64 lines
1.4 KiB
R
64 lines
1.4 KiB
R
# The follow script rebuilds a local copy of the MIMIC-IV database
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# for the purpose of this project only the patients, labitems, and labevents
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# tables are included, and the csv's need to be in the data-unshared folder
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# this script only needs to be run once on any computer performing analysis
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rm(list = ls(all.names = TRUE)) # Clear the memory of variables from previous run.
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cat("\014") # Clear the console
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# load packages -----------------------------------------------------------
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box::use(
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magrittr[`%>%`]
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,RSQLite
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,DBI[dbConnect,dbDisconnect,dbWriteTable]
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,here[here]
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,readr
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)
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# globals -----------------------------------------------------------------
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# create database ---------------------------------------------------------
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mimicDB <- dbConnect(
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RSQLite$SQLite()
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,here("ML","data-unshared","mimicDB.sqlite")
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)
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# create labevents table
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readr$read_csv_chunked(
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here("ML","data-unshared", "labevents.csv")
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,callback = function(chunk,dummy){
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dbWriteTable(mimicDB, "labevents", chunk, append = TRUE)
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}
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,chunk_size = 10000
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,col_types = "_d_ddTT_d______"
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)
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# create patient table
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readr$read_csv(
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here("ML","data-unshared","patients.csv")
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) %>%
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dbWriteTable(mimicDB,"patients", .)
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# create labitems table
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readr$read_csv(
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here("ML","data-unshared","d_labitems.csv")
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) %>%
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dbWriteTable(mimicDB,"labitems", .)
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# close database ----------------------------------------------------------
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dbDisconnect(mimicDB)
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