Retrieve antimicrobial drugs from clinical text — ab_from

Use this function on e.g. clinical texts from health care records. It returns a list with all antimicrobial drugs found in the texts.

ab_from_text(text, collapse = NULL, translate_ab = FALSE, ...)

Arguments

text	text to analyse
collapse	character to pass on to `paste(..., collapse = ...)` to only return one character per element of `text`, see Examples
translate_ab	a column name of the antibiotics data set to translate the antibiotic abbreviations to, using `ab_property()`. Defaults to `FALSE`. Using `TRUE` is equal to using "name".
...	parameters passed on to `as.ab()`

Value

A list, or a character if collapse is not NULL

Details

Without using collapse, this function will return a list. This can be convenient to use e.g. inside a mutate()):
df %>% mutate(abx = ab_from_text(clinical_text))

The returned AB codes can be transformed to official names, groups, etc. with all ab_property() functions like ab_name() and ab_group(), or by using the translate_ab parameter.

With using collapse, this function will return a character:
df %>% mutate(abx = ab_from_text(clinical_text, collapse = "|"))

This function is also internally used by as.ab(), although it then only returns the first hit and will throw a note if more results could have been returned.

Examples

# mind the bad spelling of amoxicillin in this line, 
# straight from a true health care record:
ab_from_text("28/03/2020 regular amoxicilliin 500mg po tds")

ab_from_text("administered amoxi/clav and cipro")
ab_from_text("administered amoxi/clav and cipro", collapse = ", ")

# if you want to know which antibiotic groups were administered, check it:
abx <- ab_from_text("administered amoxi/clav and cipro")
ab_group(abx[[1]])

if (require(dplyr)) {
  tibble(clinical_text = c("given cipro and mero",
                           "started on doxy today")) %>%
    mutate(abx = ab_from_text(clinical_text),
           abx2 = ab_from_text(clinical_text,
                               collapse = "|"),
           abx3 = ab_from_text(clinical_text,
                               collapse = "|",
                               translate_ab = "name"))

}