Illustration of FHIR ingestion and transformation using R

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Documentation for package ‘BiocFHIR’ version 1.9.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

add_procedures	update a fhir graph on patients and conditions with procedures
allin	collection of synthea FHIR documents ingested
available_retention_schemas	list available 'retention schemas'
build_proccond_igraph	build graph with patients, conditions and procedures
display_proccond_igraph	make network visualization
FHIRtabs	table app
FHIR_ResourceTypes	FHIR Resource types recognized in package
FHIR_retention_schemas	collection of FHIR Resource components to be retained
freq_app	produce interactive tables with FHIR resources from a list of ingested bundles
getHumanName	get human name from a BiocFHIR.Patient instance
make_condition_graph	create graph with links from patients to conditions
make_test_json_set	produce 50 json FHIR files in a folder
print.BiocFHIR.FHIRgraph	show a combination of graph and patient attributes
print.FHIR.bundle	print method
process_AllergyIntolerance	extract information from retained fields in AllergyIntolerance component of FHIR Bundle, produce simple data.frame
process_CarePlan	extract information from retained fields in CarePlan component of FHIR Bundle, produce simple data.frame
process_Claim	extract information from retained fields in Claim component of FHIR Bundle, produce simple data.frame
process_Condition	extract information from retained fields in Condition component of FHIR Bundle, produce simple data.frame
process_Encounter	extract information from retained fields in Encounter component of FHIR Bundle, produce simple data.frame
process_fhir_bundle	process a bundle of FHIR R4 JSON
process_Immunization	extract information from retained fields in Immunization component of FHIR Bundle, produce simple data.frame
process_MedicationRequest	extract information from retained fields in MedicationRequest component of FHIR Bundle, produce simple data.frame
process_Observation	extract information from retained fields in Observation component of FHIR Bundle, produce simple data.frame
process_Patient	flatten information in Patient component of a bundle to a one-line data.frame
process_Procedure	extract information from retained fields in Procedure component of FHIR Bundle, produce simple data.frame
stack_fhir	convert data of a given FHIR type in a list of bundles to a data.frame
summarise_bundles	produce tables summarizing FHIR data
summary_selections	vector of fields to be selected for summarization