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AMR v3.0.1

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@msberends msberends released this 20 Sep 16:16
· 2 commits to main since this release
v3.0.1
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msberends Matthijs Berends
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Learn about vigilant mode.

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
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