m4_microbiologyevents: Access microbiology cultures

In hdshea/MIMIC4db: Package for building, loading and referencing the Google BigQuery verion of the MIMIC-IV

Description

This function provides base access to the microbiologyevents table containing data on all microbiology tests which are a common procedure to check for infectious growth and to assess which antibiotic treatments are most effective.

Usage

m4_microbiologyevents(con, cohort = NULL, ...)

Arguments

con	A bigrquery::bigquery() DBIConnection object, as returned by DBI::dbConnect() with an appropriate bigrquery::bigquery() DBI driver specified in the call.
cohort	an optional vector of patient IDs defining the cohort of interest
...	additional optional passed along parameters.

Details

Table attributes for microbiologyevents table:

(PKEY microevent_id)

(FKEY subject_id) -> patients table

(FKEY hadm_id) -> admissions table

Value

a tibble with the results.

Examples

# To run examples, you must have the BIGQUERY_TEST_PROJECT environment
# variable set to name of project which has billing set up and to which
# you have write access.
con <- bigrquery::dbConnect(
  bigrquery::bigquery(),
  project = bigrquery::bq_test_project(),
  quiet = TRUE
)

evt <- m4_microbiologyevents(con, cohort = 10137012)
dim(evt)

bigrquery::dbDisconnect(con)

hdshea/MIMIC4db documentation built on Dec. 20, 2021, 3:45 p.m.