# Illustration of FHIR ingestion and transformation using R

## Documentation for package ‘BiocFHIR’ version 1.2.0

- 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