reorganize repository structure

MIT-LCP · d38180c22b623c83c19fb700cb089a30570ecb3f · alistairewj committed Jan 4, 2017 · Jan 4, 2017 · d38180c
1 parent 48300e8
commit d38180c22b623c83c19fb700cb089a30570ecb3f
diff --git a/etc/Makefile → concepts/Makefile b/etc/Makefile → concepts/Makefile
diff --git a/etc/README.md → concepts/README.md b/etc/README.md → concepts/README.md
diff --git a/etc/clean.sql → concepts/clean.sql b/etc/clean.sql → concepts/clean.sql
diff --git a/etc/code-status.sql → concepts/code-status.sql b/etc/code-status.sql → concepts/code-status.sql
diff --git a/comorbidity/mysql/4-elixhauser.sql → concepts/comorbidity/mysql/4-elixhauser.sql b/comorbidity/mysql/4-elixhauser.sql → concepts/comorbidity/mysql/4-elixhauser.sql
diff --git a/comorbidity/postgres/Makefile → concepts/comorbidity/postgres/Makefile b/comorbidity/postgres/Makefile → concepts/comorbidity/postgres/Makefile
diff --git a/comorbidity/postgres/clean.sql → concepts/comorbidity/postgres/clean.sql b/comorbidity/postgres/clean.sql → concepts/comorbidity/postgres/clean.sql
diff --git a/...postgres/elixhauser-ahrq-v37-with-drg.sql → ...postgres/elixhauser-ahrq-v37-with-drg.sql b/...postgres/elixhauser-ahrq-v37-with-drg.sql → ...postgres/elixhauser-ahrq-v37-with-drg.sql
diff --git a/comorbidity/postgres/elixhauser-quan.sql → .../comorbidity/postgres/elixhauser-quan.sql b/comorbidity/postgres/elixhauser-quan.sql → .../comorbidity/postgres/elixhauser-quan.sql
diff --git a/...bidity/postgres/elixhauser-score-ahrq.sql → ...bidity/postgres/elixhauser-score-ahrq.sql b/...bidity/postgres/elixhauser-score-ahrq.sql → ...bidity/postgres/elixhauser-score-ahrq.sql
diff --git a/...bidity/postgres/elixhauser-score-quan.sql → ...bidity/postgres/elixhauser-score-quan.sql b/...bidity/postgres/elixhauser-score-quan.sql → ...bidity/postgres/elixhauser-score-quan.sql
diff --git a/cookbook/postgres/basic_patient_info.sql → concepts/cookbook/basic_patient_info.sql b/cookbook/postgres/basic_patient_info.sql → concepts/cookbook/basic_patient_info.sql
diff --git a/cookbook/postgres/bun.sql → concepts/cookbook/bun.sql b/cookbook/postgres/bun.sql → concepts/cookbook/bun.sql
diff --git a/cookbook/postgres/gcs.sql → concepts/cookbook/gcs.sql b/cookbook/postgres/gcs.sql → concepts/cookbook/gcs.sql
diff --git a/cookbook/postgres/glucose.sql → concepts/cookbook/glucose.sql b/cookbook/postgres/glucose.sql → concepts/cookbook/glucose.sql
diff --git a/cookbook/postgres/hco.sql → concepts/cookbook/hco.sql b/cookbook/postgres/hco.sql → concepts/cookbook/hco.sql
diff --git a/cookbook/postgres/heart_rate.sql → concepts/cookbook/heart_rate.sql b/cookbook/postgres/heart_rate.sql → concepts/cookbook/heart_rate.sql
diff --git a/cookbook/postgres/icd9agelimited.sql → concepts/cookbook/icd9agelimited.sql b/cookbook/postgres/icd9agelimited.sql → concepts/cookbook/icd9agelimited.sql
diff --git a/cookbook/postgres/icd9count.sql → concepts/cookbook/icd9count.sql b/cookbook/postgres/icd9count.sql → concepts/cookbook/icd9count.sql
diff --git a/cookbook/postgres/icd9vagehistogram.sql → concepts/cookbook/icd9vagehistogram.sql b/cookbook/postgres/icd9vagehistogram.sql → concepts/cookbook/icd9vagehistogram.sql
diff --git a/cookbook/postgres/icd9vicd9agelimited.sql → concepts/cookbook/icd9vicd9agelimited.sql b/cookbook/postgres/icd9vicd9agelimited.sql → concepts/cookbook/icd9vicd9agelimited.sql
diff --git a/cookbook/postgres/icd9vicd9count.sql → concepts/cookbook/icd9vicd9count.sql b/cookbook/postgres/icd9vicd9count.sql → concepts/cookbook/icd9vicd9count.sql
diff --git a/etc/icustay_days.sql → concepts/cookbook/icustay-days.sql b/etc/icustay_days.sql → concepts/cookbook/icustay-days.sql
diff --git a/cookbook/postgres/min_surviving_bp.sql → concepts/cookbook/min_surviving_bp.sql b/cookbook/postgres/min_surviving_bp.sql → concepts/cookbook/min_surviving_bp.sql
diff --git a/cookbook/postgres/mortality.sql → concepts/cookbook/mortality.sql b/cookbook/postgres/mortality.sql → concepts/cookbook/mortality.sql
diff --git a/cookbook/postgres/number_of_patients.sql → concepts/cookbook/number_of_patients.sql b/cookbook/postgres/number_of_patients.sql → concepts/cookbook/number_of_patients.sql
diff --git a/cookbook/postgres/potassium.sql → concepts/cookbook/potassium.sql b/cookbook/postgres/potassium.sql → concepts/cookbook/potassium.sql
diff --git a/cookbook/postgres/rr.sql → concepts/cookbook/rr.sql b/cookbook/postgres/rr.sql → concepts/cookbook/rr.sql
diff --git a/cookbook/postgres/sbp.sql → concepts/cookbook/sbp.sql b/cookbook/postgres/sbp.sql → concepts/cookbook/sbp.sql
diff --git a/cookbook/postgres/sodium.sql → concepts/cookbook/sodium.sql b/cookbook/postgres/sodium.sql → concepts/cookbook/sodium.sql
diff --git a/cookbook/postgres/temp.sql → concepts/cookbook/temp.sql b/cookbook/postgres/temp.sql → concepts/cookbook/temp.sql
diff --git a/cookbook/postgres/uo.sql → concepts/cookbook/uo.sql b/cookbook/postgres/uo.sql → concepts/cookbook/uo.sql
diff --git a/cookbook/postgres/wbc.sql → concepts/cookbook/wbc.sql b/cookbook/postgres/wbc.sql → concepts/cookbook/wbc.sql
diff --git a/demographics/README.md → concepts/demographics/README.md b/demographics/README.md → concepts/demographics/README.md
diff --git a/cookbook/postgres/age_hist.sql → concepts/demographics/age-histogram.sql b/cookbook/postgres/age_hist.sql → concepts/demographics/age-histogram.sql
diff --git a/cookbook/postgres/height.sql → concepts/demographics/height.sql b/cookbook/postgres/height.sql → concepts/demographics/height.sql
diff --git a/demographics/postgres/HeightWeightQuery.sql → ...mographics/postgres/HeightWeightQuery.sql b/demographics/postgres/HeightWeightQuery.sql → ...mographics/postgres/HeightWeightQuery.sql
diff --git a/demographics/postgres/Makefile → concepts/demographics/postgres/Makefile b/demographics/postgres/Makefile → concepts/demographics/postgres/Makefile
diff --git a/demographics/postgres/clean.sql → concepts/demographics/postgres/clean.sql b/demographics/postgres/clean.sql → concepts/demographics/postgres/clean.sql
diff --git a/demographics/postgres/icustay_detail.sql → .../demographics/postgres/icustay_detail.sql b/demographics/postgres/icustay_detail.sql → .../demographics/postgres/icustay_detail.sql
diff --git a/etc/echo-data.sql → concepts/echo-data.sql b/etc/echo-data.sql → concepts/echo-data.sql
diff --git a/etc/firstday/Makefile → concepts/firstday/Makefile b/etc/firstday/Makefile → concepts/firstday/Makefile
diff --git a/...firstday/blood-gas-first-day-arterial.sql → ...firstday/blood-gas-first-day-arterial.sql b/...firstday/blood-gas-first-day-arterial.sql → ...firstday/blood-gas-first-day-arterial.sql
diff --git a/etc/firstday/blood-gas-first-day.sql → concepts/firstday/blood-gas-first-day.sql b/etc/firstday/blood-gas-first-day.sql → concepts/firstday/blood-gas-first-day.sql
diff --git a/etc/firstday/clean.sql → concepts/firstday/clean.sql b/etc/firstday/clean.sql → concepts/firstday/clean.sql
diff --git a/etc/firstday/gcs-first-day.sql → concepts/firstday/gcs-first-day.sql b/etc/firstday/gcs-first-day.sql → concepts/firstday/gcs-first-day.sql
diff --git a/etc/firstday/height-first-day.sql → concepts/firstday/height-first-day.sql b/etc/firstday/height-first-day.sql → concepts/firstday/height-first-day.sql
diff --git a/etc/firstday/labs-first-day.sql → concepts/firstday/labs-first-day.sql b/etc/firstday/labs-first-day.sql → concepts/firstday/labs-first-day.sql
diff --git a/etc/firstday/rrt-first-day.sql → concepts/firstday/rrt-first-day.sql b/etc/firstday/rrt-first-day.sql → concepts/firstday/rrt-first-day.sql
diff --git a/etc/firstday/urine-output-first-day.sql → concepts/firstday/urine-output-first-day.sql b/etc/firstday/urine-output-first-day.sql → concepts/firstday/urine-output-first-day.sql
diff --git a/etc/firstday/ventilation-first-day.sql → concepts/firstday/ventilation-first-day.sql b/etc/firstday/ventilation-first-day.sql → concepts/firstday/ventilation-first-day.sql
diff --git a/etc/firstday/vitals-first-day.sql → concepts/firstday/vitals-first-day.sql b/etc/firstday/vitals-first-day.sql → concepts/firstday/vitals-first-day.sql
diff --git a/etc/firstday/weight-first-day.sql → concepts/firstday/weight-first-day.sql b/etc/firstday/weight-first-day.sql → concepts/firstday/weight-first-day.sql
diff --git a/etc/auroc.sql → concepts/functions/auroc.sql b/etc/auroc.sql → concepts/functions/auroc.sql
diff --git a/etc/rrt.sql → concepts/rrt.sql b/etc/rrt.sql → concepts/rrt.sql
diff --git a/sepsis/Makefile → concepts/sepsis/Makefile b/sepsis/Makefile → concepts/sepsis/Makefile
diff --git a/sepsis/angus.sql → concepts/sepsis/angus.sql b/sepsis/angus.sql → concepts/sepsis/angus.sql
diff --git a/sepsis/angus2001.pdf → concepts/sepsis/angus2001.pdf b/sepsis/angus2001.pdf → concepts/sepsis/angus2001.pdf
diff --git a/sepsis/clean.sql → concepts/sepsis/clean.sql b/sepsis/clean.sql → concepts/sepsis/clean.sql
diff --git a/severityscores/Makefile → concepts/severityscores/Makefile b/severityscores/Makefile → concepts/severityscores/Makefile
diff --git a/severityscores/README.md → concepts/severityscores/README.md b/severityscores/README.md → concepts/severityscores/README.md
diff --git a/severityscores/apsiii.sql → concepts/severityscores/apsiii.sql b/severityscores/apsiii.sql → concepts/severityscores/apsiii.sql
diff --git a/severityscores/clean.sql → concepts/severityscores/clean.sql b/severityscores/clean.sql → concepts/severityscores/clean.sql
diff --git a/severityscores/lods-paper.pdf → concepts/severityscores/lods-paper.pdf b/severityscores/lods-paper.pdf → concepts/severityscores/lods-paper.pdf
diff --git a/severityscores/lods.sql → concepts/severityscores/lods.sql b/severityscores/lods.sql → concepts/severityscores/lods.sql
diff --git a/severityscores/make-severity-scores.sql → ...s/severityscores/make-severity-scores.sql b/severityscores/make-severity-scores.sql → ...s/severityscores/make-severity-scores.sql
diff --git a/severityscores/mlods.sql → concepts/severityscores/mlods.sql b/severityscores/mlods.sql → concepts/severityscores/mlods.sql
diff --git a/severityscores/oasis.sql → concepts/severityscores/oasis.sql b/severityscores/oasis.sql → concepts/severityscores/oasis.sql
diff --git a/severityscores/qsofa.sql → concepts/severityscores/qsofa.sql b/severityscores/qsofa.sql → concepts/severityscores/qsofa.sql
diff --git a/severityscores/saps.sql → concepts/severityscores/saps.sql b/severityscores/saps.sql → concepts/severityscores/saps.sql
diff --git a/severityscores/sapsii.sql → concepts/severityscores/sapsii.sql b/severityscores/sapsii.sql → concepts/severityscores/sapsii.sql
diff --git a/severityscores/sirs.sql → concepts/severityscores/sirs.sql b/severityscores/sirs.sql → concepts/severityscores/sirs.sql
diff --git a/severityscores/sofa.sql → concepts/severityscores/sofa.sql b/severityscores/sofa.sql → concepts/severityscores/sofa.sql
diff --git a/...pressor-durations/adenosine-durations.sql → ...pressor-durations/adenosine-durations.sql b/...pressor-durations/adenosine-durations.sql → ...pressor-durations/adenosine-durations.sql
diff --git a/...ressor-durations/dobutamine-durations.sql → ...ressor-durations/dobutamine-durations.sql b/...ressor-durations/dobutamine-durations.sql → ...ressor-durations/dobutamine-durations.sql
diff --git a/...opressor-durations/dopamine-durations.sql → ...opressor-durations/dopamine-durations.sql b/...opressor-durations/dopamine-durations.sql → ...opressor-durations/dopamine-durations.sql
diff --git a/...essor-durations/epinephrine-durations.sql → ...essor-durations/epinephrine-durations.sql b/...essor-durations/epinephrine-durations.sql → ...essor-durations/epinephrine-durations.sql
diff --git a/...sopressor-durations/isuprel-durations.sql → ...sopressor-durations/isuprel-durations.sql b/...sopressor-durations/isuprel-durations.sql → ...sopressor-durations/isuprel-durations.sql
diff --git a/...pressor-durations/milrinone-durations.sql → ...pressor-durations/milrinone-durations.sql b/...pressor-durations/milrinone-durations.sql → ...pressor-durations/milrinone-durations.sql
diff --git a/...or-durations/norepinephrine-durations.sql → ...or-durations/norepinephrine-durations.sql b/...or-durations/norepinephrine-durations.sql → ...or-durations/norepinephrine-durations.sql
diff --git a/...sor-durations/phenylephrine-durations.sql → ...sor-durations/phenylephrine-durations.sql b/...sor-durations/phenylephrine-durations.sql → ...sor-durations/phenylephrine-durations.sql
diff --git a/...essor-durations/vasopressin-durations.sql → ...essor-durations/vasopressin-durations.sql b/...essor-durations/vasopressin-durations.sql → ...essor-durations/vasopressin-durations.sql
diff --git a/...essor-durations/vasopressor-durations.sql → ...essor-durations/vasopressor-durations.sql b/...essor-durations/vasopressor-durations.sql → ...essor-durations/vasopressor-durations.sql
diff --git a/etc/ventilation-durations.sql → concepts/ventilation-durations.sql b/etc/ventilation-durations.sql → concepts/ventilation-durations.sql
@@ -24,6 +24,7 @@ select
       when itemid is null or value is null then 0 -- can't have null values
       when itemid = 720 and value != 'Other/Remarks' THEN 1  -- VentTypeRecorded
       when itemid = 223848 and value != 'Other' THEN 1
+      when itemid = 223849 then 1 -- ventilator mode
       when itemid = 467 and value = 'Ventilator' THEN 1 -- O2 delivery device == ventilator
       when itemid = 648 and value = 'Intubated/trach' THEN 1 -- Speech = intubated
       when itemid = 223900 and value = 'No Response-ETT' THEN 1
diff --git a/migrating/labid.csv b/migrating/labid.csv