Package: AMRvalid Title: Population-Aware Evaluation of Antimicrobial Resistance Predictions Version: 1.0.0 Authors@R: person("Md Omar", "Faruqe", , "faruqe@ru.ac.bd", role = c("aut", "cre", "cph"), comment = c(ORCID = "0000-0002-1226-7226")) Description: Evaluates antimicrobial resistance phenotype predictions made by external models and rule-based tools against phenotypic reference results, accounting for the population structure of bacterial isolates. Provides a documented data contract and input validation; classification and probability metrics and antimicrobial susceptibility testing agreement metrics (categorical agreement, very major, major and minor errors, essential agreement) per species and antimicrobial; checks for overlap between training and test isolates; performance by genomic distance to the training data; cluster bootstrap intervals and paired model comparisons; calibration; prevalence-adjusted predictive values; and reports aligned with the TRIPOD+AI checklist (Collins et al. (2024) ). Organism and antimicrobial identifiers use the classes of the 'AMR' package. Models are not trained inside the package. License: MIT + file LICENSE URL: https://github.com/omarfaruqe/AMRvalid BugReports: https://github.com/omarfaruqe/AMRvalid/issues Depends: R (>= 4.1.0) Imports: AMR (>= 3.0.0), stats, utils Suggests: jsonlite, knitr, rmarkdown, testthat (>= 3.0.0) VignetteBuilder: knitr Config/testthat/edition: 3 Encoding: UTF-8 Language: en-GB Roxygen: list(markdown = TRUE) Config/roxygen2/version: 8.1.1 Repository: https://omarfaruqe.r-universe.dev Date/Publication: 2026-11-12 04:01:37 UTC RemoteUrl: https://github.com/omarfaruqe/AMRvalid RemoteRef: HEAD RemoteSha: a39901ba953d62eb8b67dcffc541173e21eb0a11 NeedsCompilation: no Packaged: 2026-11-12 04:52:20 UTC; root Author: Md Omar Faruqe [aut, cre, cph] (ORCID: ) Maintainer: Md Omar Faruqe