EHRtemporalVariability v1.0.4
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Delineating Temporal Dataset Shifts in Electronic Health Records
The 'EHRtemporalVariability' package contains functions to delineate temporal dataset shifts 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. Dataset shifts can be explored and identified 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 temporal dataset shifts in Eletronic Health Records
What is this repository for?
The EHRtemporalVariability package contains functions to delineate temporal dataset shifts 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. Dataset shifts can be explored and identified 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: 1.0.3
- Authors: Carlos Sáez (UPV-HMS), Alba Gutiérrez-Sacristán (HMS), Isaac Kohane (HMS), Juan M García-Gómez (UPV), Paul Avillach (HMS)
Maintainer: Carlos Sáez (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, Kohane I, García-Gómez JM, Avillach P. EHRtemporalVariability: delineating temporal dataset shifts in electronic health records. (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
Install the latest released version from CRAN
install.packages("EHRtemporalVariability")
Download the latest development code of EHRtemporalVariability from GitHub using devtools with
devtools::install_github("hms-dbmi/EHRtemporalVariability")
Functions in EHRtemporalVariability
| Name | Description | |
| plotDataTemporalMap | Data Temporal heatmap | |
| formatDate | Function to transform dates into "Date" R format | |
| trimDataTemporalMap | Trims a DataTemporalMap | |
| DataTemporalMap-class | Class DataTemporalMap | |
| icd9toPheWAS | Function to transform ICD9-CM codification into PheWAS code | |
| plotIGTProjection | Information Geometric Temporal plot | |
| estimateDataTemporalMap | Estimates DataTemporalMap objects from raw data | |
| estimateIGTProjection | Estimates an Information Geometric Temporal plot projection | |
| No Results! | ||
Vignettes of EHRtemporalVariability
| Name | ||
| EHRtemporalVariability.Rmd | ||
| EHRtemporalVariabilityHelp.pdf | ||
| biomed-central.csl | ||
| createAutomaticPDFfunctions.R | ||
| general-overview.bib | ||
| rpackageworkflow.png | ||
| No Results! | ||
Last month downloads
Details
| Type | Package |
| Date | 2020-03-27 |
| Encoding | UTF-8 |
| License | Apache License 2.0 | file LICENSE |
| LazyData | true |
| VignetteBuilder | knitr |
| NeedsCompilation | no |
| RoxygenNote | 7.1.0 |
| URL | http://github.com/hms-dbmi/EHRtemporalVariability |
| Packaged | 2020-03-27 20:44:44 UTC; Carlos |
| Repository | CRAN |
| Date/Publication | 2020-03-28 08:20:31 UTC |
| suggests | BiocStyle , devtools , knitr , rmarkdown |
| depends | dplyr , R (>= 3.3.0) |
| imports | lubridate , methods , plotly , RColorBrewer , scales , shiny , viridis , xts , zoo |
| Contributors | Alba Guti<c3><a9>rrez-Sacrist<c3><a1>n, Paul Avillach, Juan M Garc<c3><ad>a-G<c3><b3>mez, Biomedical Data Science Lab, Universitat Polit<c3><a8>cnica de Val<c3><a8>ncia (Spain) , Department of Biomedical Informatics, Harvard Medical School , Isaac Kohane |
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