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Replace RSI with SIR

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This commit is contained in:
Dr. Matthijs Berends
2023-01-21 23:47:20 +01:00
committed by GitHub
parent 24b12024ce
commit 98e62c9af2
127 changed files with 1746 additions and 1648 deletions
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10
vignettes/resistance_predict.Rmd
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@ -80,13 +80,13 @@ plot(predict_TZP)
This is the fastest way to plot the result. It automatically adds the right axes, error bars, titles, number of available observations and type of model.
We also support the `ggplot2` package with our custom function `ggplot_rsi_predict()` to create more appealing plots:
We also support the `ggplot2` package with our custom function `ggplot_sir_predict()` to create more appealing plots:
```{r}
ggplot_rsi_predict(predict_TZP)
ggplot_sir_predict(predict_TZP)
# choose for error bars instead of a ribbon
ggplot_rsi_predict(predict_TZP, ribbon = FALSE)
ggplot_sir_predict(predict_TZP, ribbon = FALSE)
```
### Choosing the right model
@ -97,7 +97,7 @@ Resistance is not easily predicted; if we look at vancomycin resistance in Gram-
example_isolates %>%
filter(mo_gramstain(mo, language = NULL) == "Gram-positive") %>%
resistance_predict(col_ab = "VAN", year_min = 2010, info = FALSE, model = "binomial") %>%
ggplot_rsi_predict()
ggplot_sir_predict()
```
Vancomycin resistance could be 100% in ten years, but might remain very low.
@ -118,7 +118,7 @@ For the vancomycin resistance in Gram-positive bacteria, a linear model might be
example_isolates %>%
filter(mo_gramstain(mo, language = NULL) == "Gram-positive") %>%
resistance_predict(col_ab = "VAN", year_min = 2010, info = FALSE, model = "linear") %>%
ggplot_rsi_predict()
ggplot_sir_predict()
```
The model itself is also available from the object, as an `attribute`: