data | ||
man | ||
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DESCRIPTION | ||
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NAMESPACE | ||
README.md |
AMR
This is an R package to simplify the analysis of Antimicrobial Resistance (AMR).
This R package was created for academic research by PhD students of the Medical Microbiology & Infection Prevention (mmb) department 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
can be used in conjunction with summarise
to calculate the resistance percentages of different antibiotic columns of a table.
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
interpretive_reading(...)
# 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"
# Calculate age of patients
age(...)
# Categorize patients age to age groups
age.group(...)
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 MS1,2
- Luz CF1
- Hassing EEA2 (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