Package: MIC 1.0.2

Alessandro Gerada

MIC: Analysis of Antimicrobial Minimum Inhibitory Concentration Data

Analyse, plot, and tabulate antimicrobial minimum inhibitory concentration (MIC) data. Validate the results of an MIC experiment by comparing observed MIC values to a gold standard assay, in line with standards from the International Organization for Standardization (2021) <https://www.iso.org/standard/79377.html>. Perform MIC prediction from whole genome sequence data stored in the Pathosystems Resource Integration Center (2013) <doi:10.1093/nar/gkt1099> database or locally.

Authors:Alessandro Gerada [aut, cre, cph]

MIC_1.0.2.tar.gz
MIC_1.0.2.tar.gz(r-4.5-noble)MIC_1.0.2.tar.gz(r-4.4-noble)
MIC_1.0.2.tgz(r-4.4-emscripten)MIC_1.0.2.tgz(r-4.3-emscripten)
MIC.pdf |MIC.html✨
MIC/json (API)
NEWS

# Install 'MIC' in R:
install.packages('MIC', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/agerada/mic/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

Conda:

cpp

1.70 score 306 downloads 34 exports 81 dependencies

Last updated 1 months agofrom:960c91f26b. Checks:3 OK. Indexed: no.

TargetResultLatest binary
Doc / VignettesOKMar 09 2025
R-4.5-linux-x86_64OKMar 09 2025
R-4.4-linux-x86_64OKMar 09 2025

Exports:biasclean_raw_miccombined_file_systemcompare_miccompare_sirdownload_patric_dbessential_agreementfill_dilution_levelsforce_micgenome_to_libsvmgenomes_to_kmer_libsvmget_mickmersload_patric_dbmic_censormic_r_breakpointmic_rangemic_s_breakpointmic_uncensormove_filespull_PATRIC_genomesqc_in_rangeqc_on_targetreverse_complementsplit_and_combine_filessqueezed_index_to_strsqueezed_mersstandardise_mictabletidy_patric_meta_datatrain_test_filesystemunsqueezed_index_to_strunsqueezed_mersxgb.cv.lowmem

Dependencies:AMRaskpassBiocGenericsBiostringsbitbit64clicliprcodetoolscolorspacecpp11crayoncurldata.tabledigestdplyrevaluatefansifarverforcatsfuturefuture.applygenericsGenomeInfoDbGenomeInfoDbDataggplot2globalsgluegridExtragtablehighrhmshttrIRangesisobandjsonliteknitrlabelinglatticelemonlifecyclelistenvmagrittrMASSMatrixmgcvmimemunsellnlmeopensslparallellypillarpkgconfigplyrprettyunitsprogressprogressrpurrrR6RColorBrewerRcppreadrrlangS4VectorsscalesstringistringrsystibbletidyrtidyselecttzdbUCSC.utilsutf8vctrsviridisLitevroomwithrxfunXVectoryaml

Readme and manuals

Help Manual

Help pageTopics
Calculate MIC biasbias
Clean up raw MIC for use as a featureclean_raw_mic
Combine train and test filesystem into single foldercombined_file_system
Compare and validate MIC valuescompare_mic
Compare SIR results and generate categorical agreementcompare_sir
Download PATRIC databasedownload_patric_db
ECOFF dataecoffs
Essential agreement for MIC validationessential_agreement
Example MIC dataexample_mics
Fill MIC dilution levelsfill_dilution_levels
Force MIC-like into MIC-compatible formatforce_mic
Converts a genome to kmers stored in libsvm format on diskgenome_to_libsvm
Convert genomes to kmers in libsvm formatgenomes_to_kmer_libsvm
Get MIC meta-data from feature databaseget_mic
Generates genome kmerskmers
Load PATRIC databaseload_patric_db
Censor MIC valuesmic_censor
R breakpoint for MICmic_r_breakpoint
Generate dilution seriesmic_range
S breakpoint for MICmic_s_breakpoint
Uncensor MICsmic_uncensor
Move or copy files using logical vectormove_files
Plot MIC validation resultsplot.mic_validation
Print MIC validation objectprint.mic_validation
Print MIC validation summaryprint.mic_validation_summary
Automated download of genomes from PATRIC databasepull_PATRIC_genomes
Check that MIC is within QC rangeqc_in_range
Check that QC measurement is at the required target *[Experimental]*qc_on_target
Removes multiple slashes in a path or urlreplace_multiple_slashes
Reverse complement of DNA stringreverse_complement
Create test train files from a number of filessplit_and_combine_files
Get str conversion of squeezed kmer using indexsqueezed_index_to_str
Generates all permutations of squeezed kmerssqueezed_mers
Standardise MIC to control strain *[Experimental]*standardise_mic
Summary of MIC validation resultssummary.mic_validation
Tabletable table.default table.mic_validation
Tidy PATRIC datatidy_patric_meta_data
Organise files into a train-test filesystemtrain_test_filesystem
Get str conversion of unsqueezed kmer using indexunsqueezed_index_to_str
Generates all permutations of unsqueezed kmersunsqueezed_mers
Low memory cross-validation wrapper for XGBoostxgb.cv.lowmem