Fix custom reference_data support in as.sir() (#239) (PR #279)

* Fix custom reference_data support in as.sir() (#239)

- custom guideline names now correctly classify values as R: CLSI convention
  (>= breakpoint_R for MIC, <= for disk) applies only when guideline contains
  "CLSI"; all other guidelines including custom ones use the EUCAST convention
  (> breakpoint_R for MIC, < for disk)
- guideline argument is now optional when reference_data is manually set: if
  omitted or if its value does not match any row in the custom data, all rows
  in reference_data are used; if set to a value present in the data, only
  matching rows are filtered — useful for multi-guideline custom tables
- host = NA in custom reference_data now acts as a host-agnostic fallback
  when no host-specific breakpoint row exists for the current animal species
- updated reference_data argument documentation to explain these conventions

https://claude.ai/code/session_01Q8KtFFGG9qrjAgLJBbxG2U

* Refactor R-classification logic using custom_breakpoints_set flag

Introduce custom_breakpoints_set <- !identical(reference_data, AMR::clinical_breakpoints)
at the top of as_sir_method() and replace all identical() calls inside that
function with this variable.

In the case_when_AMR interpretation blocks (MIC and disk), the R-classification
now has three explicit arms:
- !custom_breakpoints_set & EUCAST guideline -> open interval (> / <)
- !custom_breakpoints_set & CLSI guideline  -> closed interval (>= / <=)
- custom_breakpoints_set                    -> open interval (> / <), always,
  regardless of the guideline name in the custom data (e.g. "CLSI_custom"
  must not accidentally trigger CLSI convention)

https://claude.ai/code/session_01Q8KtFFGG9qrjAgLJBbxG2U

* Fix unit tests for custom reference_data (#239)

- Do not override my_bp$mo / my_bp$ab in tests: assigning plain character
  strips the <mo>/<ab> class, which check_reference_data() rejects. Use the
  mo/ab values already present in the source row instead.
- Use NA_character_ instead of NA for my_bp$host so the host column keeps
  its character class.
- Pass breakpoint_type = "animal" explicitly in the host-fallback test since
  the custom reference_data only contains animal-type breakpoints.

https://claude.ai/code/session_01Q8KtFFGG9qrjAgLJBbxG2U

* Add coerce_reference_data_columns() for lenient reference_data validation

check_reference_data() now returns the (possibly coerced) reference_data and
the call site captures the result so downstream code sees the fixed columns.

A new coerce_reference_data_columns() helper is called before the strict class
check inside check_reference_data(). It coerces columns to the expected types:
- mo  -> as.mo() if not already <mo> class
- ab  -> as.ab() if not already <ab> class
- character columns -> as.character() (e.g. host = NA becomes NA_character_)
- numeric columns  -> as.double()
- logical columns  -> as.logical()

This allows users to build a custom reference_data from a plain data.frame
without having to pre-apply as.mo()/as.ab() or worry about NA column types.

Updated the reference_data roxygen argument to document the auto-coercion and
restored the tests to the simpler form that uses plain character assignments,
relying on the new coercion instead of workarounds.

https://claude.ai/code/session_01Q8KtFFGG9qrjAgLJBbxG2U

---------

Co-authored-by: Claude <noreply@anthropic.com>

NEWS.md

@@ -21,6 +21,7 @@
 * Two new `NA` objects, `NA_ab_` and `NA_mo_`, analogous to base R's `NA_character_` and `NA_integer_`, for use in pipelines that require typed missing values
 
 ### Fixes
+* `as.sir()` with `reference_data`: custom guideline names now correctly classify values as R using EUCAST convention (`> breakpoint_R` for MIC, `< breakpoint_R` for disk); custom breakpoints with `host = NA` now serve as a host-agnostic fallback when no host-specific row matches (fixes #239)
 * Fixed multiple bugs in the `parallel = TRUE` mode of `as.sir()` for data frames: (1) PSOCK workers (Windows / R < 4.0) now correctly load the AMR package before processing, with a graceful fallback to sequential mode when the package cannot be loaded; (2) resolved stale-environment issue where the PSOCK path read a frozen copy of `AMR_env` instead of the live one, causing the wrong log entries to be captured; (3) fixed log-entry duplication in the fork-based path (`mclapply`) where pre-existing `sir_interpretation_history` rows were included in every worker's captured log; (4) removed use of non-exported internal functions (`%pm>%`, `pm_pull`, `as.sir.default`) from the worker closure, which made PSOCK workers fail; (5) suppressed per-column progress messages inside workers to prevent interleaved console output; (6) fixed a malformed Unicode escape `\u00a` (3 digits) in the "DONE" status message
 * Fixed a bug in `as.sir()` where values that were purely numeric (e.g., `"1"`) and matched the broad SIR-matching regex would be incorrectly stripped of all content by the Unicode letter filter
 * Fixed a bug in `as.mic()` where MIC values in scientific notation (e.g., `"1e-3"`) were incorrectly handled because the letter `e` was removed along with other Unicode letters; scientific notation `e` is now preserved