Package: fhircrackr 2.2.0.9000
Julia Palm
fhircrackr: Handling HL7 FHIR® Resources in R
Useful tools for conveniently downloading FHIR resources in xml format and converting them to R data.frames. The package uses FHIR-search to download bundles from a FHIR server, provides functions to save and read xml-files containing such bundles and allows flattening the bundles to data.frames using XPath expressions. FHIR® is the registered trademark of HL7 and is used with the permission of HL7. Use of the FHIR trademark does not constitute endorsement of this product by HL7.
Authors:
fhircrackr_2.2.0.9000.tar.gz
fhircrackr_2.2.0.9000.zip(r-4.5)fhircrackr_2.2.0.9000.zip(r-4.4)fhircrackr_2.2.0.9000.zip(r-4.3)
fhircrackr_2.2.0.9000.tgz(r-4.4-any)fhircrackr_2.2.0.9000.tgz(r-4.3-any)
fhircrackr_2.2.0.9000.tar.gz(r-4.5-noble)fhircrackr_2.2.0.9000.tar.gz(r-4.4-noble)
fhircrackr_2.2.0.9000.tgz(r-4.4-emscripten)fhircrackr_2.2.0.9000.tgz(r-4.3-emscripten)
fhircrackr.pdf |fhircrackr.html✨
fhircrackr/json (API)
NEWS
| # Install 'fhircrackr' in R: |
| install.packages('fhircrackr', repos = c('https://polar-fhir.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/polar-fhir/fhircrackr/issues
- example_bundles1 - Toy example bundles for multiple entries
- example_bundles2 - Toy example bundles for multiple entries
- example_bundles3 - Toy example bundles for multiple entries
- example_bundles4 - Toy example bundles for multiple entries
- example_bundles5 - Toy example bundles for multiple entries
- example_bundles6 - Toy example bundles for multiple entries
- example_bundles7 - Toy example bundles for multiple entries
- example_resource1 - Toy examples to POST/PUT on a server
- example_resource2 - Toy examples to POST/PUT on a server
- example_resource3 - Toy examples to POST/PUT on a server
- medication_bundles - Exemplary FHIR bundles
- patient_bundles - Exemplary FHIR bundles
- transaction_bundle_example - Toy examples to POST/PUT on a server
Last updated 3 months agofrom:d397f91566. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 13 2024 |
| R-4.5-win | OK | Sep 13 2024 |
| R-4.5-linux | OK | Sep 13 2024 |
| R-4.4-win | OK | Sep 13 2024 |
| R-4.4-mac | OK | Sep 13 2024 |
| R-4.3-win | OK | Sep 13 2024 |
| R-4.3-mac | OK | Sep 13 2024 |
Exports:as_fhirfhir_authenticatefhir_bodyfhir_build_bundlefhir_build_resourcefhir_bundle_listfhir_bundle_xmlfhir_canonical_designfhir_capability_statementfhir_castfhir_collapsefhir_columnsfhir_common_columnsfhir_count_resourcefhir_crackfhir_current_requestfhir_designfhir_get_resource_idsfhir_get_resources_by_idsfhir_loadfhir_load_designfhir_meltfhir_melt_allfhir_next_bundle_urlfhir_postfhir_putfhir_recent_http_errorfhir_requestfhir_resource_typefhir_resource_xmlfhir_rm_divfhir_rm_indicesfhir_rm_tagfhir_sample_resourcesfhir_sample_resources_by_idsfhir_savefhir_save_designfhir_searchfhir_serializefhir_stylefhir_table_descriptionfhir_treefhir_unserializefhir_urlfhir_xpath_expressionpaste_pathspastep
Dependencies:askpassclicurldata.tablegluehttrjsonlitelifecyclemagrittrmimeopensslR6rlangstringistringrsysvctrsxml2
fhircrackr Intro: Handling HL7® FHIR® Resources in R
Rendered fromfhircrackr_intro.Rmdusingknitr::rmarkdownon Sep 13 2024.Last update: 2024-03-21
Started: 2021-03-12
fhircrackr: Download FHIR resources
Rendered fromdownloadResources.Rmdusingknitr::rmarkdownon Sep 13 2024.Last update: 2023-12-04
Started: 2021-03-12
fhircrackr: Flatten FHIR resources
Rendered fromflattenResources.Rmdusingknitr::rmarkdownon Sep 13 2024.Last update: 2024-06-27
Started: 2021-03-12
fhircrackr: Recreate FHIR resources
Rendered fromrecreateResources.Rmdusingknitr::rmarkdownon Sep 13 2024.Last update: 2022-07-13
Started: 2021-09-28
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Coerce character vector to fhir_bundle_list | as_fhir |
| Toy example bundles for multiple entries | example_bundles1 example_bundles2 example_bundles3 example_bundles4 example_bundles5 example_bundles6 example_bundles7 |
| Create token for Authentication | fhir_authenticate |
| Create fhir_body object | fhir_body fhir_body,character,character-method fhir_body,character,character-methods fhir_body,list,character-method fhir_body,list,character-methods fhir_body,list,missing-method fhir_body,list,missing-methods |
| An s4 class to represent a body for a POST to a FHIR server | fhir_body-class |
| Build a FHIR bundle | fhir_build_bundle fhir_build_bundle,data.frame-method fhir_build_bundle,list-method |
| Build a single FHIR resource | fhir_build_resource |
| Create fhir_bundle_list object | fhir_bundle_list |
| S4 class to represent a list of FHIR bundles | fhir_bundle_list-class |
| An S4 class to represent a FHIR bundle in serialized form | fhir_bundle_serialized-class |
| Create fhir_bundle_xml object | fhir_bundle_xml |
| An S4 class to represent a FHIR bundle in xml form | fhir_bundle_xml-class |
| An S4 class to represent FHIR bundles | fhir_bundle-class |
| Retrieve design of last call to fhir_crack | fhir_canonical_design |
| Get capability statement | fhir_capability_statement |
| Cast table with multiple entries This function divides multiple entries in a compact indexed table as produced by 'fhir_crack()' into separate columns. | fhir_cast |
| Collapse multiple entries | fhir_collapse |
| Create fhir_columns object | fhir_columns fhir_columns,character,character-method fhir_columns,character,missing-method fhir_columns,list,missing-method fhir_columns,missing,missing-method fhir_columns,NULL,missing-method |
| A S4 class to represent columns in a fhir_table_description | fhir_columns-class |
| Find common columns | fhir_common_columns |
| Get Resources' Counts | fhir_count_resource |
| Flatten list of FHIR bundles | fhir_crack fhir_crack,ANY,fhir_design-method fhir_crack,ANY,fhir_table_description-method fhir_crack,fhir_design-method fhir_crack,fhir_table_description-method |
| Return FHIR search request used in last call to 'fhir_search()' or 'fhir_url()' | fhir_current_request |
| Create a fhir_design object | fhir_design fhir_design,fhir_table_description-method fhir_design,fhir_table_list-method fhir_design,list-method |
| A S4 class containing a design for 'fhir_crack()' | fhir_design-class |
| List of data.frames as returned by 'fhir_crack()' | fhir_df_list-class |
| List of data.tables as returned by 'fhir_crack()' | fhir_dt_list-class |
| Get Resources' IDs | fhir_get_resource_ids |
| Get Resources by their IDs | fhir_get_resources_by_ids |
| Load bundles from xml-files | fhir_load |
| Load design from xml | fhir_load_design |
| Melt multiple entries | fhir_melt |
| Melt all columns with multiple entries | fhir_melt_all |
| Next Bundle's URL | fhir_next_bundle_url |
| POST to a FHIR server | fhir_post fhir_post,ANY,fhir_body-method fhir_post,ANY,fhir_bundle_xml-method fhir_post,ANY,fhir_resource-method fhir_post,fhir_body-method fhir_post,fhir_bundle_xml-method fhir_post,fhir_resource-method |
| PUT to a FHIR server | fhir_put |
| Return most recent http error from 'fhir_search()' | fhir_recent_http_error |
| fhir_request | fhir_request |
| An S4 class to represent a FHIR resource in serialized form | fhir_resource_serialized-class |
| Create fhir_resource_type object | fhir_resource_type |
| A representation of a FHIR resource type | fhir_resource_type-class |
| Create fhir_resource_xml object | fhir_resource_xml fhir_resource_xml,character-method fhir_resource_xml,xml_document-method fhir_resource_xml,xml_node-method |
| An S4 class to represent a FHIR resource in xml form | fhir_resource_xml-class |
| An S4 class to represent FHIR resources | fhir_resource-class |
| Remove html elements | fhir_rm_div |
| Remove indices from data.frame/data.table | fhir_rm_indices |
| Remove a certain xml tag | fhir_rm_tag fhir_rm_tag,character-method fhir_rm_tag,fhir_bundle_list-method fhir_rm_tag,fhir_bundle_xml-method |
| Randomly sample resources from a FHIR server | fhir_sample_resources |
| Download a random sample of resources from a vector of resource IDs. | fhir_sample_resources_by_ids |
| Save FHIR bundles as xml-files | fhir_save |
| Write design to xml | fhir_save_design |
| Download FHIR search result | fhir_search |
| Serialize a fhir_bundle, fhir_bundle_list or fhir_resource | fhir_serialize fhir_serialize,fhir_bundle_list-method fhir_serialize,fhir_bundle_serialized-method fhir_serialize,fhir_bundle_xml-method fhir_serialize,fhir_resource_serialized-method fhir_serialize,fhir_resource_xml-method |
| Create fhir_table_description object | fhir_table_description |
| A S4 class describing the form of a table produced by 'fhir_crack()' | fhir_table_description-class |
| Represent a wide cast table as a tree | fhir_tree |
| Unserialize a fhir_bundle, fhir_bundle_list or fhir_resource | fhir_unserialize fhir_unserialize,fhir_bundle_list-method fhir_unserialize,fhir_bundle_serialized-method fhir_unserialize,fhir_bundle_xml-method fhir_unserialize,fhir_resource_serialized-method fhir_unserialize,fhir_resource_xml-method |
| Create FHIR URL | fhir_url fhir_url,character,character,character-method fhir_url,character,character,list-method fhir_url,character,character,missing-method fhir_url,character,missing,missing-method |
| An S4 object to represent a URL for a FHIR server | fhir_url-class |
| Create fhir_xpath_expression | fhir_xpath_expression |
| An S4 class for xpath_expressions Objects of this class are essentially character vectors, but can only be valid XPath (1.0) expressions. They are mostly used in the 'fhir_columns' class. | fhir_xpath_expression-class |
| Exemplary FHIR bundles | medication_bundles patient_bundles |
| Concatenate two paths | paste_paths |
| Concatenate paths | pastep |
| Toy examples to POST/PUT on a server | example_resource1 example_resource2 example_resource3 transaction_bundle_example |
