Reference

All functions

FHIR_ResourceTypes()

FHIR Resource types recognized in package

FHIR_retention_schemas()

collection of FHIR Resource components to be retained

FHIRtabs()

table app

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

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_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

process_fhir_bundle()

process a bundle of FHIR R4 JSON

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