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Replace RSI with SIR

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This commit is contained in:
Dr. Matthijs Berends
2023-01-21 23:47:20 +01:00
committed by GitHub
parent 24b12024ce
commit 98e62c9af2
127 changed files with 1746 additions and 1648 deletions
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12
vignettes/WHONET.Rmd
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@ -48,15 +48,15 @@ library(cleaner) # to create frequency tables
We will have to transform some variables to simplify and automate the analysis:
* Microorganisms should be transformed to our own microorganism codes (called an `mo`) using [our Catalogue of Life reference data set](https://msberends.github.io/AMR/reference/catalogue_of_life), which contains all ~70,000 microorganisms from the taxonomic kingdoms Bacteria, Fungi and Protozoa. We do the tranformation with `as.mo()`. This function also recognises almost all WHONET abbreviations of microorganisms.
* Antimicrobial results or interpretations have to be clean and valid. In other words, they should only contain values `"S"`, `"I"` or `"R"`. That is exactly where the `as.rsi()` function is for.
* Antimicrobial results or interpretations have to be clean and valid. In other words, they should only contain values `"S"`, `"I"` or `"R"`. That is exactly where the `as.sir()` function is for.
```{r}
# transform variables
data <- WHONET %>%
# get microbial ID based on given organism
mutate(mo = as.mo(Organism)) %>%
# transform everything from "AMP_ND10" to "CIP_EE" to the new `rsi` class
mutate_at(vars(AMP_ND10:CIP_EE), as.rsi)
# transform everything from "AMP_ND10" to "CIP_EE" to the new `sir` class
mutate_at(vars(AMP_ND10:CIP_EE), as.sir)
```
No errors or warnings, so all values are transformed succesfully.
@ -77,13 +77,13 @@ data %>% freq(AMC_ND2)
### A first glimpse at results
An easy `ggplot` will already give a lot of information, using the included `ggplot_rsi()` function:
An easy `ggplot` will already give a lot of information, using the included `ggplot_sir()` function:
```{r, eval = FALSE}
data %>%
group_by(Country) %>%
select(Country, AMP_ND2, AMC_ED20, CAZ_ED10, CIP_ED5) %>%
ggplot_rsi(translate_ab = "ab", facet = "Country", datalabels = FALSE)
ggplot_sir(translate_ab = "ab", facet = "Country", datalabels = FALSE)
```
```{r, echo = FALSE}
@ -91,7 +91,7 @@ data %>%
tryCatch(data %>%
group_by(Country) %>%
select(Country, AMP_ND2, AMC_ED20, CAZ_ED10, CIP_ED5) %>%
ggplot_rsi(translate_ab = "ab", facet = "Country", datalabels = FALSE) %>%
ggplot_sir(translate_ab = "ab", facet = "Country", datalabels = FALSE) %>%
print(),
error = function(e) base::invisible()
)