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refactored map to phen; refactored to standard directories for phenotypes that...
refactored map to phen; refactored to standard directories for phenotypes that user can set with subdirectory codes, config.json, phen_output.csv; defaults to build/phen if not specified as makes cli much simpler
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- .gitignore 1 addition, 6 deletions.gitignore
- acmc.py 27 additions, 51 deletionsacmc.py
- example/codes/clinical-codes-org/About the source.docx 0 additions, 0 deletionsexample/codes/clinical-codes-org/About the source.docx
- example/codes/clinical-codes-org/Behaviours code lists/Alcohol intake/Where this code list comes from .docx 0 additions, 0 deletions...ists/Alcohol intake/Where this code list comes from .docx
- example/codes/clinical-codes-org/Behaviours code lists/Alcohol intake/res47-alcohol-intake.csv 0 additions, 0 deletions...viours code lists/Alcohol intake/res47-alcohol-intake.csv
- example/codes/clinical-codes-org/Behaviours code lists/Physical activity/Where this code list comes from .docx 0 additions, 0 deletions...s/Physical activity/Where this code list comes from .docx
- example/codes/clinical-codes-org/Behaviours code lists/Physical activity/res47-physical-activity.csv 0 additions, 0 deletions... code lists/Physical activity/res47-physical-activity.csv
- example/codes/clinical-codes-org/Behaviours code lists/Smoking status/Where this code list comes from .docx 0 additions, 0 deletions...ists/Smoking status/Where this code list comes from .docx
- example/codes/clinical-codes-org/Behaviours code lists/Smoking status/res56-smoking-status.csv 0 additions, 0 deletions...viours code lists/Smoking status/res56-smoking-status.csv
- example/codes/clinical-codes-org/Cardiovascular events (ICD10)/Where this code list comes from .docx 0 additions, 0 deletions...ular events (ICD10)/Where this code list comes from .docx
- example/codes/clinical-codes-org/Cardiovascular events (ICD10)/res52-cardiovascular-events-icd10.csv 0 additions, 0 deletions...ular events (ICD10)/res52-cardiovascular-events-icd10.csv
- example/codes/clinical-codes-org/Motor neurone disease/Where this code list comes from .docx 0 additions, 0 deletions...tor neurone disease/Where this code list comes from .docx
- example/codes/clinical-codes-org/Motor neurone disease/phenotype_PH62_ver_124_concepts_20230719T112819.csv 0 additions, 0 deletions...sease/phenotype_PH62_ver_124_concepts_20230719T112819.csv
- example/codes/clinical-codes-org/Non-attendance codes/Where this code list comes from .docx 0 additions, 0 deletions...on-attendance codes/Where this code list comes from .docx
- example/codes/clinical-codes-org/Non-attendance codes/res201-did-not-attend-appointment.csv 0 additions, 0 deletions...on-attendance codes/res201-did-not-attend-appointment.csv
- example/codes/clinical-codes-org/Obsessive Compulsive Disorder/Where this code list comes from .docx 0 additions, 0 deletions...Compulsive Disorder/Where this code list comes from .docx
- example/codes/clinical-codes-org/Obsessive Compulsive Disorder/phenotype_PH223_ver_446_concepts_20230719T114228.csv 0 additions, 0 deletions...rder/phenotype_PH223_ver_446_concepts_20230719T114228.csv
- example/codes/clinical-codes-org/Palliative care codes/Where this code list comes from .docx 0 additions, 0 deletions...lliative care codes/Where this code list comes from .docx
- example/codes/clinical-codes-org/Palliative care codes/res176-palliative-and-end-of-life-care.csv 0 additions, 0 deletions...ive care codes/res176-palliative-and-end-of-life-care.csv
- example/codes/clinical-codes-org/Peptic ulcer/Where this code list comes from .docx 0 additions, 0 deletions...es-org/Peptic ulcer/Where this code list comes from .docx
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