P281424/AMR
1
0 Fork 0
mirror of https://github.com/msberends/AMR.git synced 2026-10-01 04:13:33 +02:00
Code Releases Activity

(v1.7.0.9001) CLSI 2020 guideline

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends committed 2021-06-01 15:33:06 +02:00
1 parent f406319503
commit bef0f42f66
140 files changed
+23553 -931
Download Patch File Download Diff File Expand all files Collapse all files

No files matched your search

vignettes/WHONET.Rmd
+1 -1
View File
@@ -47,7 +47,7 @@ library(cleaner) # to create frequency tables
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 [our Catalogue of Life reference data set](https://msberends.github.io/AMR/reference/catalogue_of_life), which contains all ~70,000 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.
* Microorganisms should be transformed to our own microorganism codes (called an `mo`) using [our Catalogue of Life reference data set](https://msberends.github.io/AMR/reference/catalogue_of_life), which contains all ~70,000 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}