# Analysis of Antimicrobial Minimum Inhibitory Concentration Data

## Documentation for package ‘MIC’ version 1.2.0

- DESCRIPTION file.
- Package NEWS.

## Help Pages

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
genomes_to_kmer_libsvm | Convert genomes to kmers in libsvm format
genome_to_libsvm | Converts a genome to kmers stored in libsvm format on disk
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_range | Generate dilution series
mic_r_breakpoint | R breakpoint for MIC
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
table.default | Table
table.mic_validation | 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