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Changelog

Source: NEWS.md

AMR 2.1.1.9106

(this beta version will eventually become v3.0. We’re happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using the instructions here.)

A New Milestone: AMR v3.0 with One Health Support (= Human + Veterinary + Environmental)

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

  • Removed all functions and references that used the deprecated rsi class, which were all replaced with their sir equivalents over a year ago

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 CLSI VET09 guideline has been implemented to address cases where veterinary breakpoints are missing (only applies when guideline is set to CLSI)
    • The clinical_breakpoints data set contains all these breakpoints, and can be downloaded on our download page.
    • The antibiotics data set contains all veterinary antibiotics, such as pradofloxacin and enrofloxacin. All WHOCC codes for veterinary use have been added as well.
    • ab_atc() now supports ATC codes of veterinary antibiotics (that all start with “Q”)
    • ab_url() now supports retrieving the WHOCC url of their ATCvet pages
  • 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
    • EUCAST 2024 and CLSI 2024 are now supported, by adding all of their over 4,000 new clinical breakpoints to the clinical_breakpoints data set for usage in as.sir(). EUCAST 2024 is now the new default guideline for all MIC and disk diffusion interpretations.
    • 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”.
  • New forms for MIC plotting and transforming
    • New function group scale_*_mic(), namely: scale_x_mic(), scale_y_mic(), scale_colour_mic() and scale_fill_mic(). They are advanced ggplot2 extensions to allow easy plotting of MIC values. They allow for manual range definition and plotting missing intermediate log2 levels.
    • 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.
  • Other
    • 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.

Changed

  • SIR interpretation
    • It is now possible to use column names for argument 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.
  • antibiogram() function
    • New argument formatting_type to set any of the 12 options for the formatting of all ‘cells’. This defaults to 10, changing the output of antibiograms to cells with 5% (15/300) instead of the previous standard of just 5.
    • For this reason, add_total_n is now FALSE at default since the denominators are added to the cells
    • The ab_transform argument now defaults to "name", displaying antibiotic column names instead of codes
  • antibiotics data set
    • Added “clindamycin inducible screening” as CLI1. Since clindamycin is a lincosamide, the antibiotic selector lincosamides() now contains the argument only_treatable = TRUE (similar to other antibiotic selectors that contain non-treatable drugs)
    • Added Amorolfine (AMO, D01AE16), which is now also part of the antifungals() selector
  • Antibiotic selectors
    • Added selectors nitrofurans() and rifamycins()
    • When using antibiotic selectors such as aminoglycosides() that exclude non-treatable drugs like gentamicin-high, the function now always returns a warning that these can be included using only_treatable = FALSE
  • MICs
    • Added as valid levels: 4096, 6 powers of 0.0625, and 5 powers of 192 (192, 384, 576, 768, 960)
    • 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
  • 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 antibiotics and antibiotic 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 antibiotic DDDs from WHOCC
  • Added over 1,500 trade names for antibiotics
  • Fix for using a manual value for mo_transform in antibiogram()
  • Fix for mapping ‘high level’ antibiotics 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
  • 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 when antibiogram() returns an empty data set
  • 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

Other

  • 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
  • Added Larisse Bolton, Jordan Stull, Matthew Saab, and Javier Sanchez as contributors, to thank them for their valuable input
  • 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 (October 2024) and later.