query: Query your data and generates a 'comoRbidity'

In aGutierrezSacristan/comorbidity: Analyze comorbidities from electronic health record data

Description

Given 4 files (patientData.txt, diagnosisData.txt, admissionData.txt and indexDiseaseCodes.txt), generates some RData and create an object of type comoRbidity.

Usage

query(databasePth, codesPth, birthDataSep, admissionDataSep,
  intraCodes = FALSE, aggregatedDis = FALSE, python = FALSE,
  verbose = FALSE, warnings = TRUE)

Arguments

databasePth	Determines the path where the three required input files (patientData, diagnosisData, admissionData) are located.
codesPth	Determines the path where the file with the index diseases is located (indexDiseaseCode)
birthDataSep	Determines the separator symbol used in the birth date.
admissionDataSep	Determines the separator symbol used in the admission date.
intraCodes	Comorbidities will be estimated only between the index diseases. By default FALSE
aggregatedDis	Data extraction is done using the Agg column from the index disease file, that collapse the diseases in a supperior class. By default FALSE
python	By default FALSE. Change it to TRUE to run the query quicklier using python. It is necessary to have python installed.
verbose	By default FALSE. Change it to TRUE to get a on-time log from the function.
warnings	By default TRUE. Change it to FALSE to don't see the warnings.

Value

An object of class comoRbidity

Examples

ex1 <- query( databasePth      = system.file("extdata", package="comoRbidity"),
              codesPth         = system.file("extdata", package="comoRbidity"),
              birthDataSep     = "-",
              admissionDataSep = "-",
              python           = FALSE)

aGutierrezSacristan/comorbidity documentation built on April 10, 2020, 5:54 p.m.