AMR

This is an R package to simplify the analysis and prediction of Antimicrobial Resistance (AMR).

This R package was created for academic research by PhD students of the Faculty of Medical Sciences of the University of Groningen and the Medical Microbiology & Infection Prevention department of the University Medical Center Groningen (UMCG). They also maintain this package, see Authors.

Why this package?

This R package contains functions to make microbiological, epidemiological data analysis easier. It allows the use of some new S3 classes to work with MIC values and antimicrobial interpretations (i.e. values S, I and R).

AMR can also be predicted for the forthcoming years with the rsi_predict function. For use with the dplyr package, the rsi function can be used in conjunction with summarise to calculate the resistance percentages of different antibiotic columns of a table.

It also contains functions to translate antibiotic codes from the lab (like "AMOX") or the WHO (like "J01CA04") to trivial names (like "amoxicillin") and vice versa.

How to use it?

# Call it with:
library(AMR)

# For a list of functions:
help(package = "AMR")

Databases included in package

# Dataset with ATC antibiotics codes, official names and DDD's (oral and parenteral)
ablist        # A tibble: 420 x 12

# Dataset with bacteria codes and properties like gram stain and aerobic/anaerobic
bactlist      # A tibble: 2,507 x 10

New classes

This package contains two new S3 classes: mic for MIC values (e.g. from Vitek or Phoenix) and rsi for antimicrobial drug interpretations (i.e. S, I and R). Both are actually ordered factors under the hood (an MIC of 2 being higher than <=1 but lower than >=32, and for class rsi factors are ordered as S < I < R). Both classes have extensions for existing generic functions like print, summary and plot.

# Transform values to new classes
mic_data <- as.mic(c(">=32", "1.0", "8", "<=0.128", "8", "16", "16"))
rsi_data <- as.rsi(c(rep("S", 474), rep("I", 36), rep("R", 370)))

These functions also try to coerce valid values.

Quick overviews when just printing objects:

mic_data
# Class 'mic': 7 isolates
# 
# <NA>  0
# 
# <=0.128       1       8      16    >=32
#       1       1       2       2       1

rsi_data
# Class 'rsi': 880 isolates
# 
# <NA>:       0 
# Sum of S:   474 
# Sum of IR:  406 
# - Sum of R: 370 
# - Sum of I: 36 
# 
#   %S  %IR   %I   %R 
# 53.9 46.1  4.1 42.0 

A plot of rsi_data:

plot(rsi_data)

Other epidemiological functions:

# Apply EUCAST Expert Rules v3.1 (latest) to antibiotic columns
EUCAST_rules(...)

# Determine key antibiotic based on bacteria ID
key_antibiotics(...)
# Check if key antibiotics are equal
key_antibiotics_equal(...)

# Selection of first isolates of any patient
first_isolate(...)

# Calculate resistance levels of antibiotics
rsi(...)
# Predict resistance levels of antibiotics
rsi_predict(...)

# Get name of antibiotic by ATC code
abname(...)
abname("J01CR02", from = "atc", to = "umcg") # "AMCL"

How to get it?

This package is only available here on GitHub, but respects the CRAN Repository Policy.

Installation commands:

library(devtools)
install_github("msberends/AMR")

Working behind a proxy? Then use:

library(httr)
library(devtools)
set_config(use_proxy("yourproxydomain.com",
                     8080,
                     "username",
                     "password",
                     "any")) # change "any" to "basic" or "digest" if needed
install_github("msberends/AMR")
reset_config()

Authors

• Berends MS^1,2, PhD Student
• Luz CF¹, PhD Student
• Hassing EEA², Data Analyst (contributor)

¹ Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands

² Department of Medical, Market and Innovation (MMI), Certe Medische diagnostiek & advies, Groningen, the Netherlands

Copyright

This R package is licensed under the GNU General Public License (GPL) v2.0. In a nutshell, this means that this package:

• May be used for commercial purposes

• May be used for private purposes

• May be modified, although:

  • Modifications must be released under the same license when distributing the package
  • Changes made to the code must be documented

• May be distributed, although:

  • Source code must be made available when the package is distributed
  • A copy of the license and copyright notice must be included with the package.

• Comes with a LIMITATION of liability

• Comes with NO warranty