In DHLab-CGU/emr: An analysis tool for diagnosis and procedure records

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

Getting started with dxpr package

I. Introduction

The proposed open-source dxpr package is a software tool aimed at expediting an integrated analysis of electronic health records (EHRs). The dxpr package provides mechanisms to integrate, analyze, and visualize clinical data, including diagnosis and procedure records.

Feature

• Data integration Transform codes into uniform format and group code into several categories.
• Data Wrangling Generate statistical information about dataset and transform data into wide format, which fits better to other analytical and plotting packages.
• Visualization Provide overviews for the result of diagnoses standardization and the grouped categories of diagnosis codes.

Getting started

• Diagnostic part
  English: https://dhlab-tseng.github.io/dxpr/articles/Eng_Diagnosis.html
  Chinese: https://dhlab-tseng.github.io/dxpr/articles/Chi_Diagnosis.html
• Procedure part
  English: https://dhlab-tseng.github.io/dxpr/articles/Eng_Procedure.html
  Chinese: https://dhlab-tseng.github.io/dxpr/articles/Chi_Procedure.html

Development version

# install.packages("remotes")
remotes::install_github("DHLab-TSENG/dxpr")

knitr::opts_chunk$set(collapse = T, comment = "#>")
options(tibble.print_min = 4L, tibble.print_max = 4L)
remotes::install_github("DHLab-TSENG/dxpr")

Overview

Usage

library(dxpr)  

head(sampleDxFile)  

# I. Data integration
#   1. Data standardization
short <- icdDxDecimalToShort(dxDataFile = sampleDxFile, 
                             icdColName = ICD, 
                             dateColName = Date,
                             icd10usingDate = "2015/10/01")
head(short$ICD)

tail(short$Error)

#   2. Data grouping
ELIX <- icdDxToComorbid(dxDataFile = sampleDxFile, 
                        idColName = ID, 
                        icdColName = ICD, 
                        dateColName = Date, 
                        icd10usingDate = "2015/10/01", 
                        comorbidMethod = elix)
head(ELIX$groupedDT)

head(ELIX$summarised_groupedDT)

# II. Data wrangling
groupedDataWide <- groupedDataLongToWide(dxDataFile = ELIX$groupedDT, 
                                         idColName = ID, 
                                         categoryColName = Comorbidity, 
                                         dateColName = Date)
head(groupedDataWide[,1:4])

# IV. Visualization
plot_errorICD <- plotICDError(short$Error)  
plot_groupedData <- plotDiagCat(groupedDataWide, ID)

plot_errorICD

plot_groupedData

Getting help

See the GitHub issues page (https://github.com/DHLab-TSENG/dxpr/issues) to see open issues and feature requests.

DHLab-CGU/emr documentation built on Sept. 2, 2023, 9:16 p.m.