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Matthijs Berends 8261b91b24 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>
2026-04-25 14:38:01 +02:00

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Package: AMR
Version: 3.0.1.9050
Date: 2026-04-25
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
using evidence-based methods, as described in <doi:10.18637/jss.v104.i03>.
Authors@R: c(
person(given = c("Matthijs", "S."), family = "Berends", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-7620-1800"), email = "m.s.berends@umcg.nl"),
person(given = c("Dennis"), family = "Souverein", role = c("aut", "ctb"), comment = c(ORCID = "0000-0003-0455-0336")),
person(given = c("Erwin", "E.", "A."), family = "Hassing", role = c("aut", "ctb")),
person(given = c("Aislinn"), family = "Cook", role = "ctb", comment = c(ORCID = "0000-0002-9189-7815")),
person(given = c("Andrew", "P."), family = "Norgan", role = "ctb", comment = c(ORCID = "0000-0002-2955-2066")),
person(given = c("Anita"), family = "Williams", role = "ctb", comment = c(ORCID = "0000-0002-5295-8451")),
person(given = c("Annick"), family = "Lenglet", role = "ctb", comment = c(ORCID = "0000-0003-2013-8405")),
person(given = c("Anthony"), family = "Underwood", role = "ctb", comment = c(ORCID = "0000-0002-8547-4277")),
person(given = c("Anton"), family = "Mymrikov", role = "ctb"),
person(given = c("Bart", "C."), family = "Meijer", role = "ctb"),
person(given = c("Christian", "F."), family = "Luz", role = "ctb", comment = c(ORCID = "0000-0001-5809-5995")),
person(given = c("Dmytro"), family = "Mykhailenko", role = "ctb"),
person(given = c("Eric", "H.", "L.", "C.", "M."), family = "Hazenberg", role = "ctb"),
person(given = c("Gwen"), family = "Knight", role = "ctb", comment = c(ORCID = "0000-0002-7263-9896")),
person(given = c("Jane"), family = "Hawkey", role = "ctb", comment = c(ORCID = "0000-0001-9661-5293")),
person(given = c("Jason"), family = "Stull", role = "ctb", comment = c(ORCID = "0000-0002-9028-8153")),
person(given = c("Javier"), family = "Sanchez", role = "ctb", comment = c(ORCID = "0000-0003-2605-8094")),
person(given = c("Jonas"), family = "Salm", role = "ctb"),
person(given = c("Judith", "M."), family = "Fonville", role = "ctb"),
person(given = c("Kathryn"), family = "Holt", role = "ctb", comment = c(ORCID = "0000-0003-3949-2471")),
person(given = c("Larisse"), family = "Bolton", role = "ctb", comment = c(ORCID = "0000-0001-7879-2173")),
person(given = c("Matthew"), family = "Saab", role = "ctb", comment = c(ORCID = "0009-0008-6626-7919")),
person(given = c("Natacha"), family = "Couto", role = "ctb", comment = c(ORCID = "0000-0002-9152-5464")),
person(given = c("Peter"), family = "Dutey-Magni", role = "ctb", comment = c(ORCID = "0000-0002-8942-9836")),
person(given = c("Rogier", "P."), family = "Schade", role = "ctb", comment = c(ORCID = "0000-0002-9487-4467")),
person(given = c("Sofia"), family = "Ny", role = "ctb", comment = c(ORCID = "0000-0002-2017-1363")),
person(given = c("Alex", "W."), family = "Friedrich", role = "ths", comment = c(ORCID = "0000-0003-4881-038X")),
person(given = c("Bhanu", "N.", "M."), family = "Sinha", role = "ths", comment = c(ORCID = "0000-0003-1634-0010")),
person(given = c("Casper", "J."), family = "Albers", role = "ths", comment = c(ORCID = "0000-0002-9213-6743")),
person(given = c("Corinna"), family = "Glasner", role = "ths", comment = c(ORCID = "0000-0003-1241-1328")))
Depends: R (>= 3.0.0)
Suggests:
cleaner,
cli,
crayon,
curl,
data.table,
dplyr,
ggplot2,
knitr,
openxlsx,
parallelly,
pillar,
progress,
readxl,
recipes,
rlang,
rmarkdown,
rstudioapi,
rvest,
skimr,
testthat,
tibble,
tidymodels,
tidyselect,
tinytest,
vctrs,
xml2,
usethis
VignetteBuilder: knitr,rmarkdown
URL: https://amr-for-r.org, https://github.com/msberends/AMR
BugReports: https://github.com/msberends/AMR/issues
License: GPL-2 | file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.3.3
Roxygen: list(markdown = TRUE, old_usage = TRUE)
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