Package index • AMRgen

Data Import & Preprocessing

Functions to import, harmonise, and prepare genotype and phenotype data from public repositories or internal formats.

import_amrfp(): Import and Process AMRFinderPlus Results
import_ast(): Import and Process AST Data from an EBI or NCBI antibiogram File
import_ebi_ast(): Import and Process AST Data from an EBI File
import_gtdb(): Import GTDB Output
import_ncbi_ast(): Import and Process AST Data from an NCBI File
export_ncbi_biosample(): Import/Export BioSample Antibiograms
convert_aa_code(): Convert single-letter amino acid code(s) to three-letter code(s)
convert_mutation(): Convert mutation string based on method
get_binary_matrix(): Get Binary Matrix of Genotype and Phenotype Data
as.gene(): Gene Class and AMR Parsing Functions
gtdb.mo(): Get Microorganism from GTDB Species Name

Core tools for interpreting antimicrobial resistance based on EUCAST breakpoints and custom models.

compare_estimates(): Plot to Compare Two Sets of Estimates
compare_geno_pheno_id(): Compare Genotype and Phenotype Data by Sample ID
get_eucast_amr_distribution() get_eucast_mic_distribution() get_eucast_disk_distribution() compare_mic_with_eucast() compare_disk_with_eucast(): Get and Compare Antimicrobial Wild Type Distributions from EUCAST
eucast_supported_ab_distributions(): Retrieve Available Antimicrobial Wild Type Distributions from EUCAST
merge_logreg_soloppv(): Merge Logistic Regression and Solo PPV Statistics
interpret_ast(): Interpret AST data in a standard format tibble

Statistical models for resistance prediction and inference, including logistic regression and Firth regression.

Tools to visualise results, including MIC distributions, model outputs, and genotype-phenotype relationships.

plot_combined_stats(): Plot Combined Statistics
plot_estimates(): Plot Estimates from a Table of Results
plot_solo_logReg(): Plot Combined Statistics of Logistic Regression and Solo PPV
amr_upset(): Generate a Series of Plots for AMR Gene and Combination Analysis
assay_by_var(): Generate a Stacked Bar Plot of Assay Values Colored by a Variable

Example datasets for demonstration and reproducible analysis.