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algorithm update

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dr. M.S. (Matthijs) Berends
2019-02-21 18:55:52 +01:00
parent c6e57ca456
commit 68a9a35ed6
112 changed files with 586 additions and 886 deletions
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@ -23,7 +23,7 @@ This package can be used for:
* Getting properties for any antibiotic (like name, ATC code, defined daily dose or trade name)
* Plotting antimicrobial resistance
* Determining first isolates to be used for AMR analysis
* Applying EUCAST rules
* Applying EUCAST expert rules (not the translation from MIC to RSI values)
* Determining multi-drug resistant organisms (MDRO)
* Descriptive statistics: frequency tables, kurtosis and skewness
@ -137,7 +137,7 @@ The `AMR` package basically does four important things:
2. It **enhances existing data** and **adds new data** from data sets included in this package.
* Use `eucast_rules()` to apply [EUCAST expert rules to isolates](http://www.eucast.org/expert_rules_and_intrinsic_resistance/).
* Use `eucast_rules()` to apply [EUCAST expert rules to isolates](http://www.eucast.org/expert_rules_and_intrinsic_resistance/) (not the translation from MIC to RSI values).
* Use `first_isolate()` to identify the first isolates of every patient [using guidelines from the CLSI](https://clsi.org/standards/products/microbiology/documents/m39/) (Clinical and Laboratory Standards Institute).
* You can also identify first *weighted* isolates of every patient, an adjusted version of the CLSI guideline. This takes into account key antibiotics of every strain and compares them.
* Use `mdro()` (abbreviation of Multi Drug Resistant Organisms) to check your isolates for exceptional resistance with country-specific guidelines or EUCAST rules. Currently, national guidelines for Germany and the Netherlands are supported.