BiocFHIR
Illustration of FHIR ingestion and transformation using R
Bioconductor version: Release (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("BiocFHIR")
):
Installation
To install this package, start R (version "4.4") 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 | ||
NEWS | Text |
Details
biocViews | DataImport, DataRepresentation, Infrastructure, Software |
Version | 1.6.0 |
In Bioconductor since | BioC 3.16 (R-4.2) (2 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_1.6.0.tar.gz |
Windows Binary | BiocFHIR_1.6.0.zip |
macOS Binary (x86_64) | BiocFHIR_1.6.0.tgz |
macOS Binary (arm64) | BiocFHIR_1.6.0.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 |