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AWS.md

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Computing NSIDES on AWS

Scripts

  • scripts/1.compute_file_maps.py
  • scripts/2.compute_extract_propensity_scores.py
  • scripts/3.compute_prr.py
  • scripts/4.combine_prr_clean.py

Required data files

  • data/meta/drug_exposure_matrix.npz

  • data/meta/drug_id_vector.npz

  • data/meta/outcome_matrix.npz

  • data/meta/outcome_id_vector.npz

  • data/meta/report_id_vector.npz

  • data/archives/1/scores_*.tgz

  • data/archives/2/scores_*.tgz

Files to-be-computed

  • data/meta/file_map_offsides.csv
  • data/meta/file_map_twosides.csv
  • data/scores/1/*.npz
  • data/scores/2/_.npz
  • data/prr/1/*.csv.xz
  • data/prr/2/*.csv.xz
  • data/tables/offsides.csv.xz
  • data/tables/twosides.csv.xz

Files to-be-output (not deleted)

  • data/meta/file_map_offsides.csv
  • data/meta/file_map_twosides.csv
  • data/tables/offsides.csv.xz
  • data/tables/twosides.csv.xz
  • data/output_archives/offsides_propensity_scores.tar.xz
  • data/output_archives/twosides_propensity_scores.tar.xz