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BiocFHIR

Illustration of FHIR ingestion and transformation using R

Bioconductor version: Release (3.17)

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>

Citation (from within R, enter citation("BiocFHIR")):

Installation

To install this package, start R (version "4.3") 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")
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 HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DataImport, DataRepresentation, Infrastructure, Software
Version 1.2.0
In Bioconductor since BioC 3.16 (R-4.2) (1 year)
License Artistic-2.0
Depends R (>= 4.2)
Imports DT, shiny, jsonlite, graph, tidyr, visNetwork, dplyr, utils, methods, BiocBaseUtils
Linking To
Suggests knitr, testthat, rjsoncons, igraph, BiocStyle
System Requirements
Enhances
URL https://github.com/vjcitn/BiocFHIR
Bug Reports https://github.com/vjcitn/BiocFHIR/issues
See More
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_1.2.0.tar.gz
Windows Binary BiocFHIR_1.2.0.zip
macOS Binary (x86_64) BiocFHIR_1.2.0.tgz
macOS Binary (arm64) BiocFHIR_1.2.0.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