With the function mdro(), you can determine multi-drug resistant organisms (MDRO). It currently support these guidelines:

  • “Intrinsic Resistance and Exceptional Phenotypes Tables”, by EUCAST (European Committee on Antimicrobial Susceptibility Testing)
  • “Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis”, by WHO (World Health Organization)
  • “WIP-Richtlijn Bijzonder Resistente Micro-organismen (BRMO)”, by RIVM (Rijksinstituut voor de Volksgezondheid, the Netherlands National Institute for Public Health and the Environment)

As an example, I will make a data set to determine multi-drug resistant TB:

Because all column names are automatically verified for valid drug names or codes, this would have worked exactly the same:

The data set looks like this now:

We can now add the interpretation of MDR-TB to our data set:

We also created a package dedicated to data cleaning and checking, called the clean package. It gets automatically installed with the AMR package, so we only have to load it:

library(clean)

It contains the freq() function, to create a frequency table:

freq(my_TB_data$mdr)

Frequency table

Class: factor > ordered (numeric)
Length: 5,000 (of which NA: 0 = 0.00%)
Levels: 5: Negative < Mono-resistance < Poly-resistance < Multidrug resistance…
Unique: 5

Item Count Percent Cum. Count Cum. Percent
1 Mono-resistance 3271 65.4% 3271 65.4%
2 Negative 643 12.9% 3914 78.3%
3 Multidrug resistance 582 11.6% 4496 89.9%
4 Poly-resistance 287 5.7% 4783 95.7%
5 Extensive drug resistance 217 4.3% 5000 100.0%