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@ -10,6 +10,8 @@ This R package contains functions to make microbiological, epidemiological data
AMR can also be predicted for the forthcoming years with the `rsi_predict` function. For use with the `dplyr` package, the `rsi` function can be used in conjunction with `summarise` to calculate the resistance percentages of different antibiotic columns of a table. AMR can also be predicted for the forthcoming years with the `rsi_predict` function. For use with the `dplyr` package, the `rsi` function can be used in conjunction with `summarise` to calculate the resistance percentages of different antibiotic columns of a table.
It also contains functions to translate antibiotic codes from the lab (like `"AMOX"`) or the [WHO](https://www.whocc.no/atc_ddd_index/?code=J01CA04&showdescription=no) (like `"J01CA04"`) to trivial names (like `"amoxicillin"`) and vice versa.
## How to use it? ## How to use it?
```r ```r
# Call it with: # Call it with:
@ -73,7 +75,7 @@ Other epidemiological functions:
```r ```r
# Apply EUCAST Expert Rules v3.1 (latest) to antibiotic columns # Apply EUCAST Expert Rules v3.1 (latest) to antibiotic columns
interpretive_reading(...) EUCAST_rules(...)
# Determine key antibiotic based on bacteria ID # Determine key antibiotic based on bacteria ID
key_antibiotics(...) key_antibiotics(...)
@ -91,11 +93,6 @@ rsi_predict(...)
# Get name of antibiotic by ATC code # Get name of antibiotic by ATC code
abname(...) abname(...)
abname("J01CR02", from = "atc", to = "umcg") # "AMCL" abname("J01CR02", from = "atc", to = "umcg") # "AMCL"
# Calculate age of patients
age(...)
# Categorize patients age to age groups
age.group(...)
``` ```
## How to get it? ## How to get it?