P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-12 12:21:58 +02:00
Code Releases Activity

knitr format

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2023-02-23 16:27:40 +01:00
parent a84101db08
commit e70f2cd32c
10 changed files with 236 additions and 257 deletions
Download Patch File Download Diff File Expand all files Collapse all files

36
data-raw/antibiograms.Rmd
View File

@ -22,41 +22,33 @@ example_isolates
### Traditional Antibiogram
```{r trad}
print(
antibiogram(example_isolates,
antibiotics = c(aminoglycosides(), carbapenems()))
)
antibiogram(example_isolates,
antibiotics = c(aminoglycosides(), carbapenems()))
```
### Combined Antibiogram
```{r comb}
print(
antibiogram(example_isolates,
antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"))
)
antibiogram(example_isolates,
antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"))
```
### Syndromic Antibiogram
```{r synd}
print(
antibiogram(example_isolates,
antibiotics = c(aminoglycosides(), carbapenems()),
syndromic_group = "ward")
)
antibiogram(example_isolates,
antibiotics = c(aminoglycosides(), carbapenems()),
syndromic_group = "ward")
```
### Weighted-Incidence Syndromic Combination Antibiogram (WISCA)
```{r wisca}
print(
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"))
)
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"))
```