Introduction | Examining sample data, again | A graph relating patients to conditions | Adding procedures to the graph | Interactive visualization of the graph | Conclusions | Session information
Package: BiocFHIR 1.15.0
Vincent Carey
BiocFHIR: Illustration of FHIR ingestion and transformation using R
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.
Authors:
BiocFHIR_1.15.0.tar.gz
BiocFHIR_1.15.0.zip(r-4.7)BiocFHIR_1.15.0.zip(r-4.6)BiocFHIR_1.15.0.zip(r-4.5)
BiocFHIR_1.15.0.tgz(r-4.6-any)BiocFHIR_1.15.0.tgz(r-4.5-any)
BiocFHIR_1.15.0.tar.gz(r-4.7-any)BiocFHIR_1.15.0.tar.gz(r-4.6-any)
BiocFHIR_1.15.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
BiocFHIR/json (API)
| # Install 'BiocFHIR' in R: |
| install.packages('BiocFHIR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/vjcitn/biocfhir/issues
Datasets:
- allin - Collection of synthea FHIR documents ingested
On BioConductor:BiocFHIR-1.15.0(bioc 3.24)BiocFHIR-1.14.0(bioc 3.23)
infrastructuredataimportdatarepresentationfhir
Last updated from:406f003b6d. Checks:1 FAILURE, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | FAILURE | 223 | ||
| linux-devel-x86_64 | OK | 191 | ||
| source / vignettes | OK | 277 | ||
| linux-release-x86_64 | OK | 203 | ||
| macos-release-arm64 | OK | 116 | ||
| macos-oldrel-arm64 | OK | 143 | ||
| windows-devel | OK | 115 | ||
| windows-release | OK | 117 | ||
| windows-oldrel | OK | 138 | ||
| wasm-release | OK | 128 |
Exports:add_proceduresavailable_retention_schemasbuild_proccond_igraphdisplay_proccond_igraphFHIR_ResourceTypesFHIR_retention_schemasFHIRtabsfreq_appgetHumanNamemake_condition_graphmake_test_json_setprocess_AllergyIntoleranceprocess_CarePlanprocess_Claimprocess_Conditionprocess_Encounterprocess_fhir_bundleprocess_Immunizationprocess_MedicationRequestprocess_Observationprocess_Patientprocess_Procedurestack_fhirsummarise_bundlessummary_selections
Dependencies:base64encBiocBaseUtilsBiocGenericsbslibcachemclicommonmarkcpp11crosstalkdigestdplyrDTevaluatefastmapfontawesomefsgenericsgluegraphhighrhtmltoolshtmlwidgetshttpuvjquerylibjsonliteknitrlaterlazyevallifecyclemagrittrmemoisemimeotelpillarpkgconfigpromisespurrrR6rappdirsRcpprlangrmarkdownsassshinysourcetoolsstringistringrtibbletidyrtidyselecttinytexutf8vctrsvisNetworkwithrxfunxtableyaml
Linking information between FHIR resources
Last update: 2022-11-14
Started: 2022-10-06
Handling FHIR documents with BiocFHIR
Introduction | Examining sample data, again | Choosing an approach to FHIR JSON ingestion | Working with a specific type | List-based operations | Processing with BiocFHIR | Direct querying of FHIR JSON | Session information
Last update: 2022-10-15
Started: 2022-10-05
BiocFHIR -- infrastructure for parsing and analyzing FHIR data
Introduction | The basic structure of FHIR R4 JSON | Example: a table on Conditions recorded on the patient. | A family of documents | Session information
Last update: 2022-10-14
Started: 2022-10-02
Transforming FHIR documents to tables with BiocFHIR
Introduction | Examining sample data, again | Bundle to data frames | Filtering FHIR elements | The resources extracted from a bundle | Accumulating resources across bundles | Session information
Last update: 2022-10-13
Started: 2022-10-06
Upper level FHIR concepts
Introduction | Some comments from hl7.org/fhir Executive Summary | FHIR JSON documents in BiocFHIR | Examining sample data | Session information
Last update: 2022-10-13
Started: 2022-10-05
