Man pages for MIC
Analysis of Antimicrobial Minimum Inhibitory Concentration Data
| 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 |
| 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-package | MIC: Analysis of Antimicrobial Minimum Inhibitory... |
| 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... |
| 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]* |
| 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 |
