AMR v3.0.1

This is a bugfix release following the release of v3.0.0 in June 2025.

Changed

• Fixed bugs introduced by ggplot2 v4.0.0 (#236)
  • MIC scale functions (such as scale_y_mic()) will now be applied automatically when plotting values of class mic
  • SIR scale functions (such as scale_x_sir()) will now be applied automatically when plotting values of class sir
• Fixed a bug in antibiogram() for when no antimicrobials are set
• Fixed a bug in antibiogram() to allow column names containing the + character (#222)
• Fixed a bug in as.ab() for antimicrobial codes with a number in it if they are preceded by a space
• Fixed a bug in eucast_rules() for using specific custom rules
• Fixed a bug in as.sir() to allow any tidyselect language (#220)
• Fixed a bug in as.sir() to pick right breakpoint when uti = FALSE (#216)
• Fixed a bug in ggplot_sir() when using combine_SI = FALSE (#213)
• Fixed a bug in mdro() to make sure all genes specified in arguments are acknowledged
• Fixed a bug the antimicrobials data set to remove statins (#229)
• Fixed a bug the microorganisms data set for MycoBank IDs and synonyms (#233)
• Fixed ATC J01CR05 to map to piperacillin/tazobactam rather than piperacillin/sulbactam (#230)
• Fixed skimmers (skimr package) of class ab, sir, and disk (#234)
• Fixed all plotting to contain a separate colour for SDD (susceptible dose-dependent) (#223)
• Fixed some specific Dutch translations for antimicrobials
• Added a warning to as.ab() if input resembles antiviral codes or names (#232)
• Added all reasons in verbose output of mdro() (#227)
• Added names to age_groups() so that custom names can be given (#215)
• Added note to as.sir() to make it explicit when higher-level taxonomic breakpoints are used (#218)
• Added antibiotic codes from the Comprehensive Antibiotic Resistance Database (CARD) to the antimicrobials data set (#225)
• Updated Fosfomycin to be of antibiotic class Phosphonics (#225)
• Updated random_mic() and random_disk() to set skewedness of the distribution and allow multiple microorganisms

AMR v3.0.0

This package now supports not only tools for AMR data analysis in clinical settings, but also for veterinary and environmental microbiology. This was made possible through a collaboration with the University of Prince Edward Island's Atlantic Veterinary College, Canada. To celebrate this great improvement of the package, we also updated the package logo to reflect this change.

Breaking

• Dataset antibiotics has been renamed to antimicrobials as the data set contains more than just antibiotics. Using antibiotics will still work, but now returns a warning.
• Removed all functions and references that used the deprecated rsi class, which were all replaced with their sir equivalents over two years ago.
• Functions resistance_predict() and sir_predict() are now deprecated and will be removed in a future version. Use the tidymodels framework instead, for which we wrote a basic introduction.

New

• One Health implementation
  • Function as.sir() now has extensive support for veterinary breakpoints from CLSI. Use breakpoint_type = "animal" and set the host argument to a variable that contains animal species names.
  • The clinical_breakpoints data set contains all these breakpoints, and can be downloaded on our download page.
  • The (new) antimicrobials data set contains all veterinary antimicrobials, such as pradofloxacin and enrofloxacin. All WHOCC codes for veterinary use have been added as well.
  • ab_atc() now supports ATC codes of veterinary antimicrobials (that all start with "Q")
  • ab_url() now supports retrieving the WHOCC url of their ATCvet pages
• Support for WISCA antibiograms
  • The antibiogram() function now supports creating true Weighted-Incidence Syndromic Combination Antibiograms (WISCA), a powerful Bayesian method for estimating regimen coverage probabilities using pathogen incidence and antimicrobial susceptibility data. WISCA offers improved precision for syndrome-specific treatment, even in datasets with sparse data. A dedicated wisca() function is also available for easy usage.
• More global coverage of languages
  • Added full support for 8 new languages: Arabic, Bengali, Hindi, Indonesian, Korean, Swahili, Urdu, and Vietnamese. The AMR package is now available in 28 languages.
• Major update to fungal taxonomy and tools for mycologists
  • MycoBank has now been integrated as the primary taxonomic source for fungi. The microorganisms data set has been enriched with new columns (mycobank, mycobank_parent, and mycobank_renamed_to) that provide detailed information for fungal species.
  • A remarkable addition of over 20,000 new fungal records
  • New function mo_mycobank() to retrieve the MycoBank record number, analogous to existing functions such as mo_lpsn() and mo_gbif().
  • The as.mo() function and all mo_*() functions now include an only_fungi argument, allowing users to restrict results solely to fungal species. This ensures fungi are prioritised over bacteria during microorganism identification. This can also be set globally with the new AMR_only_fungi option.
  • Also updated other kingdoms, welcoming a total of 2,149 new records from 2023 and 927 from 2024.
• Updated clinical breakpoints
  • Breakpoint of 2024 and 2025 of both CLSI and EUCAST are now supported, by adding all of their over 10,000 new clinical breakpoints to the clinical_breakpoints data set for usage in as.sir(). EUCAST 2025 is now the new default guideline for all MIC and disk diffusion interpretations.
  • Added all Expected Resistant Phenotypes from EUCAST (v1.2). The default rules for eucast_rules() are now: c("breakpoints", "expected_phenotypes").
  • Updated the intrinsic_resistant data set, which is now based on EUCAST Expected Resistant Phenotypes v1.2
  • as.sir() now brings additional factor levels: "NI" for non-interpretable and "SDD" for susceptible dose-dependent. Currently, the clinical_breakpoints data set contains 24 breakpoints that can return the value "SDD" instead of "I".
  • EUCAST interpretive rules (using eucast_rules()) are now available for EUCAST 12 (2022), 13 (2023), 14 (2024), and 15 (2025).
  • EUCAST dosage tables (dosage data set) are now available for EUCAST 13 (2023), 14 (2024), and 15 (2025).
• New advanced ggplot2 extensions for MIC and SIR plotting and transforming
  • New function group scale_*_mic(), namely: scale_x_mic(), scale_y_mic(), scale_colour_mic() and scale_fill_mic(). They allow easy plotting of MIC values. They allow for manual range definition and plotting missing intermediate log2 levels.
  • New function group scale_*_sir(), namely: scale_x_sir(), scale_colour_sir() and scale_fill_sir(). They allow to plot the sir class, and translates into the system language at default. They also set colourblind-safe colours to the plots.
  • New function rescale_mic(), which allows users to rescale MIC values to a manually set range. This is the powerhouse behind the scale_*_mic() functions, but it can be used independently to, for instance, compare equality in MIC distributions by rescaling them to the same range first.
• Support for Python
  • While using R for the heavy lifting, our 'AMR' Python Package was developed to run the AMR R package natively in Python. The Python package will always have the same version number as the R package, as it is built automatically with every code change.
• Support for tidymodels
  • All antimicrobial selectors (such as aminoglycosides() and betalactams()) are now supported in tidymodels packages such as recipe and parsnip. See for more info our tutorial on using these AMR functions for predictive modelling.
• Other
  • New function top_n_microorganisms() to filter a data set to the top n of any taxonomic property, e.g., filter to the top 3 species, filter to any species in the top 5 genera, or filter to the top 3 species in each of the top 5 genera
  • New function mo_group_members() to retrieve the member microorganisms of a microorganism group. For example, mo_group_members("Strep group C") returns a vector of all microorganisms that belong to that group.
  • New functions mic_p50() and mic_p90() to retrieve the 50th and 90th percentile of MIC values.

Changed

• SIR interpretation
  • Support for parallel computing to greatly improve speed using the parallel package (part of base R). Use as.sir(your_data, parallel = TRUE) to run SIR interpretation using multiple cores.
  • It is now possible to use column names for arguments guideline, ab, mo, and uti: as.sir(..., ab = "column1", mo = "column2", uti = "column3"). This greatly improves the flexibility for users.
  • Users can now set their own criteria (using regular expressions) as to what should be considered S, I, R, SDD, and NI.
  • To get quantitative values, as.double() on a sir object will return 1 for S, 2 for SDD/I, and 3 for R (NI will become NA). Other functions using sir classes (e.g., summary()) are updated to reflect the change to contain NI and SDD.
  • Following CLSI interpretation rules, values outside the log2-dilution range will be rounded upwards to the nearest log2-level before interpretation. Only if using a CLSI guideline.
  • Combined MIC values (e.g., from CLSI) are now supported
  • The argument conserve_capped_values in as.sir() has been replaced with capped_mic_handling, which allows greater flexibility in handling capped MIC values (<, <=, >, >=). The four available options ("standard", "strict", "relaxed", "inverse") provide full control over whether these values should be interpreted conservatively or ignored. Using conserve_capped_values is now deprecated and returns a warning.
  • Added argument info to silence all console messages
• antibiogram() function
  • Argument antibiotics has been renamed to antimicrobials. Using antibiotics will still work, but now returns a warning.
  • Added argument formatting_type to set any of the 22 options for the formatting of all 'cells'. This defaults to 18 for non-WISCA and 14 for WISCA, changing the output of antibiograms to cells with more info.
  • For this reason, add_total_n is now deprecated and FALSE at default since the denominators are added to the cells dependent on the formatting_type setting
  • The ab_transform argument now defaults to "name", displaying antibiotic column names instead of codes
• Antimicrobial selectors (previously: antibiotic selectors)
  • 'Antibiotic selectors' are now called 'antimicrobial selectors' since their scope is broader than just antibiotics. All documentation have been updated, and ab_class() and ab_selector() have been replaced with amr_class() and amr_selector(). The old functions are now deprecated and will be removed in a future version.
  • Added selectors isoxazolylpenicillins(), monobactams(), nitrofurans(), phenicols(), rifamycins(), and sulfonamides()
  • When using antimicrobial selectors that exclude non-treatable drugs (such as gentamicin-high when using aminoglycosides()), the function now always returns a warning that these can be included using only_treatable = FALSE
  • Added a new argument return_all to all selectors, which defaults to TRUE to include any match. With FALSE, the old behaviour, only the first hit for each unique antimicrobial is returned.
  • All selectors can now be run as a separate command to retrieve a vector of all possible antimicrobials that the selector can select
  • The selectors lincosamides() and macrolides() do not overlap anymore - each antibiotic is now cla...