directionality: Query your data and generates a 'datafame'

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

Description

Given an object of class cAnalysis obtained from a comorbidity analysis, the comorbidity direction can be estimated. An object of class dataframe is obtained.

Usage

directionality(input, databasePth, minPairs = 1, sex, ageRange = c(0,
  100), days, dataSep = "-", correctedPval = 1,
  correctionMethod = "bonferroni", verbose)

Arguments

input	A cAnalysis object, containing the comorbidity data for a set of patients.
databasePth	Determines the path where the intermediate RData objects have been created. It is the same path where the three required input files (patientData, diagnosisData, admissionData) are located.
minPairs	Determines the minimum number of patients that must suffer the comorbidity. By default the minPairs value is set to 1. The value of the argument can be changed to any other numeric variable.
sex	Determine what is the sex of interest for performing the comorbidity analysis.
ageRange	Determines what is the age range of interest for performing the comorbidity analysis. By default it is set from 0 to 100 years old.
days	Determines the number of days of difference needed for considering two diseases as comorbid.
dataSep	Determines the separator symbol used in the admission date. By default "-".
correctionMethod	A binomial test for each pair of diseases is performed to assess the null hypothesis of independence between the two diseases. The Bonferroni correction ("bonferroni") is applied to correct for multiple testing by default. However user can select the best correction method for the analysis. The adjustment methods include the Benjamini-Hochberg false discovery rate method ("fdr"), Holm correction ("holm"), Hochberg correction ("hochberg"), Hommel ("hommel") and Benjamini & Yekutieli ("BY").
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 dataframe

Examples

load(system.file("extdata", "comorMale.RData", package="comoRbidity"))
directionEx <- directionality( input            = comorMale, 
                               databasePth      = system.file("extdata", package="comoRbidity"), 
                               minPairs         = 1, 
                               sex              = "Male",
                               ageRange         = c(0,80),
                               days             = "0",
                               dataSep          = "-", 
                               correctionMethod = "bonferroni"
              )

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