Rebuild clinical_breakpoints, and add the NEWS entries and version bump for this PR

The rebuild uses the WHONET files of today, and holds the changes of #326, #327, #328, #329 and #331. The files in data-raw/datasets are not regenerated yet.

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 3.1.0.9014
-Date: 2026-10-30
+Version: 3.1.0.9015
+Date: 2026-11-02
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
   data analysis and to work with microbial and antimicrobial properties by

NEWS.md

@@ -1,8 +1,37 @@
-# AMR 3.1.0.9014
+# AMR 3.1.0.9015
 
 This version fixes a critical bug in WISCA that biased all coverage estimates of `wisca()` and `antibiogram(..., wisca = TRUE)` downwards since AMR 3.0.0. Users are strongly advised to re-run their WISCA analyses.
 
+It also adds a `site` argument to `as.sir()`, stores EUCAST MIC breakpoints exactly as published, stores all screening breakpoints under screening agents, removes EUCAST's breakpoints in brackets, and only keeps blocking rows that have an effect.
+
+### Breaking
+* All explicit screening breakpoints in `clinical_breakpoints` moved to screening agents, e.g., from `FOX` to `FOX-S`, including the high-level aminoglycoside tests (`GEH` and `STH` to `GEN-S` and `STR1-S`), the topical cut-off values of EUCAST, and the CLSI surrogate tests of cefoxitin for staphylococci and pefloxacin for *Salmonella*. Use `as.sir(..., include_screening = TRUE)` to interpret a regular agent with these breakpoints; `GEH` and `STH` stay valid input (#328)
+* `include_screening` in `as.sir()` now defaults to `NULL`, using screening breakpoints for screening agents only. `include_screening = FALSE` now also returns `NA`, with a note, for a screening agent (#328)
+* EUCAST's breakpoints in brackets are no longer in `clinical_breakpoints`. They were blocking rows, so `as.sir()` can now use PK/PD breakpoints or the breakpoints of a broader taxon instead, e.g., for aminoglycosides in EUCAST 2020-2023. They stay available in [`data-raw/breakpoints_eucast_raw.csv`](https://github.com/msberends/AMR/blob/main/data-raw/breakpoints_eucast_raw.csv) (#327)
+* With unknown `uti`, a blocking row without UTI status no longer overrides a UTI breakpoint at the same taxonomic level, e.g., amikacin in *Acinetobacter* now gives S or R instead of `NA`, which is noted in `sir_interpretation_history()`. Use `uti = FALSE` to prevent this
+* If several breakpoints fit and no `site` is set, `as.sir()` now takes the one for the most systemic site, instead of the first one in the data set. Use `site` to choose another one
+
+### New
+* **Site of infection**
+  * `as.sir()` gained the argument `site`, in fixed codes such as `"meningitis"`, `"iv"` and `"uti"`, which can also be a column name. A breakpoint for a contradicting site is left out, a breakpoint without a site still applies, and the result is `NA` if only contradicting sites are available, without using PK/PD breakpoints. `uti = TRUE` stays available and equals `site = "uti"`
+  * `sir_interpretation_history()` now holds the site of the breakpoint used, and notes every assumption about sites
+* **Screening agents**
+  * 13 screening agents in the `antimicrobials` data set: `CHL-S`, `CIP-S`, `COL-S`, `ERY-S`, `FUS-S`, `GEN-S`, `LVX-S`, `MUP-S`, `NEO-S`, `OFX-S`, `RTP-S`, `STR1-S` and `TOB-S` (#328)
+  * EUCAST clinical breakpoints that can also be used as a screening test, e.g., erythromycin for staphylococci, have a copy under the screening agent (#328)
+* **EUCAST breakpoints stated in the Notes** (#329)
+  * Oxacillin disk for *S. pseudintermedius* and related species, and oxacillin MIC for coagulase-negative staphylococci, under `OXA-S`
+  * Mupirocin for nasal decolonisation of *S. aureus*
+  * Meropenem in other infections than meningitis for *N. meningitidis* in EUCAST 2021
+
 ### Changed
+* SIR interpretation (`as.sir()`)
+  * MIC breakpoints are compared as dilutions, so that e.g. an MIC of 0.032 and a breakpoint of 0.03 mg/L are the same (#331)
+  * A `uti` vector mixing `NA` with `TRUE` or `FALSE` no longer gives an error
+* `clinical_breakpoints` data set
+  * EUCAST MIC breakpoints are stored exactly as published, e.g., 0.03 instead of 0.032, and 0.001 instead of 0.0001 (#331)
+  * Blocking rows of EUCAST 2019-2026 that have no effect on `as.sir()` were removed, 12 243 in total (#326)
+  * The breakpoints of *Bacteroides* now also apply to zone diameters of *Parabacteroides*, *Phocaeicola dorei* and *Phocaeicola vulgatus* (#329)
+* *Morganella* is interpreted as reported, with the breakpoints of Enterobacterales or Morganellaceae and not of *M. morganii*, which is now tested (#330)
 * WISCA (`wisca()` and `antibiogram(..., wisca = TRUE)`)
   * Fixed a critical bug that systematically underestimated the coverage of every WISCA since AMR 3.0.0. Pathogens absent from a syndromic group, and pathogens without any test result for a regimen, were still included in the model with only prior information: each added a prior weight of 1 to the pathogen incidence, and untested pathogens kept their full incidence weight while counting as about 50% susceptible. The bias was largest for stratified analyses (e.g., up to 14 percentage points for meropenem in random strata of `example_isolates`). Now, only pathogens that occur in a group and have at least one test result for the regimen are included. Please re-run all WISCA analyses (#337)
   * `retrieve_wisca_parameters()` now returns only the parameters actually used in the model, and `n_total` in the `long_numeric` attribute now counts only isolates of the pathogens included for that regimen

man/clinical_breakpoints.Rd

@@ -5,7 +5,7 @@
 \alias{clinical_breakpoints}
 \title{Data Set with Clinical Breakpoints for SIR Interpretation}
 \format{
-A \link[tibble:tibble]{tibble} with 61 389 observations and 15 variables:
+A \link[tibble:tibble]{tibble} with 48 382 observations and 15 variables:
 \itemize{
 \item \code{guideline}\cr Name of the guideline
 \item \code{type}\cr Breakpoint type, either \code{"ECOFF"}, \code{"animal"}, or \code{"human"}
@@ -49,7 +49,7 @@ The default is \code{"human"}, which can also be set with the package option \co
 
 \subsection{Blocking Rows}{
 
-Where EUCAST lists an organism but gives no breakpoint for it (e.g. "IE", "-", "Note", an organism excluded with "except", or no S category for a zone diameter), \code{\link[=as.sir]{as.sir()}} must not fall back to the breakpoint of a broader taxon, such as the breakpoint for \emph{Vibrio} spp. where EUCAST gives "IE" for \emph{V. fluvialis}. Such cases are included as "blocking rows": rows in which \code{breakpoint_S} and \code{breakpoint_R} are both \code{NA} and the \code{note} starts with \code{"[No breakpoint]"} followed by the reason. \code{\link[=as.sir]{as.sir()}} returns \code{NA} for these. This currently applies to 15 660 rows. Remove them with \code{subset(clinical_breakpoints, !is.na(breakpoint_S))} if only actual breakpoints are needed.
+Where EUCAST lists an organism but gives no breakpoint for it (e.g. "IE", "-", "Note", an organism excluded with "except", or no S category for a zone diameter), \code{\link[=as.sir]{as.sir()}} must not fall back to the breakpoint of a broader taxon, such as the breakpoint for \emph{Vibrio} spp. where EUCAST gives "IE" for \emph{V. fluvialis}. Such cases are included as "blocking rows": rows in which \code{breakpoint_S} and \code{breakpoint_R} are both \code{NA} and the \code{note} starts with \code{"[No breakpoint]"} followed by the reason. \code{\link[=as.sir]{as.sir()}} returns \code{NA} for these. This currently applies to 2 406 rows. Remove them with \code{subset(clinical_breakpoints, !is.na(breakpoint_S))} if only actual breakpoints are needed.
 
 \strong{EUCAST's breakpoints in brackets} are not in this data set. EUCAST bases these on ECOFFs, and states that reporting S or I should be avoided. \code{\link[=as.sir]{as.sir()}} therefore treats them as absent, and can use PK/PD breakpoints or, for unknown UTI status, UTI breakpoints instead. All bracketed values are kept in the \href{https://github.com/msberends/AMR/blob/main/data-raw/breakpoints_eucast_raw.csv}{raw import of the EUCAST tables} (column \code{is_bracketed}).