Package: BiocFHIR 1.9.0

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:Vincent Carey [aut, cre]

BiocFHIR_1.9.0.tar.gz
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BiocFHIR_1.9.0.tgz(r-4.4-any)BiocFHIR_1.9.0.tgz(r-4.3-any)
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BiocFHIR.pdf |BiocFHIR.html✨
BiocFHIR/json (API)
NEWS

# Install 'BiocFHIR' in R:
install.packages('BiocFHIR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/vjcitn/biocfhir/issues

Datasets:
  • allin - Collection of synthea FHIR documents ingested

On BioConductor:BiocFHIR-1.9.0(bioc 3.21)BiocFHIR-1.8.0(bioc 3.20)

infrastructuredataimportdatarepresentationfhir

5.95 score 4 stars 15 scripts 122 downloads 25 exports 59 dependencies

Last updated 2 months agofrom:9b190a516a. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 29 2024
R-4.5-winOKNov 29 2024
R-4.5-linuxOKNov 29 2024
R-4.4-winNOTENov 29 2024
R-4.4-macNOTENov 29 2024
R-4.3-winNOTENov 29 2024
R-4.3-macNOTENov 29 2024

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:base64encBiocBaseUtilsBiocGenericsbslibcachemclicommonmarkcpp11crayoncrosstalkdigestdplyrDTevaluatefansifastmapfontawesomefsgenericsgluegraphhighrhtmltoolshtmlwidgetshttpuvjquerylibjsonliteknitrlaterlazyevallifecyclemagrittrmemoisemimepillarpkgconfigpromisespurrrR6rappdirsRcpprlangrmarkdownsassshinysourcetoolsstringistringrtibbletidyrtidyselecttinytexutf8vctrsvisNetworkwithrxfunxtableyaml

BiocFHIR -- infrastructure for parsing and analyzing FHIR data

Vincent J. Carey, stvjc at channing.harvard.edu

Rendered fromBiocFHIR.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2022-10-14
Started: 2022-10-02

Handling FHIR documents with BiocFHIR

Vincent J. Carey, stvjc at channing.harvard.edu

Rendered fromB_handling.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2022-10-15
Started: 2022-10-05

Linking information between FHIR resources

Vincent J. Carey, stvjc at channing.harvard.edu

Rendered fromD_linking.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2022-11-14
Started: 2022-10-06

Transforming FHIR documents to tables with BiocFHIR

Vincent J. Carey, stvjc at channing.harvard.edu

Rendered fromC_tables.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2022-10-13
Started: 2022-10-06

Upper level FHIR concepts

Vincent J. Carey, stvjc at channing.harvard.edu

Rendered fromA_upper.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2022-10-13
Started: 2022-10-05

Readme and manuals

Help Manual

Help pageTopics
update a fhir graph on patients and conditions with proceduresadd_procedures
collection of synthea FHIR documents ingestedallin
list available 'retention schemas'available_retention_schemas
build graph with patients, conditions and proceduresbuild_proccond_igraph
make network visualizationdisplay_proccond_igraph
FHIR Resource types recognized in packageFHIR_ResourceTypes
collection of FHIR Resource components to be retainedFHIR_retention_schemas
table appFHIRtabs
produce interactive tables with FHIR resources from a list of ingested bundlesfreq_app
get human name from a BiocFHIR.Patient instancegetHumanName
create graph with links from patients to conditionsmake_condition_graph
produce 50 json FHIR files in a foldermake_test_json_set
show a combination of graph and patient attributesprint.BiocFHIR.FHIRgraph
print methodprint.FHIR.bundle
extract information from retained fields in AllergyIntolerance component of FHIR Bundle, produce simple data.frameprocess_AllergyIntolerance
extract information from retained fields in CarePlan component of FHIR Bundle, produce simple data.frameprocess_CarePlan
extract information from retained fields in Claim component of FHIR Bundle, produce simple data.frameprocess_Claim
extract information from retained fields in Condition component of FHIR Bundle, produce simple data.frameprocess_Condition
extract information from retained fields in Encounter component of FHIR Bundle, produce simple data.frameprocess_Encounter
process a bundle of FHIR R4 JSONprocess_fhir_bundle
extract information from retained fields in Immunization component of FHIR Bundle, produce simple data.frameprocess_Immunization
extract information from retained fields in MedicationRequest component of FHIR Bundle, produce simple data.frameprocess_MedicationRequest
extract information from retained fields in Observation component of FHIR Bundle, produce simple data.frameprocess_Observation
flatten information in Patient component of a bundle to a one-line data.frameprocess_Patient
extract information from retained fields in Procedure component of FHIR Bundle, produce simple data.frameprocess_Procedure
convert data of a given FHIR type in a list of bundles to a data.framestack_fhir
produce tables summarizing FHIR datasummarise_bundles
vector of fields to be selected for summarizationsummary_selections