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new species groups, updated clinical breakpoints

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2023-07-08 17:30:05 +02:00
parent 2d97cca6d9
commit acb534102b
172 changed files with 44445 additions and 52835 deletions

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@ -321,3 +321,44 @@ This data set contains randomised fictitious data, but reflects reality and can
example_isolates_unclean %>%
print_df()
```
## `microorganisms.groups`: Species Groups and Microbiological Complexes
`r structure_txt(microorganisms.groups)`
This data set is in R available as `microorganisms.groups`, after you load the `AMR` package.
`r download_txt("microorganisms.groups")`
### Source
This data set contains species groups and microbiological complexes, which are used in the `clinical_breakpoints` data set.
### Example content
```{r, echo = FALSE}
microorganisms.groups %>%
print_df()
```
## `microorganisms.codes`: Common Laboratory Codes
`r structure_txt(microorganisms.codes)`
This data set is in R available as `microorganisms.codes`, after you load the `AMR` package.
`r download_txt("microorganisms.codes")`
### Source
This data set contains commonly used codes for microorganisms, from laboratory systems and [WHONET](https://whonet.org).
### Example content
```{r, echo = FALSE}
microorganisms.codes %>%
print_df()
```