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