get_data: get_data

In aneuraz/DWHtools2: Tools to query DWH

Description

For Dr.Warehouse and i2b2

Usage

get_data(num = NULL, num_type = NULL, data_type = NULL,
  ICD_prefix = "CIM10", BIO_prefix = "LOINC", use_scheme_key = FALSE,
  config = NULL)

Arguments

num	the identifier of the cohort/num_temp
num_type	type of num: one of c('num_temp', 'cohorte')
data_type	type of data: one of c('bio_num', 'cim10'). 'bio_num' for biological test results with numeric value. 'cim10' for ICD10 codes
ICD_prefix	For i2b2. prefix of the CONCEPT_CDs for ICD codes (used to filter the CONCEPT_CDs) (default = 'CIM10')
BIO_prefix	For i2b2. prefix of the CONCEPT_CDs for labtest codes (used to filter the CONCEPT_CDs) (default = 'LOINC')
use_scheme_key	For i2b2. set to 'TRUE' if you want to use a SCHEME_KEY column in OBSERVATION_FACT to filter the FACTS. if 'TRUE', the value of ICD_prefix or BIO_prefix are used to filter the FACTS.
config	a config environment created by the function getConfig.
config	a config environment created by the function getConfig.

Details

Get the data (e.g. ICD codes or laboratory test results) for the patients in a cohort/num_temp.

Value

a data.frame

aneuraz/DWHtools2 documentation built on Sept. 6, 2019, 8:11 p.m.