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 (3.22)
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 "4.5") 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 | ||
| NEWS | Text |
Details
| biocViews | DataImport, DataRepresentation, Infrastructure, Software |
| Version | 1.11.0 |
| In Bioconductor since | BioC 3.16 (R-4.2) (3 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_1.11.0.tar.gz |
| Windows Binary (x86_64) | BiocFHIR_1.11.0.zip |
| macOS Binary (x86_64) | BiocFHIR_1.11.0.tgz |
| macOS Binary (arm64) | BiocFHIR_1.11.0.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 |