AMR/reference/av_from_text.md

Retrieve Antiviral Drug Names and Doses from Clinical Text

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 "drug", "dose" or "administration", see Examples.

• collapse:

  A character to pass on to paste(, collapse = ...) to only return one character per element of text, see Examples.

• translate_av:

  If type = "drug": a column name of the antivirals data set to translate the antibiotic abbreviations to, using av_property(). The default is FALSE. Using TRUE is equal to using "name".

• thorough_search:

  A logical to indicate whether the input must be extensively searched for misspelling and other faulty input values. Setting this to TRUE will take considerably more time than when using FALSE. At default, it will turn TRUE when all input elements contain a maximum of three words.

• info:

  A logical to indicate whether a progress bar should be printed - the default is TRUE only in interactive mode.

• ...:

  Arguments passed on to as.av().

Value

A list, or a character if collapse is not NULL

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 = "|"))

Examples

av_from_text("28/03/2020 valaciclovir po tid")
#> [[1]]
#> Class 'av'
#> [1] VALA
#> 
av_from_text("28/03/2020 valaciclovir po tid", type = "admin")
#> [[1]]
#> [1] "oral"
#>