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AMR

Antimicrobial Resistance Data Analysis

Functions to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial properties by using evidence-based methods, like those defined by Leclercq et al. (2013) <doi:10.1111/j.1469-0691.2011.03703.x> and containing reference data such as LPSN <doi:10.1099/ijsem.0.004332>.

Functions (53)

AMR

The AMR Package

AMR-deprecated

Deprecated Functions

WHOCC

WHOCC: WHO Collaborating Centre for Drug Statistics Methodology

WHONET

Data Set with 500 Isolates - WHONET Example

ab_from_text

Retrieve Antimicrobial Drug Names and Doses from Clinical Text

ab_property

Get Properties of an Antibiotic

age

Age in Years of Individuals

age_groups

Split Ages into Age Groups

antibiotic_class_selectors

Antibiotic Class Selectors

antibiotics

Data Sets with 558 Antimicrobials

as.ab

Transform Input to an Antibiotic ID

as.disk

Transform Input to Disk Diffusion Diameters

as.mic

Transform Input to Minimum Inhibitory Concentrations (MIC)

as.mo

Transform Input to a Microorganism ID

as.rsi

Interpret MIC and Disk Values, or Clean Raw R/SI Data

atc_online

Get ATC Properties from WHOCC Website

availability

Check Availability of Columns

bug_drug_combinations

Determine Bug-Drug Combinations

catalogue_of_life

The Catalogue of Life

catalogue_of_life_version

Version info of included Catalogue of Life

count

Count Available Isolates

dosage

Data Set with Treatment Dosages as Defined by EUCAST

eucast_rules

Apply EUCAST Rules

example_isolates

Data Set with 2,000 Example Isolates

example_isolates_unclean

Data Set with Unclean Data

filter_ab_class

Filter Isolates on Result in Antimicrobial Class

first_isolate

Determine First (Weighted) Isolates

g.test

G-test for Count Data

get_episode

Determine (New) Episodes for Patients

ggplot_pca

PCA Biplot with ggplot2

ggplot_rsi

AMR Plots with ggplot2

guess_ab_col

Guess Antibiotic Column

intrinsic_resistant

Data Set with Bacterial Intrinsic Resistance

join

Join microorganisms to a Data Set

key_antibiotics

Key Antibiotics for First (Weighted) Isolates

kurtosis

Kurtosis of the Sample

lifecycle

Lifecycles of Functions in the AMR Package

like

Pattern Matching with Keyboard Shortcut

mdro

Determine Multidrug-Resistant Organisms (MDRO)

microorganisms

Data Set with 70,026 Microorganisms

microorganisms.codes

Data Set with 5,580 Common Microorganism Codes

microorganisms.old

Data Set with Previously Accepted Taxonomic Names

mo_matching_score

Calculate the Matching Score for Microorganisms

mo_property

Get Properties of a Microorganism

mo_source

User-Defined Reference Data Set for Microorganisms

pca

Principal Component Analysis (for AMR)

plot

Plotting for Classes rsi, mic and disk

proportion

Calculate Microbial Resistance

random

Random MIC Values/Disk Zones/RSI Generation

resistance_predict

Predict antimicrobial resistance

rsi_translation

Data Set for R/SI Interpretation

skewness

Skewness of the Sample

translate

Translate Strings from AMR Package

AMR

Antimicrobial Resistance Data Analysis

v1.6.0

GPL-2 | file LICENSE

Authors

Matthijs S. Berends [aut, cre] (<https://orcid.org/0000-0001-7620-1800>), Christian F. Luz [aut, ctb] (<https://orcid.org/0000-0001-5809-5995>), Alexander W. Friedrich [aut, ths] (<https://orcid.org/0000-0003-4881-038X>), Bhanu N. M. Sinha [aut, ths] (<https://orcid.org/0000-0003-1634-0010>), Casper J. Albers [aut, ths] (<https://orcid.org/0000-0002-9213-6743>), Corinna Glasner [aut, ths] (<https://orcid.org/0000-0003-1241-1328>), Judith M. Fonville [ctb], Erwin E. A. Hassing [ctb], Eric H. L. C. M. Hazenberg [ctb], Gwen Knight [ctb], Annick Lenglet [ctb], Bart C. Meijer [ctb], Sofia Ny [ctb], Rogier P. Schade [ctb], Dennis Souverein [ctb], Anthony Underwood [ctb]

Initial release

2021-03-14

AMR

Functions (53)

AMR

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