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(v2.1.1.9157) improved as.ab(), fixed knit_print of antibiogram

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dr. M.S. (Matthijs) Berends
2025-02-26 13:27:20 +01:00
parent b10989f431
commit 195dfb4b91
20 changed files with 107 additions and 42 deletions
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5
vignettes/AMR_with_tidymodels.Rmd
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@ -45,9 +45,6 @@ We begin by loading the required libraries and preparing the `example_isolates`
library(tidymodels) # For machine learning workflows, and data manipulation (dplyr, tidyr, ...)
library(AMR) # For AMR data analysis
# Load the example_isolates dataset
data("example_isolates") # Preloaded dataset with AMR results
# Select relevant columns for prediction
data <- example_isolates %>%
# select AB results dynamically
@ -168,7 +165,7 @@ metrics
- `predict()` generates predictions on the testing set.
- `metrics()` computes evaluation metrics like accuracy and kappa.
It appears we can predict the Gram based on AMR results with a `r round(metrics$.estimate[1], 3)` accuracy based on AMR results of aminoglycosides and beta-lactam antibiotics. The ROC curve looks like this:
It appears we can predict the Gram based on AMR results with a `r round(metrics$.estimate[1], 3) * 100`% accuracy based on AMR results of aminoglycosides and beta-lactam antibiotics. The ROC curve looks like this:
```{r}
predictions %>%