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dr. M.S. (Matthijs) Berends
2023-01-23 15:01:21 +01:00
parent af139a3c82
commit 19fd0ef121
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vignettes/AMR.Rmd
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@ -48,15 +48,16 @@ For this tutorial, we will create fake demonstration data to work with.
You can skip to [Cleaning the data](#cleaning-the-data) if you already have your own data ready. If you start your analysis, try to make the structure of your data generally look like this:
```{r example table, echo = FALSE, results = 'asis'}
knitr::kable(data.frame(
date = Sys.Date(),
patient_id = c("abcd", "abcd", "efgh"),
mo = "Escherichia coli",
AMX = c("S", "S", "R"),
CIP = c("S", "R", "S"),
stringsAsFactors = FALSE
),
align = "c"
knitr::kable(
data.frame(
date = Sys.Date(),
patient_id = c("abcd", "abcd", "efgh"),
mo = "Escherichia coli",
AMX = c("S", "S", "R"),
CIP = c("S", "R", "S"),
stringsAsFactors = FALSE
),
align = "c"
)
```
@ -129,14 +130,15 @@ sample_size <- 20000
data <- data.frame(
date = sample(dates, size = sample_size, replace = TRUE),
patient_id = sample(patients, size = sample_size, replace = TRUE),
hospital = sample(c(
"Hospital A",
"Hospital B",
"Hospital C",
"Hospital D"
),
size = sample_size, replace = TRUE,
prob = c(0.30, 0.35, 0.15, 0.20)
hospital = sample(
c(
"Hospital A",
"Hospital B",
"Hospital C",
"Hospital D"
),
size = sample_size, replace = TRUE,
prob = c(0.30, 0.35, 0.15, 0.20)
),
bacteria = sample(bacteria,
size = sample_size, replace = TRUE,
@ -293,10 +295,11 @@ data_1st %>%
```
```{r bug_drg 2b, echo = FALSE, results = 'asis'}
knitr::kable(data_1st %>%
filter(any(aminoglycosides() == "R")) %>%
head(),
align = "c"
knitr::kable(
data_1st %>%
filter(any(aminoglycosides() == "R")) %>%
head(),
align = "c"
)
```
@ -309,10 +312,11 @@ data_1st %>%
```
```{r bug_drg 1b, echo = FALSE, results = 'asis'}
knitr::kable(data_1st %>%
bug_drug_combinations() %>%
head(),
align = "c"
knitr::kable(
data_1st %>%
bug_drug_combinations() %>%
head(),
align = "c"
)
```
@ -325,10 +329,11 @@ data_1st %>%
```{r bug_drg 3b, echo = FALSE, results = 'asis'}
knitr::kable(data_1st %>%
select(bacteria, aminoglycosides()) %>%
bug_drug_combinations(),
align = "c"
knitr::kable(
data_1st %>%
select(bacteria, aminoglycosides()) %>%
bug_drug_combinations(),
align = "c"
)
```