Where is "public.sepsis3" created?

spfohl / cs238_sepsis_rl

Learning to reinforcement learn and treating sepsis on the side

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Where is "public.sepsis3" created? #1

Closed sgfin closed 6 years ago

sgfin commented 6 years ago

Trying to rerun the mimic scripts, and was able to run the scripts of the form "*_all_rl.sql", but when I try to run "create_cohort_table.sql", I get the following error:

DROP MATERIALIZED VIEW psql:create_cohort_table.sql:34: ERROR: relation "sepsis3" does not exist LINE 19: FROM sepsis3 as s3

Searching through the repo, I can't see where sepsis3 is created. Is there another script where that happens, or am I just missing something?

sgfin commented 6 years ago

Nevermind looks like it's from here:

https://github.com/alistairewj/sepsis3-mimic

paulrich1234 commented 5 years ago

hello @sgfin,did you finally get the original data ? if so ,could you tell me how to get it ? thank you

spfohl commented 5 years ago

Hi @paulrich1234, you'll need to get MIMIC-III from Physionet, build the concept tables here https://github.com/MIT-LCP/mimic-code and then run make_tables.sql from here: https://github.com/alistairewj/sepsis3-mimic/tree/master/query

paulrich1234 commented 5 years ago

hello @ @spfohl Thank you for your timely reply ,i think i have got the result as your instruction recently .Thank you