AMR/data-raw/antibiograms.Rmd

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---
title: "Generating antibiograms with the AMR package"
author: "AMR package developers"
date: "`r Sys.Date()`"
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output: pdf_document
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---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE, message = FALSE)
library(AMR)
```
This is an example R Markdown file to show the use of `antibiogram()` of the AMR package.
For starters, this is what our `example_isolates` data set looks like:
```{r}
example_isolates
```
### Traditional Antibiogram
```{r trad}
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antibiogram(example_isolates,
antibiotics = c(aminoglycosides(), carbapenems()))
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```
### Combined Antibiogram
```{r comb}
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antibiogram(example_isolates,
antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"))
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```
### Syndromic Antibiogram
```{r synd}
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antibiogram(example_isolates,
antibiotics = c(aminoglycosides(), carbapenems()),
syndromic_group = "ward")
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```
### Weighted-Incidence Syndromic Combination Antibiogram (WISCA)
```{r wisca}
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antibiogram(example_isolates,
antibiotics = c("AMC", "AMC+CIP", "TZP", "TZP+TOB"),
mo_transform = "gramstain",
minimum = 10, # this should be >= 30, but now just as example
syndromic_group = ifelse(example_isolates$age >= 65 &
example_isolates$gender == "M",
"WISCA Group 1", "WISCA Group 2"))
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```