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 who 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