| Type: | Package |
| Title: | Extract Drug Dosages from Free-Text Prescriptions |
| Version: | 0.1.2 |
| Description: | Utilities for converting unstructured electronic prescribing instructions into structured medication data. Extracts drug dose, units, daily dosing frequency and intervals from English-language prescriptions. Based on Karystianis et al. (2015) <doi:10.1186/s12911-016-0255-x>. |
| BugReports: | https://github.com/Selbosh/doseminer/issues |
| License: | MIT + file LICENSE |
| Encoding: | UTF-8 |
| LazyData: | true |
| Imports: | magrittr(≥ 2.0.1), stringr(≥ 1.4.0) |
| Suggests: | rmarkdown, knitr, testthat, tidyr, dplyr, ggplot2, prettydoc |
| RoxygenNote: | 7.1.1 |
| Depends: | R (≥ 3.5.0) |
| VignetteBuilder: | knitr |
| Language: | en-GB |
| NeedsCompilation: | no |
| Packaged: | 2021-07-19 10:27:42 UTC; David |
| Author: | David Selby  [aut,
cre],
Belay Birlie Yimer [ctb],
Ben Marwick [ctb] |
| Maintainer: | David Selby <david.selby@manchester.ac.uk> |
| Repository: | CRAN |
| Date/Publication: | 2021-07-19 10:40:05 UTC |
doseminer: Extract Drug Dosages from Free-Text Prescriptions
Description
Utilities for converting unstructured electronic prescribing instructions into structured medication data. Extracts drug dose, units, daily dosing frequency and intervals from English-language prescriptions. Based on Karystianis et al. (2015) <doi:10.1186/s12911-016-0255-x>.
Author(s)
Maintainer: David Selby david.selby@manchester.ac.uk (ORCID)
Other contributors:
Belay Birlie Yimer belaybirlie.yimer@manchester.ac.uk [contributor]
Ben Marwick benmarwick@gmail.com [contributor]
See Also
Useful links:
Report bugs at https://github.com/Selbosh/doseminer/issues
Clean up raw prescription freetext
Description
Clean up raw prescription freetext
Usage
clean_prescription_text(txt)
Arguments
txt |
a character vector |
Value
a character vector the same length as txt
Examples
clean_prescription_text(example_prescriptions)
Sample electronic prescribing dataset
Description
A dataset containing product codes, patient identifiers, quantities, dates and free-text dose instructions, similar to data provided by the Clinical Practice Research Datalink (CPRD).
Usage
cprd
Format
An object of class data.frame with 714 rows and 6 columns.
Details
Variables in the data include
- id
record identifier
- patid
patient identifier
- date
date of start of prescription
- prodcode
product code; identifier for the prescribed medication
- qty
total quantity of medication prescribed
- text
free text prescribing instructions
Medication dosage units
Description
A named character vector. Names represent patterns to match dose units and values represent standardised names for those units.
Usage
drug_units
Format
An object of class character of length 28.
Details
Use with a function like str_replace_all
to standardise a freetext prescription. Used internally in
extract_from_prescription.
Example freetext prescriptions
Description
Adapted from CPRD common dosages
Usage
example_cprd
Format
An object of class character of length 28.
See Also
Example freetext prescriptions
Description
Various examples of how prescription data may be represented in free text.
Usage
example_prescriptions
Format
An object of class character of length 27.
See Also
Extract units of dose from freetext prescriptions.
Description
A function used internally in extract_from_prescription to
parse the dosage units, such as millilitres, tablets, grams and so on.
If there are multiple units mentioned in a string, only the first is returned.
Usage
extract_dose_unit(txt)
Arguments
txt |
a character vector |
Value
A character vector the same length as txt, containing
standardised units, or NA if no units were found in the prescription.
A simple wrapper around str_replace_all and
str_extract.
Based on add_dose_unit.py from original Python/Java algorithm.
See Also
Extract dosage information from free-text English-language prescriptions
Description
This is the main workhorse function for the doseminer package.
Pass in a character vector of prescribing instructions and it will extract
structured dosage information.
Usage
extract_from_prescription(txt)
Arguments
txt |
A character vector of freetext prescriptions |
Details
To avoid redundant computation, it is recommended to remove duplicate
elements from the input vector. The results can be joined back to the
original data using the raw column.
Value
A data.frame with seven columns:
- raw
the input character vector
- output
a residual character vector of 'non-extracted' text. For debugging.
- freq
number of doses administered per day
- itvl
number of days between doses
- dose
quantity of medication in each dose
- unit
unit of measurement of medication, if any
- optional
integer. Can the dose be zero? 1 if yes, otherwise 0
Examples
extract_from_prescription(example_prescriptions)
Convert hourly to daily frequency
Description
Convert hourly to daily frequency
Usage
hourly_to_daily(txt)
Arguments
txt |
String of the form 'every n hours' |
Value
An equivalent string of the form 'x / day'
List of Latin medical and pharmaceutical abbreviations
Description
A named character vector. Names represent Latin terms and values the English translations. Used for converting terms like "q4h" into "every 4 hours", which can then be parsed into a dosage frequency/interval.
Usage
latin_medical_terms
Format
An object of class character of length 47.
Details
Use with a function like str_replace_all
to translate a prescription from Latin to English (thence to numbers).
Source
https://en.wikipedia.org/wiki/List_of_abbreviations_used_in_medical_prescriptions
Examples
stringr::str_replace_all('Take two tablets q4h', latin_medical_terms)
Evaluate a multiplicative plaintext expression
Description
Replaces written phrases like "2 x 5" with their arithmetic result (i.e. 10)
Usage
multiply_dose(axb)
Arguments
axb |
An string expression of the form 'A x B' where A, B are numeric |
Value
An equivalent string giving the product of A and B.
If A is a range of values, a range of values is returned.
See Also
Used internally within extract_from_prescription
Dictionary of English names of numbers
Description
For internal use in words2number. When passed as a replacement
to a function like
str_replace_all, it turns the
string into an arithmetic expression that can be evaluated to give an integer
representation of the named number.
Usage
numb_replacements
Format
An object of class character of length 49.
Details
Lifted from Ben Marwick's words2number package and converted into
a named vector (previously a chain of gsub calls).
Note
Does not yet fully support decimals, fractions or mixed fractions. Some limited support for 'half' expressions, e.g. 'one and a half'.
Source
https://github.com/benmarwick/words2number
Examples
## Not run:
stringr::str_replace_all('one hundred and forty-two', numb_replacements)
## End(Not run)
Regular expression to match numbers in English
Description
A regex pattern to identify natural language English number phrases, such as
"one hundred and fifty" or "thirty-seven". Used internally by
replace_numbers to identify substrings to replace with their
decimal representation.
Usage
regex_numbers
Format
An object of class character of length 1.
Details
This is a PCRE (Perl type) regular expression, so it must be used with
perl = TRUE in base R regex functions. The packages stringr
and stringi are based on the alternative ICU regular expression
engine, so they cannot use this pattern.
Note
There is limited support for fractional expressions like "one half". The original pattern did not support expressions like "a thousand", but it has been adapted to offer (experimental) support for this. Phrases like "million" or "thousand" with no prefix will not match.
Source
https://www.rexegg.com/regex-trick-numbers-in-english.html
Replace English number phrases with their decimal representations
Description
Uses numb_replacements to match parts of a string corresponding
to numbers, then invokes words2number to convert these
substrings to numeric. The rest of the string (the non-number words) is
left intact.
Usage
replace_numbers(string)
Arguments
string |
A character vector. Can contain numbers and other text |
Details
Works on non-negative integer numbers under one billion (one thousand million). Does not support fractions or decimals (yet).
Value
A character vector the same length as string, with words
replaced by their decimal representations.
See Also
words2number, for use on cleaned text that does not contain
any non-number words
Examples
replace_numbers('Two plus two equals four')
replace_numbers('one hundred thousand dollars!')
replace_numbers(c('A vector', 'containing numbers', 'like thirty seven'))
Convert weekly interval to daily interval
Description
Convert weekly interval to daily interval
Usage
weekly_to_daily(Dperweek)
Arguments
Dperweek |
String of the form 'n / week' |
Value
An equivalent string of the form 'x / day'
Convert English names of numbers to their numerical values
Description
Convert English names of numbers to their numerical values
Usage
words2number(txt)
Arguments
txt |
A character vector containing names of numbers (only). |
Value
A named numeric vector of the same length as phrase.
Source
Originally adapted from the
words2number package by
Ben Marwick.
Examples
words2number('seven')
words2number('forty-two')
words2number(c('three', 'one', 'twenty two thousand'))