Package index • AMRgen

All functions

AMRgen_barplot_mic_gen(): Generate a Stacked Bar Plot of MIC Values Colored by Gene Symbol for Each Antibiotic

amr_complexUpset(): Create an Upset plot for AMR data

amr_logistic(): AMR Logistic Regression Analysis

amr_upset(): amr_upset: Generate a series of plots for AMR gene and combination analysis

as.gene(): Gene Class and AMR Parsing Functions

compare_estimates(): Plot to Compare Two Sets of Estimates

compare_geno_pheno_id(): Compare Genotype and Phenotype Data by Sample ID

ecoli_ast: E. coli NCBI AST example data, re-interpreted with AMR package

ecoli_ast_raw: E. coli NCBI AST example data

ecoli_geno_raw: E. coli genotype example data

eucast_supported_ab_distributions(): Retrieve Available Antimicrobial Wild Type Distributions from EUCAST

export_ncbi_biosample(): Import/Export BioSample Antibiograms

get_binary_matrix(): Get Binary Matrix of Genotype and Phenotype Data

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

glm_details(): Extract Details from a Generalized Linear Model

gtdb.mo(): Get Microorganism from GTDB Species Name

harmonize_data(): hamronize_data

import_amrfp(): Import and process AMRFinderPlus results

import_gtdb(): Import GTDB Output

import_ncbi_ast(): Import and process AST data from an NCBI file

logistf_details(): Extract Details from a logistf Model

merge_logreg_soloppv(): Merge Logistic Regression and Solo PPV Statistics

plot_combined_stats(): Plot Combined Statistics

plot_estimates(): Plot Estimates from a Table of Results

solo_ppv_analysis(): Perform Solo PPV Analysis for AMR Markers

stripRangeValues(): Strip Range Values from MIC Object