Package: MIC 1.0.2.9000

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_1.0.2.9000.tar.gz
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MIC.pdf |MIC.html✨
MIC/json (API)
NEWS

# Install 'MIC' in R:

install.packages('MIC', repos = c('https://agerada.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:

ecoffs - ECOFF data
example_mics - Example MIC data

On CRAN:

cpp

3.85 score 10 scripts 53 downloads 34 exports 81 dependencies

Last updated 29 days agofrom:42e24220b9. Checks:8 OK. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Feb 11 2025
R-4.5-win-x86_64	OK	Feb 11 2025
R-4.5-mac-x86_64	OK	Feb 11 2025
R-4.5-mac-aarch64	OK	Feb 11 2025
R-4.5-linux-x86_64	OK	Feb 11 2025
R-4.4-win-x86_64	OK	Feb 11 2025
R-4.4-mac-x86_64	OK	Feb 11 2025
R-4.4-mac-aarch64	OK	Feb 11 2025

Exports:bias clean_raw_mic combined_file_system compare_mic compare_sir download_patric_db essential_agreement fill_dilution_levels force_mic genome_to_libsvm genomes_to_kmer_libsvm get_mic kmers load_patric_db mic_censor mic_r_breakpoint mic_range mic_s_breakpoint mic_uncensor move_files pull_PATRIC_genomes qc_in_range qc_on_target reverse_complement split_and_combine_files squeezed_index_to_str squeezed_mers standardise_mic table tidy_patric_meta_data train_test_filesystem unsqueezed_index_to_str unsqueezed_mers xgb.cv.lowmem

Dependencies:AMR askpass BiocGenerics Biostrings bit bit64 cli clipr codetools colorspace cpp11 crayon curl data.table digest dplyr evaluate fansi farver forcats future future.apply generics GenomeInfoDb GenomeInfoDbData ggplot2 globals glue gridExtra gtable highr hms httr IRanges isoband jsonlite knitr labeling lattice lemon lifecycle listenv magrittr MASS Matrix mgcv mime munsell nlme openssl parallelly pillar pkgconfig plyr prettyunits progress progressr purrr R6 RColorBrewer Rcpp readr rlang S4Vectors scales stringi stringr sys tibble tidyr tidyselect tzdb UCSC.utils utf8 vctrs viridisLite vroom withr xfun XVector yaml

Citation

Development and contributors

Readme and manuals

Help Manual

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