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EHR (version 0.4-11)

Electronic Health Record (EHR) Data Processing and Analysis Tool

Description

Process and analyze electronic health record (EHR) data. The 'EHR' package provides modules to perform diverse medication-related studies using data from EHR databases. Especially, the package includes modules to perform pharmacokinetic/pharmacodynamic (PK/PD) analyses using EHRs, as outlined in Choi, Beck, McNeer, Weeks, Williams, James, Niu, Abou-Khalil, Birdwell, Roden, Stein, Bejan, Denny, and Van Driest (2020) . Additional modules will be added in future. In addition, this package provides various functions useful to perform Phenome Wide Association Study (PheWAS) to explore associations between drug exposure and phenotypes obtained from EHR data, as outlined in Choi, Carroll, Beck, Mosley, Roden, Denny, and Van Driest (2018) .

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Version

Install

install.packages('EHR')

Monthly Downloads

351

Version

0.4-11

License

GPL (>= 3)

Maintainer

Leena Choi

Last Published

December 19th, 2022

Functions in EHR (0.4-11)

Logistf

Firth's penalized-likelihood logistic regression with more decimal places of p-value than logistf function in the R package ‘logistf’
extractMed

Extract medication information from clinical notes
collapseDose

Collapse Dose Data
collapse-internal

Internal functions for collapseDose process
dataTransformation

Data Transformation
freqNum

Convert Character Frequency to Numeric
parseMedExtractR

Parse medExtractR NLP Output
dd.small

dd.small
dd.baseline.small

dd.baseline.small
dd.baseline

dd.baseline
build_lastdose

PK oral functions
lam_metadata

Example of Metadata for Lamotrigine Data
lam_mxr_parsed

Example of Lamotrigine Output from `parseMedExtractR`
dd

dd
run_MedStrI

Run Str Data I
run_MedStrII

Run Structured E-Prescription Data
processLastDose

Process and standardize extracted last dose times
extractMed-internal

Internal functions for Extract-Med module
pk-internal

Internal functions for pk analysis
pullFakeId

Pull Fake/Mod ID
makeDose

Make Dose Data
lastdose-internal

Internal functions for lastdose
stdzStrength

Standardize Strength Entity
pullRealId

Pull Real ID
tac_lab

Example of Lab Time Data for Tacrolimus
stdzDoseSchedule

Standardize Dose Schedule Entity
stdzDuration

Standardize Duration Entity
idCrosswalk

Create ID Crosswalk
parse-internal

Internal functions for parse process
readTransform

Read and Transform
parseMedXN

Parse MedXN NLP Output
mod-internal

Internal functions for EHR modules
zeroOneTable

Make Zero One Contingency Tables
writeCheckData

Write Check File as CSV
run_Demo

Run Demographic Data
run_Build_PK_Oral

Build-PK-Oral Module
run_Build_PK_IV

Build-PK-IV Module
tac_metadata

Example of Metadata for Tacrolimus Data
stdzDose

Standardize Dose Entity
stdzDoseChange

Standardize Dose Change Entity
tac_mxr_parsed

Example of Tacrolimus Output from `parseMedExtractR`
run_DrugLevel

Run Drug Level Data
parseMedEx

Parse MedEx NLP Output
stdzRoute

Standardize Route Entity
parseCLAMP

Parse CLAMP NLP Output
run_Labs

Run Lab Data
stdzFreq

Standardize Frequency Entity
addLastDose

Add Lastdose Data
analysisPheWAS

Statistical Analysis for PheWAS
build-internal

Internal functions for buildDose process
buildDose

Combine Dose Data
EHR-package

Electronic Health Record (EHR) Data Processing and Analysis Tool