Package: fhircrackr 2.4.0

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. 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:Thomas Peschel [aut], Julia Palm [aut, cre], Jens Przybilla [aut], Frank Meineke [aut]

fhircrackr_2.4.0.tar.gz
fhircrackr_2.4.0.zip(r-4.7)fhircrackr_2.4.0.zip(r-4.6)fhircrackr_2.4.0.zip(r-4.5)
fhircrackr_2.4.0.tgz(r-4.6-any)fhircrackr_2.4.0.tgz(r-4.5-any)
fhircrackr_2.4.0.tar.gz(r-4.7-any)fhircrackr_2.4.0.tar.gz(r-4.6-any)
fhircrackr_2.4.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
fhircrackr/json (API)

# 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

Datasets:

On CRAN:

Conda:

fhirfhir-client

7.28 score 39 stars 61 scripts 644 downloads 48 exports 18 dependencies

Last updated from:5480069af6. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK128
source / vignettesOK193
linux-release-x86_64OK131
macos-release-arm64OK126
macos-oldrel-arm64OK171
windows-develOK92
windows-releaseOK101
windows-oldrelOK88
wasm-releaseOK104

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_is_emptyfhir_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: Flatten FHIR resources
Preparation | Extracting one resource type | The table_description | The resource argument | The cols argument | Other arguments | Examples | Extract all available attributes | Extract specific elements | Extracting more than one resource type | Saving and reading designs | Multiple entries | Process resources with multiple entries | Select values using predicates in XPath expression | Melt tables with multiple entries | Remove indices | Melt all multiple entries at once | Cast tables with multiple entries | Collapse multiple entries
Rendered fromflattenResources.Rmdusingknitr::rmarkdown

Last update: 2024-06-27
Started: 2021-03-12

fhircrackr Intro: Handling HL7® FHIR® Resources in R
Introduction | Prerequisites | Downloading resources | Flattening resources | Multiple entries | Process Tables with multiple Entries | Melt tables with multiple entries | Remove indices | Save and load downloaded bundles | Save and load bundles as R objects | Save and load bundles as xml files | Acknowledgments
Rendered fromfhircrackr_intro.Rmdusingknitr::rmarkdown

Last update: 2024-03-21
Started: 2021-03-12

fhircrackr: Download FHIR resources
FHIR search requests | Accessing the current request | Download FHIR resources from a server | Basic request | More than one resource type | Authentication | Search via POST | Deal with HTTP Errors | Save the downloaded bundles | Save bundles as R objects | Save and load bundles as xml files | Dealing with large data sets | Saving memory | 1. Download trimmed resources using _elements | 2. Batch process bundles by saving them to hard drive | 3. Batch process bundles by downloading them piece by piece | Saving download time | Operating system | Breaking pointers | Splitting up requests | Download random samples from a server | Download Capability Statement | A note on HTML in resources | Next steps
Rendered fromdownloadResources.Rmdusingknitr::rmarkdown

Last update: 2023-12-04
Started: 2021-03-12

fhircrackr: Recreate FHIR resources
Preparation | Crack to wide format | Modify the data | Recreate a single resource | Recreate a bundle of resources | Different attributes | Upload resources to a server | Upload a single resource | Upload a bundle of resources | Linked resources
Rendered fromrecreateResources.Rmdusingknitr::rmarkdown

Last update: 2022-07-13
Started: 2021-09-28

Readme and manuals

Help Manual

Help pageTopics
Coerce character vector to fhir_bundle_listas_fhir
Toy example bundles for multiple entriesexample_bundles1 example_bundles2 example_bundles3 example_bundles4 example_bundles5 example_bundles6 example_bundles7 example_bundles_empty
Create token for Authenticationfhir_authenticate
Create fhir_body objectfhir_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 serverfhir_body-class
Build a FHIR bundlefhir_build_bundle fhir_build_bundle,data.frame-method fhir_build_bundle,list-method
Build a single FHIR resourcefhir_build_resource
Create fhir_bundle_list objectfhir_bundle_list
S4 class to represent a list of FHIR bundlesfhir_bundle_list-class
An S4 class to represent a FHIR bundle in serialized formfhir_bundle_serialized-class
Create fhir_bundle_xml objectfhir_bundle_xml
An S4 class to represent a FHIR bundle in xml formfhir_bundle_xml-class
An S4 class to represent FHIR bundlesfhir_bundle-class
Retrieve design of last call to fhir_crackfhir_canonical_design
Get capability statementfhir_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 entriesfhir_collapse
Create fhir_columns objectfhir_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_descriptionfhir_columns-class
Find common columnsfhir_common_columns
Get Resources' Countsfhir_count_resource
Flatten list of FHIR bundlesfhir_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 objectfhir_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' IDsfhir_get_resource_ids
Get Resources by their IDsfhir_get_resources_by_ids
Check if Bundle/Bundlelist is emptyfhir_is_empty fhir_is_empty,fhir_bundle_list-method fhir_is_empty,fhir_bundle_xml-method
Load bundles from xml-filesfhir_load
Load design from xmlfhir_load_design
Melt multiple entriesfhir_melt
Melt all columns with multiple entriesfhir_melt_all
Internal function to melt multiple entries in a data.tablefhir_melt_internal
Next Bundle's URLfhir_next_bundle_url
POST to a FHIR serverfhir_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 serverfhir_put
Return most recent http error from 'fhir_search()'fhir_recent_http_error
fhir_requestfhir_request
An S4 class to represent a FHIR resource in serialized formfhir_resource_serialized-class
Create fhir_resource_type objectfhir_resource_type
A representation of a FHIR resource typefhir_resource_type-class
Create fhir_resource_xml objectfhir_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 formfhir_resource_xml-class
An S4 class to represent FHIR resourcesfhir_resource-class
Remove html elementsfhir_rm_div
Remove indices from data.frame/data.tablefhir_rm_indices
Remove a certain xml tagfhir_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 serverfhir_sample_resources
Download a random sample of resources from a vector of resource IDs.fhir_sample_resources_by_ids
Save FHIR bundles as xml-filesfhir_save
Write design to xmlfhir_save_design
Download FHIR search resultfhir_search
Serialize a fhir_bundle, fhir_bundle_list or fhir_resourcefhir_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 objectfhir_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 treefhir_tree
Unserialize a fhir_bundle, fhir_bundle_list or fhir_resourcefhir_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 URLfhir_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 serverfhir_url-class
Create fhir_xpath_expressionfhir_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 bundlesmedication_bundles patient_bundles
Concatenate two pathspaste_paths
Concatenate pathspastep
Toy examples to POST/PUT on a serverexample_resource1 example_resource2 example_resource3 transaction_bundle_example