as.sir_vectorised       Convert MIC or Disk Diffusion to SIR,
                        vectorised over antimicrobials
bias                    Calculate MIC bias
clean_raw_mic           Clean up raw MIC for use as a feature
combined_file_system    Combine train and test filesystem into single
                        folder
compare_mic             Compare and validate MIC values
compare_sir             Compare SIR results and generate categorical
                        agreement
download_patric_db      Download PATRIC database
droplevels.mic_validation
                        Droplevels for MIC validation object
ecoffs                  ECOFF data
essential_agreement     Essential agreement for MIC validation
example_mics            Example MIC data
fill_dilution_levels    Fill MIC dilution levels
force_mic               Force MIC-like into MIC-compatible format
genome_to_libsvm        Converts a genome to kmers stored in libsvm
                        format on disk
genomes_to_kmer_libsvm
                        Convert genomes to kmers in libsvm format
get_mic                 Get MIC meta-data from feature database
kmers                   Generates genome kmers
load_patric_db          Load PATRIC database
mic_censor              Censor MIC values
mic_r_breakpoint        R breakpoint for MIC
mic_range               Generate dilution series
mic_s_breakpoint        S breakpoint for MIC
mic_uncensor            Uncensor MICs
move_files              Move or copy files using logical vector
plot.mic_validation     Plot MIC validation results
print.mic_validation    Print MIC validation object
print.mic_validation_summary
                        Print MIC validation summary
pull_PATRIC_genomes     Automated download of genomes from PATRIC
                        database
qc_in_range             Check that MIC is within QC range
qc_on_target            Check that QC measurement is at the required
                        target *[Experimental]*
replace_multiple_slashes
                        Removes multiple slashes in a path or url
reverse_complement      Reverse complement of DNA string
split_and_combine_files
                        Create test train files from a number of files
squeezed_index_to_str   Get str conversion of squeezed kmer using index
squeezed_mers           Generates all permutations of squeezed kmers
standardise_mic         Standardise MIC to control strain
                        *[Experimental]*
subset.mic_validation   Subset MIC validation object
summary.mic_validation
                        Summary of MIC validation results
table                   Table
tidy_patric_meta_data   Tidy PATRIC data
train_test_filesystem   Organise files into a train-test filesystem
unsqueezed_index_to_str
                        Get str conversion of unsqueezed kmer using
                        index
unsqueezed_mers         Generates all permutations of unsqueezed kmers
xgb.cv.lowmem           Low memory cross-validation wrapper for XGBoost
