Package index

Data Import & Preprocessing

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

import_abricate()

Import and Process ABRicate Results

import_amrfp()

Import and Process AMRFinderPlus Results

import_amrfp_ebi()

Import EBI-processed AMRFinderPlus Genotypes

import_amrfp_ebi_ftp()

Import EBI-processed AMRFinderPlus Genotypes from FTP

import_amrfp_ebi_web()

Import EBI-processed AMRFinderPlus Genotypes from Web

import_amrrules_predictions()

Import phenotype predictions from AMRrules output

import_ebi_pheno()

Import and process antimicrobial susceptibility phenotype data from the EBI AMR web portal

import_ebi_pheno_ftp()

Import and process antimicrobial phenotype data files retrieved from the EBI AMR portal FTP site

import_geno()

Import and process antimicrobial genotype data from common sources

import_kleborate()

Import and Process Kleborate Results

import_microscan_pheno()

Import and process antimicrobial phenotype data exported from MicroScan instruments

import_ncbi_biosample()

Import and process antimicrobial phenotype data retrieved from NCBI BioSamples

import_ncbi_pheno()

Import and process antimicrobial susceptibility phenotype data from the NCBI AST browser

import_pheno()

Import and process antimicrobial phenotype data from common sources

import_phoenix_pheno()

Import and process antimicrobial phenotype data exported from BD Phoenix instruments

import_rgi()

Import and Process Resistance Gene Identifier (RGI) Results

import_sensititre_pheno()

Import and process antimicrobial phenotype data exported from Sensititre instruments

import_sirscan_pheno()

Import and process antimicrobial susceptibility data from SIRscan (Bio-Rad)

import_vitek_pheno()

Import and process antimicrobial phenotype data exported from Vitek instruments

import_whonet_pheno()

Import and process antimicrobial phenotype data from WHONET files

export_ebi_pheno()

Export EBI Antibiogram

export_ncbi_pheno()

Export NCBI BioSample Antibiogram

convert_aa_code()

Convert single-letter amino acid code(s) to three-letter code(s)

convert_mutation()

Convert mutation string based on method

download_ebi()

Download antimicrobial genotype or phenotype data from the EBI AMR Portal

download_ncbi_pheno()

Download NCBI antimicrobial susceptibility testing (AST) data

summarise_geno()

Summarise a Genotype Table

summarise_geno_pheno()

Summarise the intersection of a genotype table and a phenotype table

summarise_pheno()

Summarise a Phenotype Table

format_ebi_json()

Generate EBI antibiogram submission in JSON

format_pheno()

Import and process antimicrobial phenotype data from a generic format

get_binary_matrix()

Get Binary Matrix of Genotype and Phenotype Data

get_combo_matrix()

Add marker combinations to a binary geno-pheno matrix

query_ncbi_bq_geno()

Query antimicrobial genotype (MicroBIGG-E) data from NCBI Pathogen Detection BigQuery

query_ncbi_bq_pheno()

Query antimicrobial phenotype data from NCBI Pathogen Detection BigQuery

Resistance Interpretation

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_pheno()

Interpret antimicrobial susceptibility phenotype data in a standard format tibble

Modelling and analysis

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

amr_upset()

Generate Upset Plot

solo_ppv()

Perform Solo PPV Analysis for AMR Markers

amr_ppv()

Generate PPV Plot

amr_logistic()

AMR Logistic Regression Analysis

glm_details()

Extract Details from a Generalised Linear Model

logistf_details()

Extract Details from a logistf Model

getBreakpoints()

Get Clinical Breakpoints for an Antibiotic

checkBreakpoints()

Check and Retrieve Breakpoints for an Antibiotic

concordance()

Calculate genotype-phenotype concordance from binary matrix

concordance_from_tables()

Assess concordance between tables of observed and predicted phenotypes

print(<amr_concordance>)

Print method for amr_concordance objects

Visualisation & Reporting

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

assay_by_var()

Plot Assay Values Colored by a Variable

Data

Example datasets for demonstration and reproducible analysis.

ecoli_pheno

E. coli NCBI AST Example Data, Re-interpreted with AMR Package

ecoli_pheno_raw

E. coli NCBI AST Example Data

ecoli_geno_raw

E. coli Genotype Example Data

ecoli_cip_vs_ref

E. coli Ciprofloxacin MIC Distribution Example Data

ecoli_cip_mic_data

EUCAST Reference distribution for Ciprofloxacin in E. coli

staph_pheno_ncbi

S. aureus Example of Imported NCBI Phenotype Data

staph_pheno_ncbi_raw

S. aureus Example of Raw Phenotype Data Downloaded from NCBI BioSamples via Entrez API

staph_pheno_ncbi_cloud_raw

S. aureus Example of Raw Phenotype Data Downloaded from NCBI via Google Cloud BigQuery

staph_geno_ncbi_cloud_raw

S. aureus Example of Raw Genotype Data Downloaded from NCBI via Google Cloud BigQuery

staph_pheno_ebi

S. aureus Example of Imported EBI Phenotype Data

staph_geno_ebi

S. aureus Example of Imported EBI Genotype Data

amrfp_drugs_table

NCBI Subclass mapping to drug class

pheno_eco_2075

E. coli AST data from Mills et al 2022

geno_eco_2075

E. coli genotype data from Mills et al 2022

eurogasp_geno_raw

N. gonorrhoeae Euro-GASP Genotype Data Use Case 1

ngono_cro_geno_raw

N. gonorrhoeae PBP2 Mutations Genotype Data Use Case 2

ngono_tet_geno_raw

N. gonorrhoeae Tetracycline Resistance Genotype Data Use Case 3

ngono_cro_pheno_raw

N. gonorrhoeae PBP2 Mutations Phenotype Data Use Case 2

eurogasp_pheno_raw

N. gonorrhoeae Euro-GASP Phenotype Data Use Case 1

azm_comparison

N. gonorrhoeae Euro-GASP azithromycin data vs EUCAST reference distribution

cip_comparison

N. gonorrhoeae Euro-GASP ciprofloxacin data vs EUCAST reference distribution

cro_comparison

N. gonorrhoeae Euro-GASP ceftriaxone data vs EUCAST reference distribution

cfm_comparison

N. gonorrhoeae Euro-GASP cefixime data vs EUCAST reference distribution

ngono_tet_pheno_raw

N. gonorrhoeae Tetracycline Resistance Phenotype Data Use Case 3

salm_raw

Example Salmonella Genotype-Phenotype Data

kleborate_raw

Example Kleborate Genotype Data from EuSCAPE project

kleborate_raw_v313

Example Kleborate v3.1.3 Genotype Data from EuSCAPE project

kleborate_classes

Table mapping Kleborate drug class columns

pheno_CLI_public

Clindamycin MIC data for 5914 Staphylococcus aureus isolates

afp_CLI_public

S. aureus Clindamycin Resistance Genotype Data

ST_data_CLI

ST data for Staphylococcus aureus genomes for clindamycin vignette

DASSIM_pheno_raw

DASSIM phenotype metadata

btESBL_pheno

blantyreESBL AST data

DASSIM_geno

DASSIM genotype data (AMRFinderPlus)

NCBI_Ecoli_pheno_chl

NCBI AST for Escherichia coli tested against chloramphenicol

MICROBIGGE_Ecoli_CHLR

MicroBIGG-E for E.coli containing all chloramphenicol resistance genes

rgi_raw

Example Resistance Gene Identifier (RGI) v6.0.6 Genotype Data

rgi_short_name_table

Table mapping CARD/RGI Model ID and CARD Short Name

rgi_drugs_table

Table mapping CARD/RGI drug class and antibiotic columns

rgi_EuSCAPE_raw

Example Resistance Gene Identifier (RGI) v6.0.6 Genotype Data from EuSCAPE project

kp_mero_euscape

Meropenem Phenotype Data from EuSCAPE project

kp_mero_amrfp

Example AMRFinderPlus Genotype Data from EuSCAPE project

sirscan_codes

SIRscan antibiotic code mapping