BiocFHIR
Bioc currentIllustration of FHIR ingestion and transformation using R
Release Lineage
Entered 3.16 · Nov 2, 2022
Current · Requires R 4.6
Description
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.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
29 25 exported
Complexity
1.6 avg / 6 max
Call network
29 nodes / 27 edges
Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.
Call graph
Open call graph →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
2,340
Files
62
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
25
Internal functions
5
Testing
Has tests
Yes
Test-to-code ratio
0.12
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.2
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
8
First release
2022-11-01
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
2
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 28
- Examples that run
- 100%25 run in a plain check (2 of them under a condition)
- Exported functions with examples
- 92%
- Documented parameters
- 98%
- Return-value docs
- 100%
- Help pages citing references
- 0%
Repository practices
2 development-tooling and community-health practices detected across 2 families in the upstream repository
Checks run against github.com/vjcitn/biocfhir on 2026-10-21.
GitHub Pages site last deployed 2023-08-24
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| allin | list | 50 elements | No other package |
Topics
People
- Vincent Carey author maintainer
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("BiocFHIR")This package has no citation file, so citation() returns this entry built from DESCRIPTION.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.