BiocFHIR

DOI: 10.18129/B9.bioc.BiocFHIR  

Illustration of FHIR ingestion and transformation using R

Bioconductor version: Release (3.16)

FHIR R4 bundles in JSON format are derived from https://synthea.mitre.org/downloads. Transformation inspired by a kaggle notebook published by Dr Alexander Scarlat, https://www.kaggle.com/code/drscarlat/fhir-starter-parse-healthcare-bundles-into-tables. This is a very limited illustration of some basic parsing and reorganization processes. Additional tooling will be required to move beyond the Synthea data illustrations.

Author: Vincent Carey [aut, cre]

Maintainer: Vincent Carey <stvjc at channing.harvard.edu>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("BiocFHIR")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("BiocFHIR")

 

HTML	R Script	BiocFHIR -- infrastructure for parsing and analyzing FHIR data
HTML	R Script	Handling FHIR documents with BiocFHIR
HTML	R Script	Linking information between FHIR resources
HTML	R Script	Transforming FHIR documents to tables with BiocFHIR
HTML	R Script	Upper level FHIR concepts
PDF		Reference Manual
Text		NEWS

Details

biocViews	DataImport, DataRepresentation, Infrastructure, Software
Version	1.0.0
In Bioconductor since	BioC 3.16 (R-4.2) (< 6 months)
License	Artistic-2.0
Depends	R (>= 4.2)
Imports	DT, shiny, jsonlite, graph, tidyr, visNetwork, igraph, utils, methods, BiocBaseUtils
LinkingTo
Suggests	knitr, testthat, rjsoncons
SystemRequirements
Enhances
URL	https://github.com/vjcitn/BiocFHIR
BugReports	https://github.com/vjcitn/BiocFHIR/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	BiocFHIR_1.0.0.tar.gz
Windows Binary	BiocFHIR_1.0.0.zip
macOS Binary (x86_64)	BiocFHIR_1.0.0.tgz
macOS Binary (arm64)	BiocFHIR_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/BiocFHIR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/BiocFHIR
Bioc Package Browser	https://code.bioconductor.org/browse/BiocFHIR/
Package Short Url	https://bioconductor.org/packages/BiocFHIR/
Package Downloads Report	Download Stats