure_csv2b: output/measures/measure_emot_distAEbyRegion*_rate.csv
measure_csv2c: output/measures/measure_emot_distAEbyIMD*_rate.csv
measure_csv2d: output/measures/measure_emot_distAEbyEthnicity*_rate.csv
measure_csv2e: output/measures/measure_emot_distAEbyAge*_rate.csv
measure_csv2f: output/measures/measure_emot_distHo*_rate.csv
measure_csv2g: output/measures/measure_emot_distHobyRegion*_rate.csv
measure_csv2h: output/measures/measure_emot_distHobyIMD*_rate.csv
measure_csv2i: output/measures/measure_emot_distHobyEthnicity*_rate.csv
measure_csv2j: output/measures/measure_emot_distHobyAge*_rate.csv
# measure_csv2k: output/measures/measure_emot_distDe*_rate.csv
# measure_csv2l: output/measures/measure_emot_distDebyRegion*_rate.csv
# measure_csv2m: output/measures/measure_emot_distDebyIMD*_rate.csv
# measure_csv2n: output/measures/measure_emot_distDebyEthnicity*_rate.csv
# measure_csv2o: output/measures/measure_emot_distDebyAge*_rate.csv
measure_csv3a: output/measures/measure_eat_disorAE*_rate.csv
measure_csv3b: output/measures/measure_eat_disorAEbyRegion*_rate.csv
measure_csv3c: output/measures/measure_eat_disorAEbyIMD*_rate.csv
measure_csv3d: output/measures/measure_eat_disorAEbyEthnicity*_rate.csv
measure_csv3e: output/measures/measure_eat_disorAEbyAge*_rate.csv
measure_csv3f: output/measures/measure_eat_disorHo*_rate.csv
measure_csv3g: output/measures/measure_eat_disorHobyRegion*_rate.csv
measure_csv3h: output/measures/measure_eat_disorHobyIMD*_rate.csv
measure_csv3i: output/measures/measure_eat_disorHobyEthnicity*_rate.csv
measure_csv3j: output/measures/measure_eat_disorHobyAge*_rate.csv
# measure_csv3k: output/measures/measure_eat_disorDe*_rate.csv
# measure_csv3l: output/measures/measure_eat_disorDebyRegion*_rate.csv
# measure_csv3m: output/measures/measure_eat_disorDebyIMD*_rate.csv
# measure_csv3n: output/measures/measure_eat_disorDebyEthnicity*_rate.csv
# measure_csv3o: output/measures/measure_eat_disorDebyAge*_rate.csv
measure_csv4a: output/measures/measure_lifestyleAE*_rate.csv
measure_csv4b: output/measures/measure_lifestyleAEbyRegion*_rate.csv
measure_csv4c: output/measures/measure_lifestyleAEbyIMD*_rate.csv
measure_csv4d: output/measures/measure_lifestyleAEbyEthnicity*_rate.csv
measure_csv4e: output/measures/measure_lifestyleAEbyAge*_rate.csv
measure_csv4f: output/measures/measure_lifestyleHo*_rate.csv
measure_csv4g: output/measures/measure_lifestyleHobyRegion*_rate.csv
measure_csv4h: output/measures/measure_lifestyleHobyIMD*_rate.csv
measure_csv4i: output/measures/measure_lifestyleHobyEthnicity*_rate.csv
measure_csv4j: output/measures/measure_lifestyleHobyAge*_rate.csv
# measure_csv4k: output/measures/measure_lifestyleDe*_rate.csv
# measure_csv4l: output/measures/measure_lifestyleDebyRegion*_rate.csv
# measure_csv4m: output/measures/measure_lifestyleDebyIMD*_rate.csv
# measure_csv4n: output/measures/measure_lifestyleDebyEthnicity*_rate.csv
# measure_csv4o: output/measures/measure_lifestyleDebyAge*_rate.csv
measure_csv5a: output/measures/measure_violence_AE*_rate.csv
measure_csv5b: output/measures/measure_violence_AEbyRegion*_rate.csv
measure_csv5c: output/measures/measure_violence_AEbyIMD*_rate.csv
measure_csv5d: output/measures/measure_violence_AEbyEthnicity*_rate.csv
measure_csv5e: output/measures/measure_violence_AEbyAge*_rate.csv
measure_csv5f: output/measures/measure_violence_Ho*_rate.csv
measure_csv5g: output/measures/measure_violence_HobyRegion*_rate.csv
measure_csv5h: output/measures/measure_violence_HobyIMD*_rate.csv
measure_csv5i: output/measures/measure_violence_HobyEthnicity*_rate.csv
measure_csv5j: output/measures/measure_violence_HobyAge*_rate.csv
# measure_csv5k: output/measures/measure_violence_De*_rate.csv
# measure_csv5l: output/measures/measure_violence_DebyRegion*_rate.csv
# measure_csv5m: output/measures/measure_violence_DebyIMD*_rate.csv
# measure_csv5n: output/measures/measure_violence_DebyEthnicity*_rate.csv
# measure_csv5o: output/measures/measure_violence_DebyAge*_rate.csv
measure_csv6a: output/measures/measure_s_m_illn_AE*_rate.csv
measure_csv6b: output/measures/measure_s_m_illn_AEbyRegion*_rate.csv
measure_csv6c: output/measures/measure_s_m_illn_AEbyIMD*_rate.csv
measure_csv6d: output/measures/measure_s_m_illn_AEbyEthnicity*_rate.csv
measure_csv6e: output/measures/measure_s_m_illn_AEbyAge*_rate.csv
measure_csv6f: output/measures/measure_s_m_illn_Ho*_rate.csv
measure_csv6g: output/measures/measure_s_m_illn_HobyRegion*_rate.csv
measure_csv6h: output/measures/measure_s_m_illn_HobyIMD*_rate.csv
measure_csv6i: output/measures/measure_s_m_illn_HobyEthnicity*_rate.csv
measure_csv6j: output/measures/measure_s_m_illn_HobyAge*_rate.csv
# measure_csv6k: output/measures/measure_s_m_illn_De*_rate.csv
# measure_csv6l: output/measures/measure_s_m_illn_DebyRegion*_rate.csv
# measure_csv6m: output/measures/measure_s_m_illn_DebyIMD*_rate.csv
# measure_csv6n: output/measures/measure_s_m_illn_DebyEthnicity*_rate.csv
# measure_csv6o: output/measures/measure_s_m_illn_DebyAge*_rate.csv
measure_csv7a: output/measures/measure_psyc_eme_AE*_rate.csv
measure_csv7b: output/measures/measure_psyc_eme_AEbyRegion*_rate.csv
measure_csv7c: output/measures/measure_psyc_eme_AEbyIMD*_rate.csv
measure_csv7d: output/measures/measure_psyc_eme_AEbyEthnicity*_rate.csv
measure_csv7e: output/measures/measure_psyc_eme_AEbyAge*_rate.csv
describe_trends:
run: r:latest analysis/Descriptive_trends.R
needs:
[generate_measures]
outputs:
moderately_sensitive:
fig1a: output/self_harmAE.png
fig2a: output/self_harmAEbyReg.png
fig3a: output/self_harmAEbyIMD.png
fig4a: output/self_harmAEbyEth.png
fig5a: output/self_harmAEbyAge.png
csv1a: output/self_harmAE_rounded.csv
csv2a: output/self_harmAEbyReg_rounded.csv
csv3a: output/self_harmAEbyIMD_rounded.csv
csv4a: output/self_harmAEbyEth_rounded.csv
csv5a: output/self_harmAEbyAge_rounded.csv
fig6a: output/self_harmHo.png
fig7a: output/self_harmHobyReg.png
fig8a: output/self_harmHobyIMD.png
fig9a: output/self_harmHobyEth.png
fig10a: output/self_harmHobyAge.png
csv6a: output/self_harmHo_rounded.csv
csv7a: output/self_harmHobyReg_rounded.csv
csv8a: output/self_harmHobyIMD_rounded.csv
csv9a: output/self_harmHobyEth_rounded.csv
csv10a: output/self_harmHobyAge_rounded.csv
# fig11a: output/self_harmDe.png
# fig12a: output/self_harmDebyReg.png
# fig13a: output/self_harmDebyIMD.png
# fig14a: output/self_harmDebyEth.png
# fig15a: output/self_harmDebyAge.png
# csv11a: output/self_harmDe_rounded.csv
# csv12a: output/self_harmDebyReg_rounded.csv
# csv13a: output/self_harmDebyIMD_rounded.csv
# csv14a: output/self_harmDebyEth_rounded.csv
# csv15a: output/self_harmDebyAge_rounded.csv
fig1c: output/emot_distAE.png
fig2c: output/emot_distAEbyReg.png
fig3c: output/emot_distAEbyIMD.png
fig4c: output/emot_distAEbyEth.png
fig5c: output/emot_distAEbyAge.png
csv1c: output/emot_distAE_rounded.csv
csv2c: output/emot_distAEbyReg_rounded.csv
csv3c: output/emot_distAEbyIMD_rounded.csv
csv4c: output/emot_distAEbyEth_rounded.csv
csv5c: output/emot_distAEbyAge_rounded.csv
fig6c: output/emot_distHo.png
fig7c: output/emot_distHobyReg.png
fig8c: output/emot_distHobyIMD.png
fig9c: output/emot_distHobyEth.png
fig10c: output/emot_distHobyAge.png
csv6c: output/emot_distHo_rounded.csv
csv7c: output/emot_distHobyReg_rounded.csv
csv8c: output/emot_distHobyIMD_rounded.csv
csv9c: output/emot_distHobyEth_rounded.csv
csv10c: output/emot_distHobyAge_rounded.csv
# fig11c: output/emot_distDe.png
# fig12c: output/emot_distDebyReg.png
# fig13c: output/emot_distDebyIMD.png
# fig14c: output/emot_distDebyEth.png
# fig15c: output/emot_distDebyAge.png
# csv11c: output/emot_distDe_rounded.csv
# csv12c: output/emot_distDebyReg_rounded.csv
# csv13c: output/emot_distDebyIMD_rounded.csv
# csv14c: output/emot_distDebyEth_rounded.csv
# csv15c: output/emot_distDebyAge_rounded.csv
fig1b: output/eat_disorAE.png
fig2b: output/eat_disorAEbyReg.png
fig3b: output/eat_disorAEbyIMD.png
fig4b: output/eat_disorAEbyEth.png
fig5b: output/eat_disorAEbyAge.png
csv1b: output/eat_disorAE_rounded.csv
csv2b: output/eat_disorAEbyReg_rounded.csv
csv3b: output/eat_disorAEbyIMD_rounded.csv
csv4b: output/eat_disorAEbyEth_rounded.csv
csv5b: output/eat_disorAEbyAge_rounded.csv
fig6b: output/eat_disorHo.png
fig7b: output/eat_disorHobyReg.png
fig8b: output/eat_disorHobyIMD.png
fig9b: output/eat_disorHobyEth.png
fig10b: output/eat_disorHobyAge.png
csv6b: output/eat_disorHo_rounded.csv
csv7b: output/eat_disorHobyReg_rounded.csv
csv8b: output/eat_disorHobyIMD_rounded.csv
csv9b: output/eat_disorHobyEth_rounded.csv
csv10b: output/eat_disorHobyAge_rounded.csv
# fig11b: output/eat_disorDe.png
# fig12b: output/eat_disorDebyReg.png
# fig13b: output/eat_disorDebyIMD.png
# fig14b: output/eat_disorDebyEth.png
# fig15b: output/eat_disorDebyAge.png
# csv11b: output/eat_disorDe_rounded.csv
# csv12b: output/eat_disorDebyReg_rounded.csv
# csv13b: output/eat_disorDebyIMD_rounded.csv
# csv14b: output/eat_disorDebyEth_rounded.csv
# csv15b: output/eat_disorDebyAge_rounded.csv
fig1d: output/lifestyleAE.png
fig2d: output/lifestyleAEbyReg.png
fig3d: output/lifestyleAEbyIMD.png
fig4d: output/lifestyleAEbyEth.png
fig5d: output/lifestyleAEbyAge.png
csv1d: output/lifestyleAE_rounded.csv
csv2d: output/lifestyleAEbyReg_rounded.csv
csv3d: output/lifestyleAEbyIMD_rounded.csv
csv4d: output/lifestyleAEbyEth_rounded.csv
csv5d: output/lifestyleAEbyAge_rounded.csv
fig6d: output/lifestyleHo.png
fig7d: output/lifestyleHobyReg.png
fig8d: output/lifestyleHobyIMD.png
fig9d: output/lifestyleHobyEth.png
fig10d: output/lifestyleHobyAge.png
csv6d: output/lifestyleHo_rounded.csv
csv7d: output/lifestyleHobyReg_rounded.csv
csv8d: output/lifestyleHobyIMD_rounded.csv
csv9d: output/lifestyleHobyEth_rounded.csv
csv10d: output/lifestyleHobyAge_rounded.csv
# fig11d: output/lifestyleDe.png
# fig12d: output/lifestyleDebyReg.png
# fig13d: output/lifestyleDebyIMD.png
# fig14d: output/lifestyleDebyEth.png
# fig15d: output/lifestyleDebyAge.png
# csv11d: output/lifestyleDe_rounded.csv
# csv12d: output/lifestyleDebyReg_rounded.csv
# csv13d: output/lifestyleDebyIMD_rounded.csv
# csv14d: output/lifestyleDebyEth_rounded.csv
# csv15d: output/lifestyleDebyAge_rounded.csv
fig1e: output/violence_AE.png
fig2e: output/violence_AEbyReg.png
fig3e: output/violence_AEbyIMD.png
fig4e: output/violence_AEbyEth.png
fig5e: output/violence_AEbyAge.png
csv1e: output/violence_AE_rounded.csv
csv2e: output/violence_AEbyReg_rounded.csv
csv3e: output/violence_AEbyIMD_rounded.csv
csv4e: output/violence_AEbyEth_rounded.csv
csv5e: output/violence_AEbyAge_rounded.csv
fig6e: output/violence_Ho.png
fig7e: output/violence_HobyReg.png
fig8e: output/violence_HobyIMD.png
fig9e: output/violence_HobyEth.png
fig10e: output/violence_HobyAge.png
csv6e: output/violence_Ho_rounded.csv
csv7e: output/violence_HobyReg_rounded.csv
csv8e: output/violence_HobyIMD_rounded.csv
csv9e: output/violence_HobyEth_rounded.csv
csv10e: output/violence_HobyAge_rounded.csv
# fig11e: output/violence_De.png
# fig12e: output/violence_DebyReg.png
# fig13e: output/violence_DebyIMD.png
# fig14e: output/violence_DebyEth.png
# fig15e: output/violence_DebyAge.png
# csv11e: output/violence_De_rounded.csv
# csv12e: output/violence_DebyReg_rounded.csv
# csv13e: output/violence_DebyIMD_rounded.csv
# csv14e: output/violence_DebyEth_rounded.csv
# csv15e: output/violence_DebyAge_rounded.csv
fig1f: output/s_m_illn_AE.png
fig2f: output/s_m_illn_AEbyReg.png
fig3f: output/s_m_illn_AEbyIMD.png
fig4f: output/s_m_illn_AEbyEth.png
fig5f: output/s_m_illn_AEbyAge.png
csv1f: output/s_m_illn_AE_rounded.csv
csv2f: output/s_m_illn_AEbyReg_rounded.csv
csv3f: output/s_m_illn_AEbyIMD_rounded.csv
csv4f: output/s_m_illn_AEbyEth_rounded.csv
csv5f: output/s_m_illn_AEbyAge_rounded.csv
fig6f: output/s_m_illn_Ho.png
fig7f: output/s_m_illn_HobyReg.png
fig8f: output/s_m_illn_HobyIMD.png
fig9f: output/s_m_illn_HobyEth.png
fig10f: output/s_m_illn_HobyAge.png
csv6f: output/s_m_illn_Ho_rounded.csv
csv7f: output/s_m_illn_HobyReg_rounded.csv
csv8f: output/s_m_illn_HobyIMD_rounded.csv
csv9f: output/s_m_illn_HobyEth_rounded.csv
csv10f: output/s_m_illn_HobyAge_rounded.csv
# fig11f: output/s_m_illn_De.png
# fig12f: output/s_m_illn_DebyReg.png
# fig13f: output/s_m_illn_DebyIMD.png
# fig14f: output/s_m_illn_DebyEth.png
# fig15f: output/s_m_illn_DebyAge.png
# csv11f: output/s_m_illn_De_rounded.csv
# csv12f: output/s_m_illn_DebyReg_rounded.csv
# csv13f: output/s_m_illn_DebyIMD_rounded.csv
# csv14f: output/s_m_illn_DebyEth_rounded.csv
# csv15f: output/s_m_illn_DebyAge_rounded.csv
fig1g: output/psyc_eme_AE.png
fig2g: output/psyc_eme_AEbyReg.png
fig3g: output/psyc_eme_AEbyIMD.png
fig4g: output/psyc_eme_AEbyEth.png
fig5g: output/psyc_eme_AEbyAge.png
csv1g: output/psyc_eme_AE_rounded.csv
csv2g: output/psyc_eme_AEbyReg_rounded.csv
csv3g: output/psyc_eme_AEbyIMD_rounded.csv
csv4g: output/psyc_eme_AEbyEth_rounded.csv
csv5g: output/psyc_eme_AEbyAge_rounded.csv