# pubmedR 1.0.1

## Bug fixes

* `pmEnrichCitations()` no longer relies on the NCBI E-Link
  `pubmed_pubmed_refs` link, which only resolves references for articles
  whose full text is deposited in PMC. The function now extracts cited
  references directly from the PubMed XML `<ReferenceList>` block, which is
  populated for the majority of recent articles. CR coverage on typical
  bibliographic queries improved from a few percent to almost full coverage
  on tested samples.

## New functions

* `pmExtractReferences()`: parse a PubMed XML payload (the result of
  `pmApiRequest()` or `pmFetchById()`) and return a tidy data frame of
  references, one row per cited reference, with the source PMID, the raw
  `<Citation>` text, and any embedded PubMed/DOI identifiers.

## Improvements

* `pmEnrichCitations()` gains the arguments `P` (reuse a previously
  downloaded XML payload to avoid an extra `efetch` round-trip),
  `resolve_pmids` (resolve cited PMIDs to WoS-style "AUTHOR YEAR, JOURNAL,
  V, P, DOI" citation strings via batched `efetch`), `only_multiple` (only
  resolve references cited by more than one source article), `include_TC`
  (toggle the slower per-article cited-by lookup), and `batch_size`
  (forwarded to `pmFetchById()`).

* CR strings produced by `pmEnrichCitations()` are now compatible with the
  WoS conventions parsed by `bibliometrix` (`citations()`,
  `histNetwork()`, ...). References for which only a free-text `<Citation>`
  is available are kept verbatim (uppercased).

* `pmEnrichCitations()` now also writes the number of references for each
  article into the `NR` column.

# pubmedR 1.0.0

# pubmedR 0.1.0.900

## New functions

* `pmQueryBuild()`: build PubMed search queries programmatically, with support
  for terms, MeSH headings, authors, journals, language, publication type,
  and date range filters.

* `pmFetchById()`: download PubMed records directly by a vector of PMIDs,
  with batch support and full compatibility with `pmApi2df()`.

* `pmCitedBy()`: retrieve PMIDs of articles that cite a given article,
  using the NCBI E-Link service.

* `pmReferences()`: retrieve PMIDs of references cited by a given article,
  using the NCBI E-Link service.

* `pmEnrichCitations()`: batch enrich a bibliometric data frame with real
  citation counts (TC) and cited references (CR) from NCBI E-Link data.

* `pmCollect()`: one-step wrapper that covers the full workflow — query
  building, record count, download, conversion to data frame, and optional
  citation enrichment.

## Improvements

* All API calls now include error handling with automatic retry and
  exponential backoff (up to 3 retries).

* Automatic rate limiting enforces NCBI limits: 3 requests/second without
  API key, 10 requests/second with API key.

* API key is now auto-detected from environment variables `PUBMED_API_KEY`
  or `ENTREZ_KEY`, removing the need to pass it explicitly to every function.

* `pmApiRequest()` gains a `batch_size` argument (default 200) to control
  the number of records per API request.

* `pmApiRequest()` now returns an empty result gracefully when the query
  matches zero records, instead of erroring.

* Improved affiliation extraction in `pmApi2df()`: all author affiliations
  are now collected (previously only the corresponding author's affiliation
  was captured).

* Progress bars upgraded to style 3 (percentage display) across all functions.

* `pmApiRequest()` documentation now correctly references `pmQueryBuild()`
  (previously referenced a non-existent function).

## Bug fixes

* Fixed HTTP 400 error when query returns exactly one record. The
  `retstart` parameter now correctly starts at 0 instead of 1 (GitHub
  issues #7 and #9, PR #13).

* Fixed "invalid multibyte string" error in `pmApi2df()` caused by
  non-UTF-8 characters in PubMed XML records. Encoding is now sanitized
  during list-to-character conversion (GitHub issues #3 and #6).

* Fixed `txtProgressBar` error in `pmApi2df()` when converting a single
  record (`min == max` when `n == 1`), by starting the progress bar at 0
  (GitHub PR #13).

## Infrastructure

* Added test suite using testthat (66 tests covering utilities, query building,
  query counting, and data conversion).

* New `README.Rmd` with live examples, function reference table, workflow
  diagram, and integration guide for bibliometrix/biblioshiny.

* Internal utility functions (`list2char`, `get_api_key`, `api_throttle`,
  `api_call_with_retry`) extracted into `R/utils.R`.

# pubmedR 0.0.4

* Fixed issue about entrez_fetch restart argument.

# pubmedR 0.0.2

* Fixed issue in publication year field.

# pubmedR 0.0.1

* Initial version.