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Changelog

Source: NEWS.md

AMR 3.0.1.9146

Planned as v3.1.0, mid October 2026.

Breaking

  • The former kingdoms Bacteria and Archaea are now each divided into four kingdoms, with new top-level domains Bacteria and Archaea (Göker and Oren, 2024, DOI: 10.1099/ijsem.0.006242). Following this, a new domain column was added to the microorganisms data set, and mo_kingdom() now returns the formal kingdom (e.g., "Pseudomonadati" instead of "Bacteria"). Use mo_domain() for the old behaviour. For non-prokaryotic kingdoms (Fungi, Protozoa, etc.), kingdom and domain are identical.

    mo_kingdom() < 3.1.0 mo_kingdom() now mo_domain() (unchanged)
    Bacteria Bacillati Bacteria
    Fusobacteriati Bacteria
    Pseudomonadati Bacteria
    Thermotogati Bacteria
    Archaea Methanobacteriati Archaea
    Nanobdellati Archaea
    Promethearchaeati Archaea
    Thermoproteati Archaea
    Fungi Fungi Fungi
    Protozoa Protozoa Protozoa

    Previously, mo_domain() was an alias of mo_kingdom(); it is now a distinct function. Its output is therefore unchanged, while mo_kingdom() now returns the new formal kingdom. A one-time note per session explains this change when bacterial or archaeal records are queried.

  • Parallel computing in as.sir(), antibiogram(), and wisca() now uses the future and future.apply packages, which is faster. A non-sequential plan (e.g., future::plan(future::multisession)) must be active before using parallel = TRUE (#281).

  • The options of capped_mic_handling in as.sir() have been redefined as "none", "conservative", "standard" (default), and "lenient". The option "inverse" is no longer available (#243).

  • as.sir() now returns WT/NWT (Wildtype/Non-wildtype) instead of S/R when using ECOFF-based interpretation with breakpoint_type = "ECOFF". WT/NWT results are fully supported in all resistance and susceptibility functions and in all plots (#254).

  • Aggregated analyses now follow the guideline for the ‘I’ category, set with the new guideline argument or the AMR_guideline option: EUCAST considers ‘I’ susceptible and CLSI considers ‘I’ resistant, while SDD and WT are always considered susceptible, and NWT and NS always resistant (see section Interpretation of SIR in ?as.sir). This applies to count_df(), proportion_df(), sir_df(), ggplot_sir(), geom_sir(), and labels_sir_count(), which with CLSI now return "S" vs. "IR" instead of "SI" vs. "R", and to antibiogram(), wisca(), and format() on the output of bug_drug_combinations(). Previously, these functions always considered ‘I’ susceptible, as with EUCAST. Use guideline = "EUCAST" for the old behaviour.

  • The combine_SI argument of these functions is deprecated in favour of guideline. While set, it is followed literally and takes precedence over guideline. Use guideline = NULL instead of combine_SI = FALSE to keep S, I, and R separate.

New

  • Updated clinical breakpoints
    • EUCAST 2026 and CLSI 2026 are now supported, by adding over 5,700 new breakpoints to the clinical_breakpoints data set. EUCAST 2026 is now the default guideline for all MIC and disk diffusion interpretations.
    • Human EUCAST breakpoints from 2019 (v9.0) onwards are now retrieved directly from the EUCAST Excel files, instead of relying on the WHONET repository. As a result:
      • clinical_breakpoints now contains blocking rows (NA breakpoints, with the reason in note) where EUCAST gives no breakpoint for an organism, so that as.sir() no longer falls back to the breakpoint of a broader taxon
      • Restrictions in EUCAST notes are applied, e.g., zone diameter breakpoints for E. coli only
      • EUCAST PK-PD (non-species related) breakpoints of 2019-2023 and H. parainfluenzae MIC breakpoints are now included
  • Unified interpretive rules
    • New function interpretive_rules() applies the interpretive rules of both EUCAST and CLSI. eucast_rules() is now a wrapper around this function (#235, #259).
    • Species named in a rule now also match all other names of the same accepted taxon (e.g., ‘Clostridium ramosum’ for Thomasclavelia ramosa). This also updated the intrinsic_resistant data set.
  • Support for tidymodels pipelines
  • Morphology of bacteria
    • New morphology column in the microorganisms data set, with the corresponding function mo_morphology() to return the cell shape of bacteria. Data are sourced from BacDive; values prefixed with “likely” are extrapolated from the consensus at genus level.
    • New argument add_morphology in mo_gramstain() to return combined results, such as "Gram-negative rods"
  • Antimicrobials
    • New function sir_combine() to combine SIR results of multiple antimicrobials into one variable, for combination therapy (method = "most_susceptible") or for resistance within a group (method = "most_resistant") (#321)
    • New function add_custom_antimicrobial_synonyms() to add local names, such as trade names, to existing antimicrobials (#307)
    • New antimicrobial selectors ionophores(), peptides(), phosphonics(), and spiropyrimidinetriones()
    • New antimicrobials: cefepime/taniborbactam (FTA), ceftibuten/avibactam (CTA), clorobiocin (CLB), kasugamycin (KAS), ostreogrycin (OST), sulbactam/durlobactam (SUD1, #308), taniborbactam (TAN), thiostrepton (THS), xeruborbactam (XER), and zorbamycin (ZOR)
  • Other
    • New function wisca_plot() to assess the distributions of susceptibility and incidence from the Monte Carlo simulations of WISCA
    • New function amr_course() to download and unpack course or webinar materials from GitHub in one call
    • New typed missing value constants NA_ab_ and NA_mo_, for use in pipelines that need missing values of a specific class
    • A registry of all MO codes since v2.0.0 now prevents existing codes from being reused or mixed up. Codes of earlier releases are translated to the current code of the same taxon.

Changed

  • SIR interpretation (as.sir())
    • New argument enforce_method ("auto", "mic", or "disk") to force the interpretation method when S3 class information is lost, e.g., when called from Python (#291)
    • When input consists of whole numbers only, disk zones are now assumed rather than MIC values (#291)
    • Capped MICs (e.g., <=0.5) now return I instead of S or NI if there is no S category, i.e., in case of an off-scale S breakpoint such as EUCAST’s 0.001 mg/L (#295)
    • Capped MICs are no longer forced to S or R if there is no breakpoint for the drug-bug combination
    • Fixed the documented default of capped_mic_handling, which is "standard"
    • On data frames, already-converted SIR columns are no longer dropped on a re-run (#278)
    • Metadata columns (e.g., patient, ward) are no longer misidentified as antimicrobial columns
    • info = FALSE now suppresses all messages, including those for columns without breakpoints
    • Combined MIC/SIR input values (e.g., "<= 0.002; S" or "S; 0.002") are now parsed correctly (#252)
    • Setting a year-qualified guideline, such as options(AMR_guideline = "EUCAST 2012"), no longer causes errors or silently wrong results in interpretive_rules(), resistance(), susceptibility(), count_resistant(), count_susceptible(), and the SIR plotting and printing functions (#298)
  • clinical_breakpoints data set
    • Fixed EUCAST breakpoint rules for Aerococcus (v12 onwards), which were never applied, and for Pasteurella, which were partly filed under Neisseria meningitidis (#290)
    • Fixed streptomycin breakpoints imported from WHONET, which were coded as streptoduocin (STR) instead of streptomycin (STR1)
    • Fixed CLSI breakpoints for sulbactam/durlobactam, which were coded as sulfadimethoxine (SUD), and added the missing EUCAST 2011 breakpoints for roxithromycin (#308)
    • Fixed some EUCAST Expert Rules, mostly on S. pneumoniae
  • Microorganism coercion (as.mo()) and properties (mo_*())
    • Considerably faster through one consistent session cache design, which is cleared when lookup tables change, e.g., after add_custom_microorganisms() (#313)
    • mo_*() functions now retrieve properties of valid mo input directly, and only for unique values
    • The mapping of outdated taxonomic names to their current names is now remembered per code
    • Previously coerced input is now recognised again, e.g., for an unknown species of a known genus, instead of being matched again on every call (#313)
    • mo_uncertainties() now also lists uncertainties of previously coerced input
    • Translated names in the set language are now recognised, such as the output of mo_name(x, language = "fr"), and cached per language
    • Input of the form "X complex" now falls back to "X" when the complex is not a distinct taxon, preventing NA for valid clinical descriptions such as "Proteus vulgaris complex" (#287)
    • Abbreviated genus input now ranks candidates with an exactly matching species epithet above more prevalent organisms, so that e.g. "S. apiospermum" returns Scedosporium apiospermum instead of a Staphylococcus species (#288)
    • Abbreviated genus input for species with subspecies (e.g., "P. ovale") now returns the species instead of a more prevalent organism, while explicit subspecies (e.g., "P. ovale curtisi") are preserved (#288)
    • Salmonella serovars written with the species, such as "Salmonella enterica serovar Typhi", no longer return Salmonella bongori or another subspecies
    • as.mo() and mo_current() now find the current name of synonyms with multiple sources (e.g., Chaetomium abuense)
    • mo_taxonomy() and mo_info() now contain an extra element domain
  • Own microorganism codes (set_mo_source() and get_mo_source())
    • Fixed get_mo_source() removing the mo_source file at the default location in interactive sessions, when called with a destination that does not exist
    • Fixed get_mo_source() returning the mo_source already loaded instead of the one at the requested destination
    • Fixed get_mo_source(), and therefore as.mo() and all mo_*() functions, throwing an error in interactive sessions after the original file of the mo_source was moved or deleted. The mo_source file is now removed, as documented.
    • An updated original file now updates the mo_source file at its own destination instead of at the default location
  • microorganisms data set
    • Taxonomic update of all microorganisms, now based on COL 2026-04-18 XR, LPSN and BacDive of October 2026, and MycoBank of January 2026
    • Names listed twice by a source now take the correct record (e.g., Eggerthella lenta, Gordonia amarae, and Anisakis simplex were synonyms without a current name)
    • Synonyms without a current name are now linked via LPSN or removed, with their codes retired. The M. tuberculosis complex is always kept.
    • Higher taxonomy and parent records are now consistent, and all data sets refer only to current names (except intrinsic_resistant)
    • Erysipelatoclostridium and its species are now synonyms of Thomasclavelia; E. merdavium is retired
    • Author references now strip emend. and everything after it, so that ref reflects the combination authority rather than the emendation author (e.g., Rhodococcus equi now returns “Goodfellow et al., 1977” instead of “Nouioui et al., 2018”)
  • Antimicrobial coercion (as.ab()) and antimicrobials data set
    • Considerably faster through the same session cache design as as.mo() (#313)
    • Input that is not a known name or code is now coerced up to 70 times faster, with identical results, as LOINC codes, synonyms, and abbreviations are looked up in one step instead of per antimicrobial, and translated names are built once per language
    • Fixed a bug where results of fast_mode (used internally) were remembered and reused by later regular calls, which could return NA for valid input (#313)
    • Codes containing “PH” or “TH” (e.g., ETH, PHE) no longer return NA when mixed with unrecognised input (#245)
    • Input that is not valid UTF-8 (e.g., text exported in a local encoding such as CP949) now returns NA with a warning instead of an error
    • ab_reset_session() no longer clears the uncertainties of as.mo() (#313)
    • antimicrobials$group is now a list, so that drugs belonging to multiple groups are fully represented. Use ab_group(all_groups = TRUE) to retrieve all groups of a drug (#246).
    • Trade names of combinations (Tazocin, Timentin, Recarbrio, Exblifep) were listed under a single component, and names of screening libraries and suppliers (e.g., Prestwick, Spectrum) as synonyms. These have been corrected (#315).
  • Antibiograms (antibiogram() and wisca())
    • wisca() now follows Bielicki et al. (2016) more strictly by using Beta(1,9999)\text{Beta}(1, 9999) for intrinsically resistant pairs, forcing near-zero susceptibility regardless of observed data (based on EUCAST Expected Resistant Phenotypes)
    • Fixed a bug where both functions failed without the antimicrobials argument if tidyselect was not available, e.g., for binary installations without dplyr
    • Isolates of unknown species are now included in grouped antibiograms and in wisca(), as they already were in traditional antibiograms. They were previously excluded silently, with the warning “invalid microorganism code, NA generated”. This can change WISCA coverage estimates.
    • Grouped traditional antibiograms now show the (translated) pathogen names, as ungrouped antibiograms do, instead of microorganism codes
  • Resistance and susceptibility calculation
    • New argument guideline (default: the AMR_guideline option, otherwise EUCAST) in susceptibility(), resistance(), count_df(), proportion_df(), sir_df(), ggplot_sir(), geom_sir(), labels_sir_count(), antibiogram(), wisca(), and bug_drug_combinations() to interpret the ‘I’ category correctly per guideline. Functions that return results per category also accept guideline = NULL to keep S, I, and R separate, while functions that return a single proportion or count give an informative error.
    • When EUCAST is assumed because neither the guideline argument nor the AMR_guideline option is set, a message explains how to change this, once per session and not in R Markdown or Quarto documents
    • count_*() and proportion_*() now handle WT, NWT, NS, and NI results correctly (#321)
  • MICs and disk diffusion
    • New argument round_to_next_log2 in as.mic() and rescale_mic() to round values up to the nearest log2 dilution level (#255)
    • as.mic() now handles values in scientific notation (e.g., 1e-3) correctly
    • Input validation of as.disk() is now more strict, rejecting values that are not recognisable as a numeric disk zone diameter
  • MDRO determination (mdro())
    • Resistance can now be inferred from a drug/inhibitor combination when the column of the base drug is absent (e.g., piperacillin inferred from piperacillin/tazobactam). This is controlled with the new argument infer_from_combinations (default: TRUE) (#209).
    • BRMO classification now includes bacterial complexes (#275)
  • top_n_microorganisms()
    • New argument property_for_each for sub-grouping within the top n groups. Rank ordering is enforced, so that only lower taxonomic ranks are allowed.
    • property = NULL is now accepted
    • The inner filter now tracks the original row indices, to prevent contamination across groups
  • Translations
    • Improved French translations, kindly provided by Mathilde Garé (#322)
    • Improved translations of combination names and antimicrobial groups in 20 languages
    • Translating is now around 50 times faster, with identical results, as the translations are prepared once per language and applied to all values at once. This also makes ab_group() faster in other languages.
    • Translations are no longer translated again (e.g., “Ticarcillinee” in Dutch and “groupee” in French), and parts of combination names are no longer left untranslated
    • Fixed Italian names of CoNS and CoPS (#256), Dutch names of antimicrobials, and output of sir_df() in other languages (#272)
  • Interpretive rules (interpretive_rules(), eucast_rules(), and clsi_rules())
    • Considerably faster, around 11 to 18 times, with identical results
    • The number of added and changed values now only counts values that were actually written, so that values left untouched due to overwrite = FALSE or add_if_missing = FALSE are no longer reported as changes or additions, also not in the output of verbose = TRUE (#259)
    • The changes of custom rules are now also printed when no other rules were applied
    • The rule column of the output of verbose = TRUE no longer contains formatting markup (e.g., {.field AMC}) for the inhibitor-inheritance rules
  • custom_eucast_rules() has been renamed to custom_interpretive_rules(). The old name is now deprecated but still works (#268).
  • Logical comparison (==, !=) of the sir class with a factor is now possible on R >= 4.3
  • New argument guideline in random_mic() and random_disk(), defaulting to the AMR_guideline option (otherwise EUCAST), so that generated values are based on the latest breakpoints of one guideline instead of those of all guidelines and years combined
  • Fixed format() on the output of bug_drug_combinations(), which counted I and SDD as resistant with the default combine_SI = TRUE, contrary to its documentation. It now reads the guideline used in bug_drug_combinations(), which can be overridden with its own guideline argument, and also counts NS as resistant.
  • Fixed a bug in g.test() that returned the degrees of freedom as argument instead of parameter, so that they were not printed
  • Fixed a bug where R could crash after unloading the data.table package, and where suggested packages available on the machine that built the package were used even if they were not available to the user

Other

  • Improved console messages with clickable links throughout the package, powered by cli if it is installed (#191, #265)
  • The section Interpretation of SIR (in ?as.sir) now explains for all functions with a guideline argument for aggregated analyses how S, SDD, I, R, WT, NWT, NS, and NI are categorised per guideline. The handling of ‘I’ per MDRO guideline in mdro() will be revised in a future version (#323).
  • labels_sir_count() is now documented together with ggplot_sir()
  • The documentation of get_AMR_locale() now describes the actual order in which the language is determined: the AMR_locale option, then the LANG system variable, then LANGUAGE only if LANG is not set, and then the system locale
  • Revamped console output of interpretive_rules(), with section headers, S/I/R values styled as in the printing of sir columns in tibbles, and the summary of edits sorted by SIR level, using cli if it is installed (#259)
  • The printing of custom_interpretive_rules() and custom_mdro_guideline() now styles SIR values as in tibbles, i.e., the colour of I depends on the guideline. WT, NWT, and NS were previously shown as SDD, I, and R, and values other than S and R as I.
  • The ‘AMR for Python’ vignette now contains sections on installation channels (stable from CRAN, or development from GitHub via AMR.beta) and on using enforce_method in as_sir() from Python

AMR 3.0.1

CRAN release: 2025-09-20

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 3.0.0

CRAN release: 2025-06-02

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

  • Data set 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 data sets 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.
    • For as.sir(), it is now possible to use column names for arguments guideline, ab, mo, and uti
    • 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 classified as either of these and not both
    • Fixed selector fluoroquinolones(), which now really only selects second-generation quinolones and up (first-generation quinolones do not contain a fluorine group)
  • antimicrobials data set
    • Added agents used for screening, with an ID all ending with -S: benzylpenicillin screening test (PEN-S), beta-lactamase screening test (BLA-S), cefotaxime screening test (CTX-S), clindamycin inducible screening test (CLI-S), nalidixic acid screening test (NAL-S), norfloxacin screening test (NOR-S), oxacillin screening test (OXA-S), pefloxacin screening test (PEF-S), and tetracycline screening test (TCY-S). The ID of cefoxitin screening was renamed from FOX1 to FOX-S, while the old code remains to work.
    • For this reason, the antimicrobial selectors cephalosporins(), cephalosporins_3rd(), lincosamides(), isoxazolylpenicillins(), quinolones(), fluoroquinolones(), and tetracyclines() now contain the argument only_treatable = TRUE (similar to other antimicrobial selectors that contain non-treatable drugs)
    • Added amorolfine (AMO, D01AE16), an antimycotic, which is now also part of the antifungals() selector
    • Added cefepime/enmetazobactam (FPE), a 4th gen cephalosporin
    • Added tigemonam (TNM), a monobactam
    • Added bleomycin (BLM), a glycopeptide
    • Added efflux (EFF), to allow mapping to AMRFinderPlus
    • Updated all ATC codes, trade names, and DDDs
  • MICs
    • Added as valid levels: 4096, 6 powers of 0.0625, and 5 powers of 192 (192, 384, 576, 768, 960)
    • Fixed a bug in as.mic() that failed translation of scientifically formatted numbers
    • Added new argument keep_operators to as.mic(). This can be "all" (default), "none", or "edges". This argument is also available in the new rescale_mic() and scale_*_mic() functions.
    • Comparisons of MIC values are now more strict. For example, >32 is higher than (and never equal to) 32. Thus, as.mic(">32") == as.mic(32) now returns FALSE, and as.mic(">32") > as.mic(32) now returns TRUE.
    • Sorting of MIC values (using sort()) was fixed in the same manner; <0.001 now gets sorted before 0.001, and >0.001 gets sorted after 0.001.
    • Intermediate log2 levels used for MIC plotting are now more common values instead of following a strict dilution range
    • is.mic() now returns a vector of TRUE/FALSE if the input is a data.frame, just like as.sir()
  • eucast_rules() now has an argument overwrite (default: FALSE) to indicate whether non-NA values should be overwritten
  • Disks of 0 to 5 mm are now allowed, the newly allowed range for disk diffusion (as.disk()) is now between 0 and 50 mm
  • Updated italicise_taxonomy() to support HTML output
  • custom_eucast_rules() now supports multiple antimicrobials and antimicrobial groups to be affected by a single rule
  • mo_info() now contains an extra element rank and group_members (with the contents of the new mo_group_members() function)
  • Updated all ATC codes from WHOCC
  • Updated all antimicrobial DDDs from WHOCC
  • Fix for using a manual value for mo_transform in antibiogram()
  • Fixed a bug for when antibiogram() returns an empty data set
  • Argument only_sir_columns now defaults to TRUE if any column of a data set contains a class ‘sir’ (functions eucast_rules(), key_antimicrobials(), mdro(), etc.)
  • Added Sensititre codes for animals, antimicrobials and microorganisms
  • Fix for mapping ‘high level’ antimicrobials in as.ab() (amphotericin B-high, gentamicin-high, kanamycin-high, streptomycin-high, tobramycin-high)
  • Improved overall algorithm of as.ab() for better performance and accuracy, including the new function as_reset_session() to remove earlier coercions.
  • Improved overall algorithm of as.mo() for better performance and accuracy, specifically:
    • More weight is given to genus and species combinations in cases where the subspecies is miswritten, so that the result will be the correct genus and species
    • Genera from the World Health Organization’s (WHO) Priority Pathogen List now have the highest prevalence
  • Fixed a bug for sir_confidence_interval() when there are no isolates available
  • Updated the prevalence calculation to include genera from the World Health Organization’s (WHO) Priority Pathogen List
  • Improved algorithm of first_isolate() when using the phenotype-based method, to prioritise records with the highest availability of SIR values
  • scale_y_percent() can now cope with ranges outside the 0-100% range
  • MDRO determination (using mdro())
    • The Verbose Mode (verbose = TRUE) now includes the guideline name
    • Implemented the new Dutch national MDRO guideline (SRI-richtlijn BRMO, Nov 2024)
    • Added arguments esbl, carbapenemase, mecA, mecC, vanA, vanB to denote column names or logical values indicating presence of these genes (or production of their proteins)
    • Added upport for antimicrobial selectors to use as as a custom rule (custom_mdro_guideline())
  • Added console colours support of sir class for Positron

Other

  • New website domain: https://amr-for-r.org! The old domain will remain to work.
  • Added Dr. Larisse Bolton and Aislinn Cook as contributors for their fantastic implementation of WISCA in a mathematically solid way
  • Added Matthew Saab, Dr. Jordan Stull, and Prof. Javier Sanchez as contributors for their tremendous input on veterinary breakpoints and interpretations
  • Added Prof. Kathryn Holt, Dr. Jane Hawkey, and Dr. Natacha Couto as contributors for their many suggestions, ideas and bugfixes
  • Greatly improved vctrs integration, a Tidyverse package working in the background for many Tidyverse functions. For users, this means that functions such as dplyr’s bind_rows(), rowwise() and c_across() are now supported for e.g. columns of class mic. Despite this, this AMR package is still zero-dependent on any other package, including dplyr and vctrs.
  • Greatly updated and expanded documentation
  • Stopped support for SAS (.xpt) files, since their file structure and extremely inefficient and requires more disk space than GitHub allows in a single commit.

Older Versions

This changelog only contains changes from AMR v3.0 (June 2025) and later.