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mo codes for WHONET

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dr. M.S. (Matthijs) Berends
2019-02-08 16:06:54 +01:00
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vignettes/WHONET.Rmd
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@ -48,7 +48,7 @@ library(AMR) # this package
We will have to transform some variables to simplify and automate the analysis:
* Microorganisms should be transformed to our own microorganism IDs (called an `mo`) using [the ITIS reference data set](./reference/ITIS.html), which contains all ~20,000 microorganisms from the taxonomic kingdoms Bacteria, Fungi and Protozoa. We do the tranformation with `as.mo()`.
* Microorganisms should be transformed to our own microorganism IDs (called an `mo`) using [the ITIS reference data set](./reference/ITIS.html), which contains all ~20,000 microorganisms from the taxonomic kingdoms Bacteria, Fungi and Protozoa. We do the tranformation with `as.mo()`. This function also recognises almost all WHONET abbreviations of microorganisms.
* Antimicrobial results or interpretations have to be clean and valid. In other words, they should only contain values `"S"`, `"I"` or `"R"`. That is exactly where the `as.rsi()` function is for.
```{r}