Package: pathling 7.0.0

"Australian e-Health Research Centre, CSIRO"

pathling: A Library for using 'Pathling'

R API for 'Pathling', a tool for querying and transforming electronic health record data that is represented using the 'Fast Healthcare Interoperability Resources' (FHIR) standard - see <https://pathling.csiro.au/docs>.

Authors:Australian e-Health Research Centre, CSIRO [cph, cre], Piotr Szul [aut], John Grimes [aut]

pathling_7.0.0.tar.gz
pathling_7.0.0.tar.gz(r-4.5-noble)pathling_7.0.0.tar.gz(r-4.4-noble)
pathling_7.0.0.tgz(r-4.4-emscripten)pathling_7.0.0.tgz(r-4.3-emscripten)
pathling.pdf |pathling.html✨
pathling/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/aehrc/pathling/issues

Datasets:

45 exports 0.23 score 39 dependencies 10 scripts 849 downloads

Last updated 4 months agofrom:2de05e8ccd. Checks:OK: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 21 2024
R-4.5-linuxOKAug 21 2024

Exports:%>%ds_aggregateds_extractds_readds_write_deltads_write_ndjsonds_write_parquetds_write_tablesEquivalenceImportModeLOINC_URIMimeTypepathling_connectpathling_disconnectpathling_disconnect_allpathling_encodepathling_encode_bundlepathling_example_resourcepathling_examplespathling_install_sparkpathling_is_spark_installedpathling_read_bundlespathling_read_datasetspathling_read_deltapathling_read_ndjsonpathling_read_parquetpathling_read_tablespathling_sparkpathling_spark_infopathling_versionPropertyTypeSNOMED_URIStorageTypetx_designationtx_displaytx_member_oftx_property_oftx_subsumed_bytx_subsumestx_to_codingtx_to_ecl_value_settx_to_loinc_codingtx_to_snomed_codingtx_translateVersion

Dependencies:askpassblobclicodetoolsconfigcpp11curlDBIdbplyrdplyrfansigenericsglobalsgluehttrjsonlitelifecyclemagrittrmimeopensslpillarpkgconfigpurrrR6rlangrstudioapisparklyrstringistringrsystibbletidyrtidyselectutf8uuidvctrswithrxml2yaml

Readme and manuals

Help Manual

Help pageTopics
Synthetic conditions dataconditions
Execute an aggregate queryds_aggregate
Execute an extract queryds_extract
Get data for a resource type from a data sourceds_read
Write FHIR data to Delta filesds_write_delta
Write FHIR data to NDJSON filesds_write_ndjson
Write FHIR data to Parquet filesds_write_parquet
Write FHIR data to managed tablesds_write_tables
Concept map equivalence typesEquivalence
ImportModeImportMode
LOINC system URILOINC_URI
FHIR MIME typesMimeType
Create or retrieve the Pathling contextpathling_connect
Disconnect from the Spark sessionpathling_disconnect
Disconnect all Spark connectionspathling_disconnect_all
Encode FHIR JSON or XML to a dataframepathling_encode
Encode FHIR Bundles to a dataframepathling_encode_bundle
Read resource from Pathling example datapathling_example_resource
Get path to Pathling example datapathling_examples
Install Sparkpathling_install_spark
Check if Spark is installedpathling_is_spark_installed
Create a data source from FHIR bundlespathling_read_bundles
Create a data source from datasetspathling_read_datasets
Create a data source from Delta tablespathling_read_delta
Create a data source from NDJSONpathling_read_ndjson
Create a data source from Parquet tablespathling_read_parquet
Create a data source from managed tablespathling_read_tables
Get the Spark sessionpathling_spark
Get versions of Spark and other dependenciespathling_spark_info
Get version of Pathlingpathling_version
Coding property data typesPropertyType
SaveModeSaveMode
SNOMED CT system URISNOMED_URI
Terminology cache storage typeStorageType
Convert a vector to a SQL array literalto_array
Get designations for codingstx_designation
Get the display text for codingstx_display
Test membership within a value settx_member_of
Get properties for codingstx_property_of
Test subsumption between codingstx_subsumed_by
Test subsumption between codingstx_subsumes
Convert codes to Coding structurestx_to_coding
Convert a SNOMED CT ECL expression to a ValueSet URItx_to_ecl_value_set
Convert LOINC codes to Coding structurestx_to_loinc_coding
Convert SNOMED CT codes to Coding structurestx_to_snomed_coding
Translate between value setstx_translate
FHIR versionsVersion