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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 81c69f0)
pull_patric_genomes now takes an ab argument to only download strains
where the specified antibiotic was tested