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(v2.1.1.9186) replace antibiotics with antimicrobials!

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dr. M.S. (Matthijs) Berends
2025-03-07 20:43:26 +01:00
parent f2b2a450cb
commit f7938289eb
140 changed files with 4870 additions and 4702 deletions
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14
vignettes/datasets.Rmd
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@ -40,7 +40,7 @@ download_txt <- function(filename) {
msg <- paste0(
"It was last updated on ",
trimws(format(file.mtime(paste0("../data/", filename, ".rda")), "%e %B %Y %H:%M:%S %Z", tz = "UTC")),
". Find more info about the structure of this data set [here](https://msberends.github.io/AMR/reference/", ifelse(filename == "antivirals", "antibiotics", filename), ".html).\n"
". Find more info about the structure of this data set [here](https://msberends.github.io/AMR/reference/", ifelse(filename == "antivirals", "antimicrobials", filename), ".html).\n"
)
github_base <- "https://github.com/msberends/AMR/raw/main/data-raw/"
filename <- paste0("../data-raw/", filename)
@ -111,7 +111,7 @@ print_df <- function(x, rows = 6) {
}
```
All reference data (about microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) in this `AMR` package are reliable, up-to-date and freely available. We continually export our data sets to formats for use in R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. We also provide tab-separated text files that are machine-readable and suitable for input in any software program, such as laboratory information systems.
All reference data (about microorganisms, antimicrobials, SIR interpretation, EUCAST rules, etc.) in this `AMR` package are reliable, up-to-date and freely available. We continually export our data sets to formats for use in R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. We also provide tab-separated text files that are machine-readable and suitable for input in any software program, such as laboratory information systems.
On this page, we explain how to download them and how the structure of the data sets look like.
@ -158,13 +158,13 @@ microorganisms %>%
```
## `antibiotics`: Antibiotic (+Antifungal) Drugs
## `antimicrobials`: Antibiotic and Antifungal Drugs
`r structure_txt(antibiotics)`
`r structure_txt(antimicrobials)`
This data set is in R available as `antibiotics`, after you load the `AMR` package.
This data set is in R available as `antimicrobials`, after you load the `AMR` package.
`r download_txt("antibiotics")`
`r download_txt("antimicrobials")`
The tab-separated text, Microsoft Excel, SPSS, and Stata files all contain the ATC codes, common abbreviations, trade names and LOINC codes as comma separated values.
@ -180,7 +180,7 @@ This data set contains all EARS-Net and ATC codes gathered from WHO and WHONET,
### Example content
```{r, echo = FALSE}
antibiotics %>%
antimicrobials %>%
filter(ab %in% colnames(example_isolates)) %>%
print_df()
```