Package: EHR 0.4-11

Leena Choi

EHR: Electronic Health Record (EHR) Data Processing and Analysis Tool

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) <doi:10.1002/cpt.1787>. 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) <doi:10.1093/bioinformatics/bty306>.

Authors:Leena Choi [aut, cre], Cole Beck [aut], Hannah Weeks [aut], Elizabeth McNeer [aut], Nathan James [aut], Michael Williams [aut]

EHR_0.4-11.tar.gz
EHR_0.4-11.tar.gz(r-4.7-any)EHR_0.4-11.tar.gz(r-4.6-any)
EHR_0.4-11.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
EHR/json (API)

# Install 'EHR' in R:
install.packages('EHR', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

4.41 score 64 scripts 344 downloads 11 mentions 33 exports 6 dependencies

Last updated from:cc88321e28. Checks:2 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64WARNING170
source / vignettesOK287
linux-release-x86_64WARNING175
wasm-releaseOK130

Exports:addLastDoseanalysisPheWASbuildDosecollapseDosedataTransformationextractMedfreqNumidCrosswalkLogistfmakeDoseparseCLAMPparseMedExparseMedExtractRparseMedXNprocessLastDosepullFakeIdpullRealIdreadTransformrun_Build_PK_IVrun_Build_PK_Oralrun_Demorun_DrugLevelrun_Labsrun_MedStrIrun_MedStrIIstdzDosestdzDoseChangestdzDoseSchedulestdzDurationstdzFreqstdzRoutestdzStrengthzeroOneTable

Dependencies:cpp11data.tablegenericslubridatepkdatatimechange

EHR Vignette for Structured Data
Introduction | Example 1: Quick Data Building with Processed Datasets | Example 2: Complete Data Processing and Building from Raw Extracted Data to PK Data | Pre-Processing for Raw Extracted Data | (1) Read and clean raw data | (2) Merge data to create new ID variables | (3) Make new data for use with modules | Pro-Demographic | Pro-Med-Str | Part I: IV dose data | Part II: e-prescription data | Pro-Drug Level | Pro-Laboratory | Build-PK-IV | References
Rendered fromehr_vignette_02_str.Rmdusingknitr::rmarkdown

Last update: 2022-12-19
Started: 2021-06-09

EHR Vignette for Extract-Med and Pro-Med-NLP
Introduction | Extract-Med | Setup of extractMed | Running extractMed | Tuning the medExtractR system | Pro-Med-NLP | Part I | Parse functions (parseMedExtractR, parseMedXN, parseCLAMP, parseMedEx) | Running parseMedExtractR | Running parseMedXN | buildDose | Running buildDose | Part II | noteMetaData | Handling lastdose | collapseDose | Running collapseDose | Additional collapsing | References
Rendered fromehr_vignette_01_mxr.Rmdusingknitr::rmarkdown

Last update: 2021-10-07
Started: 2021-06-09

Dose Building Using Example Vanderbilt EHR Data
Introduction | medExtractR Output | Part I | Comparing to Gold Standard | Part II
Rendered fromehr_vignette_03_DoseBuilding.Rmdusingknitr::rmarkdown

Last update: 2021-10-07
Started: 2021-06-09

EHR Vignette for Build-PK-Oral
Introduction | Build-PK-Oral | References
Rendered fromehr_vignette_04_Build_PK_Oral.Rmdusingknitr::rmarkdown

Last update: 2021-10-07
Started: 2021-06-09

Readme and manuals

Help Manual

Help pageTopics
Electronic Health Record (EHR) Data Processing and Analysis ToolEHR-package EHR
Add Lastdose DataaddLastDose
Statistical Analysis for PheWASanalysisPheWAS
Combine Dose DatabuildDose
Collapse Dose DatacollapseDose
Data TransformationdataTransformation
dddd
dd.baselinedd.baseline
dd.baseline.smalldd.baseline.small
dd.smalldd.small
Extract medication information from clinical notesextractMed
Convert Character Frequency to NumericfreqNum
Create ID CrosswalkidCrosswalk
Example of Metadata for Lamotrigine Datalam_metadata
Example of Lamotrigine Output from `parseMedExtractR`lam_mxr_parsed
Firth's penalized-likelihood logistic regression with more decimal places of p-value than 'logistf' function in the R package 'logistf'Logistf
Make Dose DatamakeDose
Parse CLAMP NLP OutputparseCLAMP
Parse MedEx NLP OutputparseMedEx
Parse medExtractR NLP OutputparseMedExtractR
Parse MedXN NLP OutputparseMedXN
Process and standardize extracted last dose timesprocessLastDose
Pull Fake/Mod IDpullFakeId
Pull Real IDpullRealId
Read and TransformreadTransform
Build-PK-IV Modulerun_Build_PK_IV
Build-PK-Oral Modulerun_Build_PK_Oral
Run Demographic Datarun_Demo
Run Drug Level Datarun_DrugLevel
Run Lab Datarun_Labs
Run Str Data Irun_MedStrI
Run Structured E-Prescription Datarun_MedStrII
Standardize Dose EntitystdzDose
Standardize Dose Change EntitystdzDoseChange
Standardize Dose Schedule EntitystdzDoseSchedule
Standardize Duration EntitystdzDuration
Standardize Frequency EntitystdzFreq
Standardize Route EntitystdzRoute
Standardize Strength EntitystdzStrength
Example of Lab Time Data for Tacrolimustac_lab
Example of Metadata for Tacrolimus Datatac_metadata
Example of Tacrolimus Output from `parseMedExtractR`tac_mxr_parsed
Make Zero One Contingency TableszeroOneTable