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Changelog

Source: NEWS.md

AMR 2.1.1.9078

(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 animal 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 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
  • 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 disks 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”.
  • 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 to rescale MIC values to a manually set range. This is the powerhouse behind the scale_*_mic() functions, but it can be used by users directly to e.g. compare equality in MIC distributions by rescaling them to the same range first.
  • Microbiological taxonomy (microorganisms data set) updated to June 2024, with some exciting new features:
    • Added MycoBank as the primary taxonomic source for fungi
      • The microorganisms data set now contains additional columns mycobank, mycobank_parent, and mycobank_renamed_to
      • New function mo_mycobank() to get the MycoBank record number, analogous to existing functions mo_lpsn() and mo_gbif()
    • We’ve welcomed over 2,000 records from 2023, over 900 from 2024, and many thousands of new fungi
  • Improved support for mycologists:
    • The as.mo() function now includes a new argument, only_fungi (TRUE/FALSE), which limits the results to fungi only. Normally, bacteria are often prioritised by the algorithm, but setting only_fungi = TRUE ensures only fungi are returned.
    • You can also set this globally using the new R option AMR_only_fungi, e.g., options(AMR_only_fungi = TRUE).
  • 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 are in 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.
  • 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 group_members, with the contents of the new mo_group_members() function
  • 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.
  • Updated all ATC codes from WHOCC
  • Updated all antibiotic DDDs from WHOCC
  • 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.
  • Intermediate log2 levels used for MIC plotting are now more common values instead of following a strict dilution range
  • Fixed a bug for when antibiogram() returns an empty data set

Other

  • Greatly updated and expanded documentation
  • Added Jordan Stull, Matthew Saab, and Javier Sanchez as contributors, to thank them for their valuable input

AMR 2.1.1

CRAN release: 2023-10-21

  • Fix for selecting first isolates using the phenotype-based method
    • This included too many isolates when patients had altering antibiograms within the same bacterial species
    • See for more info our issue #122
  • Added 1,366 LOINC codes to the antibiotics data set and updated to the latest version (LOINC v2.76)
  • MICs can now be used in complex number calculations and allow scientific number format as input (e.g., as.mic("1.28e-2"))
  • Fix rounding MICs on latest R beta (‘R-devel’)
  • Removed unneeded note about the used language when option AMR_locale is set
  • Fixed non-ASCII characters in documentation, according to CRAN maintainers