### An [R package](https://www.r-project.org) to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and work with antibiotic properties by using evidence-based methods.
This R package was created for academic research by PhD students of the Faculty of Medical Sciences of the [University of Groningen](https://www.rug.nl) and the Medical Microbiology & Infection Prevention (MMBI) department of the [University Medical Center Groningen (UMCG)](https://www.umcg.nl).
This R package contains functions to make **microbiological, epidemiological data analysis easier**. It allows the use of some new classes to work with MIC values and antimicrobial interpretations (i.e. values S, I and R).
* Calculate the resistance (and even co-resistance) of microbial isolates with the `resistance` and `susceptibility` functions, that can also be used with the `dplyr` package (e.g. in conjunction with `summarise`)
* Predict antimicrobial resistance for the nextcoming years with the `rsi_predict` function
* Apply [EUCAST rules to isolates](http://www.eucast.org/expert_rules_and_intrinsic_resistance/) with the `EUCAST_rules` function
* Identify first isolates of every patient [using guidelines from the CLSI](https://clsi.org/standards/products/microbiology/documents/m39/) (Clinical and Laboratory Standards Institute) with the `first_isolate` function
* Get antimicrobial ATC properties from the WHO Collaborating Centre for Drug Statistics Methodology ([WHOCC](https://www.whocc.no/atc_ddd_methodology/who_collaborating_centre/)), to be able to:
* Translate antibiotic codes (like *AMOX*), official names (like *amoxicillin*) and even trade names (like *Amoxil* or *Trimox*) to an [ATC code](https://www.whocc.no/atc_ddd_index/?code=J01CA04&showdescription=no) (like *J01CA04*) and vice versa with the `abname` function
* Get the latest antibiotic properties like hierarchic groups and [defined daily dose](https://en.wikipedia.org/wiki/Defined_daily_dose) (DDD) with units and administration form from the WHOCC website with the `atc_property` function
* A recent data set with ~2500 human pathogenic microorganisms, including family, genus, species, gram stain and aerobic/anaerobic
* A recent data set with all antibiotics as defined by the [WHOCC](https://www.whocc.no/atc_ddd_methodology/who_collaborating_centre/), including ATC code, official name and DDD's
* An example data set `septic_patients`, consisting of 2000 blood culture isolates from anonymised septic patients between 2001 and 2017.
With the `MDRO` function (abbreviation of Multi Drug Resistant Organisms), you can check your isolates for exceptional resistance with country-specific guidelines or EUCAST rules. Currently guidelines for Germany and the Netherlands are supported. Please suggest addition of your own country here: [https://github.com/msberends/AMR/issues/new](https://github.com/msberends/AMR/issues/new?title=New%20guideline%20for%20MDRO&body=%3C--%20Please%20add%20your%20country%20code,%20guideline%20name,%20version%20and%20source%20below%20and%20remove%20this%20line--%3E).
The functions to calculate microbial resistance use expressions that are not evaluated by R itself, but by alternative C++ code that is 25 to 30 times faster and uses less memory. This is called *hybrid evaluation*.
- (Exploratory.io costs $40/month but the somewhat limited Community Plan is free for students and teachers, [click here to enroll](https://exploratory.io/plan?plan=Community))
Bacteria ID's can be retrieved with the `as.bactid` function. It uses any type of info about a microorganism as input. For example, all these will return value `STAAUR`, the ID of *S. aureus*:
```r
as.bactid("stau")
as.bactid("STAU")
as.bactid("staaur")
as.bactid("S. aureus")
as.bactid("S aureus")
as.bactid("Staphylococcus aureus")
as.bactid("MRSA") # Methicillin Resistant S. aureus
as.bactid("VISA") # Vancomycin Intermediate S. aureus
as.bactid("VRSA") # Vancomycin Resistant S. aureus
```
### 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`.
Base R lacks a simple function to create frequency tables. We created such a function that works with almost all data types: `freq` (or `frequency_tbl`). It can be used in two ways:
This R package is licensed under the [GNU General Public License (GPL) v2.0](https://github.com/msberends/AMR/blob/master/LICENSE). In a nutshell, this means that this package:
