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Add FHIR Resolution section to pkgdown documentation#6

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alex-omophub merged 1 commit intomainfrom
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Apr 14, 2026
Merged

Add FHIR Resolution section to pkgdown documentation#6
alex-omophub merged 1 commit intomainfrom
develop

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@alex-omophub alex-omophub commented Apr 14, 2026

  • Updated the README to clarify the output structure for bulk lexical and semantic searches, emphasizing the return types and iteration methods.
  • Added a new section on tibble output for batch resolution, demonstrating how to use as_tibble = TRUE for streamlined data manipulation with dplyr.
  • Included standalone wrapper functions for improved usability in pipe-friendly workflows and clarified the distinction between using the client methods and raw FHIR responses.

Summary by cubic

Adds a FHIR Resolution section and examples to the pkgdown docs to make FHIR-to-OMOP workflows clearer and easier in R. Also clarifies response shapes for bulk search and updates error handling guidance.

  • New Features
    • FHIR-to-OMOP docs with as_tibble = TRUE batch output, ready for dplyr pipelines; columns and batch summary are documented.
    • Pipe-friendly wrappers added: fhir_resolve, fhir_resolve_batch, fhir_resolve_codeable_concept.
    • FHIR interop documented via omophub_fhir_url() with httr2 examples (r4, r4b, r5, r6).
    • Response shapes clarified: bulk_basic returns a flat list; bulk_semantic returns an object with results, counts, and duration; hierarchy$descendants() data lives under data$descendants.
    • Error handling examples switched to httr2 condition classes (httr2_http_404, httr2_http_401, httr2_http_429, etc.); omophub_validation_error remains for client-side checks.
    • New examples referenced: inst/examples/fhir_resolver.R and inst/examples/fhir_interop.R.

Written for commit 4800128. Summary will update on new commits.

- Updated the README to clarify the output structure for bulk lexical and semantic searches, emphasizing the return types and iteration methods.
- Added a new section on tibble output for batch resolution, demonstrating how to use `as_tibble = TRUE` for streamlined data manipulation with `dplyr`.
- Included standalone wrapper functions for improved usability in pipe-friendly workflows and clarified the distinction between using the client methods and raw FHIR responses.
@alex-omophub alex-omophub merged commit 6053d4d into main Apr 14, 2026
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