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(v1.5.0.9027) website update

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dr. M.S. (Matthijs) Berends
2021-02-26 12:11:29 +01:00
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vignettes/AMR.Rmd
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@ -510,7 +510,7 @@ mic_values <- random_mic(size = 100)
mic_values
```
```{r}
```{r mic_plots}
# base R:
plot(mic_values)
# ggplot2:
@ -520,39 +520,36 @@ ggplot(mic_values)
But we could also be more specific, by generating MICs that are likely to be found in *E. coli* for ciprofloxacin:
```{r, results = 'markup', message = FALSE, warning = FALSE}
# this will generate MICs that are likely to be found in E. coli for ciprofloxacin:
mic_values_specific <- random_mic(size = 100, mo = "E. coli", ab = "cipro")
mic_values <- random_mic(size = 100, mo = "E. coli", ab = "cipro")
```
For the `plot()` and `ggplot()` function, we can define the microorganism and an antimicrobial agent the same way. This will add the interpretation of those values according to a chosen guidelines (defaults to the latest EUCAST guideline).
Default colours are colour-blind friendly, while maintaining the convention that e.g. 'susceptible' should be green and 'resistant' should be red:
```{r, message = FALSE, warning = FALSE}
```{r mic_plots_mo_ab, message = FALSE, warning = FALSE}
# base R:
plot(mic_values_specific, mo = "E. coli", ab = "cipro")
plot(mic_values, mo = "E. coli", ab = "cipro")
# ggplot2:
ggplot(mic_values_specific, mo = "E. coli", ab = "cipro")
ggplot(mic_values, mo = "E. coli", ab = "cipro")
```
For disk diffusion values, there is not much of a difference in plotting:
```{r, results = 'markup'}
# this will generate disks that are likely to be found in E. coli for ciprofloxacin:
disk_values_specific <- random_disk(size = 100, mo = "E. coli", ab = "cipro")
disk_values_specific
disk_values <- random_disk(size = 100, mo = "E. coli", ab = "cipro")
disk_values
```
```{r, message = FALSE, warning = FALSE}
```{r disk_plots, message = FALSE, warning = FALSE}
# base R:
plot(disk_values_specific, mo = "E. coli", ab = "cipro")
plot(disk_values, mo = "E. coli", ab = "cipro")
```
And when using the `ggplot2` package, but now choosing the latest implemented CLSI guideline (notice that the EUCAST-specific term "Incr. exposure" has changed to "Intermediate"):
```{r, message = FALSE, warning = FALSE}
# and ggplot2, but now choosing an old CLSI guideline:
ggplot(disk_values_specific,
```{r disk_plots_mo_ab, message = FALSE, warning = FALSE}
ggplot(disk_values,
mo = "E. coli",
ab = "cipro",
guideline = "CLSI")