EHRtemporalVariability v1.0

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Delineating Reference Changes in Electronic Health Records over Time

The 'EHRtemporalVariability' package contains functions to delineate reference changes over time in Electronic Health Records through the projection and visualization of dissimilarities among data temporal batches. This is done through the estimation of data statistical distributions over time and their projection in non-parametric statistical manifolds uncovering the patterns of the data latent temporal variability. Results can be explored through visual analytics formats such as Data Temporal heatmaps and Information Geometric Temporal (IGT) plots. An additional 'EHRtemporalVariability' Shiny app can be used to load and explore the package results and even to allow the use of these functions to those users non-experienced in R coding.

Readme

EHRtemporalVariability

EHRtemporalVariability is an R package for delineating reference changes in Eletronic Health Records over time

What is this repository for?

The EHRtemporalVariability package contains functions to delineate reference changes over time in Electronic Health Records through the projection and visualization of dissimilarities among data temporal batches. This is done through the estimation of data statistical distributions over time and their projection in non-parametric statistical manifolds uncovering the patterns of the data latent temporal variability. Results can be explored through visual analytics formats such as Data Temporal heatmaps and Information Geometric Temporal (IGT) plots 1-3. An additional EHRtemporalVariability Shiny app can be used to load and explore the package results and even to allow the use of these functions to those users non-experienced in R coding.

Package' Status

  • Version: 1.0
  • Authors: Carlos Sáez (UPV-HMS), Alba Gutiérrez-Sacristán (HMS), Paul Avillach (HMS), Juan M García-Gómez (UPV)
  • Maintainer: Carlos Saez (UPV-HMS)

    Copyright: 2019 - Biomedical Data Science Lab, Universitat Politècnica de València, Spain (UPV) - Department of Biomedical Informatics, Harvard Medical School (HMS)

Documentation

Citation

A paper describing the EHRtemporalVariability package has been submitted. If you use EHRtemporalVariability, please cite:

Sáez C, Gutiérrez-Sacristán A, Avillach P, García-Gómez JM. EHRtemporalVariability: delineating unknown reference changes in Electronic Health Records over time. (Submitted)

The original methods and case studies using the approach are described here:

[1]: Sáez C, Rodrigues PP, Gama J, Robles M, García-Gómez JM. Probabilistic change detection and visualization methods for the assessment of temporal stability in biomedical data quality. Data Mining and Knowledge Discovery. 2015;29:950–75. https://doi.org/10.1007/s10618-014-0378-6

[2]: Sáez C, Zurriaga O, Pérez-Panadés J, Melchor I, Robles M, García-Gómez JM. Applying probabilistic temporal and multisite data quality control methods to a public health mortality registry in spain: A systematic approach to quality control of repositories. Journal of the American Medical Informatics Association. 2016;23:1085–95. https://doi.org/10.1093/jamia/ocw010

[3]: Sáez C, García-Gómez JM. Kinematics of Big Biomedical Data to characterize temporal variability and seasonality of data repositories: Functional Data Analysis of data temporal evolution over non-parametric statistical manifolds. International Journal of Medical Informatics. 2018;119:109–24. https://doi.org/10.1016/j.ijmedinf.2018.09.015

Download

Download the latest development code of EHRtemporalVariability from GitHub using devtools with

devtools::install_github("hms-dbmi/EHRtemporalVariability")

Functions in EHRtemporalVariability

Name Description
plotIGTProjection Information Geometric Temporal plot
estimateDataTemporalMap Estimates DataTemporalMap objects from raw data
icd9toPheWAS Function to transform ICD9-CM codification into PheWAS code
estimateIGTProjection Estimates an Information Geometric Temporal plot projection
formatDate Function to transform dates into "Date" R format
plotDataTemporalMap Data Temporal heatmap
DataTemporalMap-class Class DataTemporalMap
trimDataTemporalMap Trims a DataTemporalMap
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Vignettes of EHRtemporalVariability

Name
EHRtemporalVariability.Rmd
EHRtemporalVariabilityHelpForAllFunctions.pdf
biomed-central.csl
createAutomaticPDFfunctions.R
general-overview.bib
rpackageworkflow.png
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Details

Type Package
Date 2019-03-01
Encoding UTF-8
License Apache License 2.0 | file LICENSE
LazyData true
VignetteBuilder knitr
NeedsCompilation no
RoxygenNote 6.1.1
URL http://github.com/hms-dbmi/EHRtemporalVariability
Packaged 2019-03-14 09:31:15 UTC; Carlos
Repository CRAN
Date/Publication 2019-03-14 12:03:34 UTC

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