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new tibble export

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dr. M.S. (Matthijs) Berends
2022-08-27 20:49:37 +02:00
parent 164886f50b
commit 303d61b473
115 changed files with 836 additions and 996 deletions
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12
vignettes/AMR.Rmd
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@ -534,7 +534,7 @@ autoplot(disk_values,
## Independence test
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 practice AMR data analysis.
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 fosfomycin (column `FOS`) in hospital A and D. The input for the `fisher.test()` can be retrieved with a transformation like this:
@ -543,11 +543,11 @@ We will compare the resistance to fosfomycin (column `FOS`) in hospital A and D.
library(tidyr)
check_FOS <- example_isolates %>%
filter(hospital_id %in% c("A", "D")) %>% # filter on only hospitals A and D
select(hospital_id, FOS) %>% # select the hospitals and fosfomycin
group_by(hospital_id) %>% # group on the hospitals
count_df(combine_SI = TRUE) %>% # count all isolates per group (hospital_id)
pivot_wider(names_from = hospital_id, # transform output so A and D are columns
filter(ward %in% c("A", "D")) %>% # filter on only hospitals A and D
select(ward, FOS) %>% # select the hospitals and fosfomycin
group_by(ward) %>% # group on the hospitals
count_df(combine_SI = TRUE) %>% # count all isolates per group (ward)
pivot_wider(names_from = ward, # transform output so A and D are columns
values_from = value) %>%
select(A, D) %>% # and only select these columns
as.matrix() # transform to a good old matrix for fisher.test()

40
vignettes/datasets.Rmd
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@ -80,6 +80,7 @@ download_txt <- function(filename) {
print_df <- function(x, rows = 6) {
x %>%
as.data.frame(stringsAsFactors = FALSE) %>%
head(n = rows) %>%
mutate_all(function(x) {
if (is.list(x)) {
@ -285,3 +286,42 @@ Currently included dosages in the data set are meant for: `r AMR:::format_eucast
dosage %>%
print_df()
```
## `example_isolates`: Example Data for Practice
`r structure_txt(example_isolates)`
This data set is in R available as `example_isolates`, after you load the `AMR` package.
`r download_txt("example_isolates")`
### Source
This data set contains randomised fictitious data, but reflects reality and can be used to practise AMR data analysis.
### Example content
```{r, echo = FALSE}
example_isolates %>%
print_df()
```
## `example_isolates_unclean`: Example Data for Practice
`r structure_txt(example_isolates_unclean)`
This data set is in R available as `example_isolates_unclean`, after you load the `AMR` package.
`r download_txt("example_isolates_unclean")`
### Source
This data set contains randomised fictitious data, but reflects reality and can be used to practise AMR data analysis.
### Example content
```{r, echo = FALSE}
example_isolates_unclean %>%
print_df()
```