Retrieve Antiviral Drug Names and Doses from Clinical TextSource:
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.
av_from_text( text, type = c("drug", "dose", "administration"), collapse = NULL, translate_av = FALSE, thorough_search = NULL, info = interactive(), ... )
text to analyse
type of property to search for, either
"administration", see Examples
a character to pass on to
paste(, collapse = ...)to only return one character per element of
text, see Examples
type = "drug": a column name of the antivirals data set to translate the antibiotic abbreviations to, using
av_property(). The default is
TRUEis equal to using "name".
a logical to indicate whether the input must be extensively searched for misspelling and other faulty input values. Setting this to
TRUEwill take considerably more time than when using
FALSE. At default, it will turn
TRUEwhen all input elements contain a maximum of three words.
a logical to indicate whether a progress bar should be printed - the default is
TRUEonly in interactive mode
arguments passed on to
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.
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.
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.
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.
collapse, this function will return a list. This can be convenient to use e.g. inside a
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_group(), or by using the
collapse, this function will return a character:
df %>% mutate(avx = av_from_text(clinical_text, collapse = "|"))