av_from_text {AMR} | R Documentation |
Retrieve Antiviral Drug Names and Doses from Clinical Text
Description
Use this function on e.g. clinical texts from health care records. It returns a list with all antiviral drugs, doses and forms of administration found in the texts.
Usage
av_from_text(
text,
type = c("drug", "dose", "administration"),
collapse = NULL,
translate_av = FALSE,
thorough_search = NULL,
info = interactive(),
...
)
Arguments
text |
text to analyse |
type |
type of property to search for, either |
collapse |
a character to pass on to |
translate_av |
if |
thorough_search |
a logical to indicate whether the input must be extensively searched for misspelling and other faulty input values. Setting this to |
info |
a logical to indicate whether a progress bar should be printed - the default is |
... |
arguments passed on to |
Details
This function is also internally used by as.av()
, although it then only searches for the first drug name and will throw a note if more drug names could have been returned. Note: the as.av()
function may use very long regular expression to match brand names of antiviral drugs. This may fail on some systems.
Argument type
At default, the function will search for antiviral drug names. All text elements will be searched for official names, ATC codes and brand names. As it uses as.av()
internally, it will correct for misspelling.
With type = "dose"
(or similar, like "dosing", "doses"), all text elements will be searched for numeric values that are higher than 100 and do not resemble years. The output will be numeric. It supports any unit (g, mg, IE, etc.) and multiple values in one clinical text, see Examples.
With type = "administration"
(or abbreviations, like "admin", "adm"), all text elements will be searched for a form of drug administration. It supports the following forms (including common abbreviations): buccal, implant, inhalation, instillation, intravenous, nasal, oral, parenteral, rectal, sublingual, transdermal and vaginal. Abbreviations for oral (such as 'po', 'per os') will become "oral", all values for intravenous (such as 'iv', 'intraven') will become "iv". It supports multiple values in one clinical text, see Examples.
Argument collapse
Without using collapse
, this function will return a list. This can be convenient to use e.g. inside a mutate()
):
df %>% mutate(avx = av_from_text(clinical_text))
The returned AV codes can be transformed to official names, groups, etc. with all av_*
functions such as av_name()
and av_group()
, or by using the translate_av
argument.
With using collapse
, this function will return a character:
df %>% mutate(avx = av_from_text(clinical_text, collapse = "|"))
Value
A list, or a character if collapse
is not NULL
Examples
av_from_text("28/03/2020 valaciclovir po tid")
av_from_text("28/03/2020 valaciclovir po tid", type = "admin")