Changes in version 2.0.0 (2025-12-04)                  

  - This is a major release that includes several breaking changes. The
    package has been refocused to on MIC analysis and validation, and
    all genomic functions have been removed. These have been ported to
    https://github.com/agerada/faLearn. To maintain previous
    functionality, please install and load the faLearn package alongside
    MIC in your scripts. As such the package now has less dependencies,
    and no longer requires compilation.

                 Changes in version 1.2.0 (2025-10-12)                  

  - Functions that download data from PATRIC/BV-BRC have now been
    updated to support changes in BV-BRC ftp.

  - As of this version the genomic functions of the package have been
    deprecated, so that future versions of MIC can focus on MIC
    analysis. Any removed functions will be ported to a new package
    (called faLearn, see: https://github.com/agerada/faLearn) that
    focuses on machine learning with genomic data. The only change for
    users will be to install and load faLearn.

  - Functionality added to handle <= and => in MIC values,
    distinguishing them from < and >. In general, inhibitory MIC assays
    report <= and >. The leq and geq arguments for force_mic can be used
    to enforce these. The essential_agreement and compare_mic functions
    now have tolerate_leq and tolerate_geq arguments. When all settings
    are kept at default values, the functions assume typical censoring,
    i.e., <= and >.

                 Changes in version 1.1.0 (2025-06-05)                  

  - revamp of the essential_agreement function to allow a more robust,
    flexible, and explicit approach to dealing with censored values.
    Now, essential_agreement (and compare_mic) have tolerate_censoring
    and tolerate_matched_censoring arguments to control how censored
    values are handled. The default values should be appropriate for
    most situations where the user is comparing an investigational
    method to a gold standard method.
  - compare_mic is faster when only one ab is provided
  - subset S3 method added for mic_validation
  - plot.mic_validation now properly matches dilutions on the lower end
    of the scale
  - droplevels.mic_validation method added that allows unnecessary MIC
    levels in a validation object to be dropped
  - tidy_patric_meta_data was missing MICs when laboratory_typing_method
    was "MIC" (see 81c69f08)
  - pull_patric_genomes now takes an ab argument to only download
    strains where the specified antibiotic was tested
  - kmer counting is now case insensitive
  - compatibility with AMR v3.0

                 Changes in version 1.0.2 (2025-02-07)                  

  - CRAN resubmission with minor changes.

                        Changes in version 1.0.1                        

  - CRAN resubmission with minor changes to DESCRIPTION file.

                        Changes in version 1.0.0                        

  - Initial release and CRAN submission.