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 >.
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
providedsubset S3 method added for
mic_validationplot.mic_validation now properly matches dilutions on
the lower end of the scaledroplevels.mic_validation method added that allows
unnecessary MIC levels in a validation object to be droppedtidy_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
testedAMR v3.0