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dr. M.S. (Matthijs) Berends
2022-05-11 10:26:58 +02:00
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vignettes/datasets.Rmd
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@ -209,6 +209,27 @@ antivirals %>%
print_df()
```
## Interpretation from MIC values / disk diameters to R/SI
`r structure_txt(rsi_translation)`
This data set is in R available as `rsi_translation`, after you load the `AMR` package.
`r download_txt("rsi_translation")`
### Source
This data set contains interpretation rules for MIC values and disk diffusion diameters. Included guidelines are CLSI (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`) and EUCAST (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`).
### Example content
```{r, echo = FALSE}
rsi_translation %>%
mutate(mo_name = mo_name(mo, language = NULL), .after = mo) %>%
mutate(ab_name = ab_name(ab, language = NULL), .after = ab) %>%
print_df()
```
## Intrinsic bacterial resistance
@ -231,31 +252,11 @@ intrinsic_resistant %>%
transmute(microorganism = mo_name(mo),
antibiotic = ab_name(ab)) %>%
filter(microorganism == "Enterobacter cloacae") %>%
arrange(antibiotic) %>%
print_df(rows = Inf)
```
## Interpretation from MIC values / disk diameters to R/SI
`r structure_txt(rsi_translation)`
This data set is in R available as `rsi_translation`, after you load the `AMR` package.
`r download_txt("rsi_translation")`
### Source
This data set contains interpretation rules for MIC values and disk diffusion diameters. Included guidelines are CLSI (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`) and EUCAST (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`).
### Example content
```{r, echo = FALSE}
rsi_translation %>%
mutate(ab = ab_name(ab), mo = mo_name(mo)) %>%
print_df()
```
## Dosage guidelines from EUCAST
`r structure_txt(dosage)`