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BiocFHIR

This is the development version of BiocFHIR; for the stable release version, see BiocFHIR.

Illustration of FHIR ingestion and transformation using R


Bioconductor version: Development (3.19)

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 "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.5.1
In Bioconductor since BioC 3.16 (R-4.2) (1.5 years)
License Artistic-2.0
Depends R (>= 4.2)
Imports DT, shiny, jsonlite, graph, tidyr, visNetwork, dplyr, utils, methods, BiocBaseUtils
System Requirements
URL https://github.com/vjcitn/BiocFHIR
Bug Reports https://github.com/vjcitn/BiocFHIR/issues
See More
Suggests knitr, testthat, rjsoncons, igraph, BiocStyle
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package BiocFHIR_1.5.1.tar.gz
Windows Binary BiocFHIR_1.5.1.zip
macOS Binary (x86_64) BiocFHIR_1.5.1.tgz
macOS Binary (arm64) BiocFHIR_1.5.1.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