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dr. M.S. (Matthijs) Berends
2023-02-18 11:57:17 +01:00
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vignettes/AMR.Rmd
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@ -1,7 +1,5 @@
---
title: "How to conduct AMR data analysis"
author: "Dr. Matthijs Berends"
date: '`r format(Sys.Date(), "%d %B %Y")`'
output:
rmarkdown::html_vignette:
toc: true
@ -18,7 +16,7 @@ editor_options:
knitr::opts_chunk$set(
warning = FALSE,
collapse = TRUE,
comment = "#",
comment = "#>",
fig.width = 7.5,
fig.height = 5
)
@ -586,13 +584,13 @@ autoplot(
The next example uses the `example_isolates` data set. This is a data set included with this package and contains 2,000 microbial isolates with their full antibiograms. It reflects reality and can be used to practise AMR data analysis.
We will compare the resistance to amoxicillin/clavulanic acid (column `FOS`) between an ICU and other clinical wards. The input for the `fisher.test()` can be retrieved with a transformation like this:
We will compare the resistance to amoxicillin/clavulanic acid (column `AMC`) between an ICU and other clinical wards. The input for the `fisher.test()` can be retrieved with a transformation like this:
```{r, results = 'markup'}
# use package 'tidyr' to pivot data:
library(tidyr)
check_FOS <- example_isolates %>%
check_AMC <- example_isolates %>%
filter(ward %in% c("ICU", "Clinical")) %>% # filter on only these wards
select(ward, AMC) %>% # select the wards and amoxi/clav
group_by(ward) %>% # group on the wards
@ -604,14 +602,18 @@ check_FOS <- example_isolates %>%
select(ICU, Clinical) %>% # and only select these columns
as.matrix() # transform to a good old matrix for fisher.test()
check_FOS
check_AMC
```
We can apply the test now with:
```{r}
# do Fisher's Exact Test
fisher.test(check_FOS)
fisher.test(check_AMC)
```
As can be seen, the p value is practically zero (`r format(fisher.test(check_FOS)$p.value, scientific = FALSE)`), which means that the amoxicillin/clavulanic acid resistance found in isolates between patients in ICUs and other clinical wards are really different.
As can be seen, the p value is practically zero (`r format(fisher.test(check_AMC)$p.value, scientific = FALSE)`), which means that the amoxicillin/clavulanic acid resistance found in isolates between patients in ICUs and other clinical wards are really different.
----
*Author: Dr. Matthijs Berends*