{"Package":"doseminer","Type":"Package","Title":"Extract Drug Dosages from Free-Text Prescriptions","Version":"0.1.2","Authors@R":"\nc(person(given = 'David',\nfamily = 'Selby',\nrole = c('aut', 'cre'),\nemail = 'david.selby@manchester.ac.uk',\ncomment = c(ORCID = '0000-0001-8026-5663')),\nperson(given = 'Belay Birlie',\nfamily = 'Yimer',\nemail = 'belaybirlie.yimer@manchester.ac.uk',\nrole = 'ctb'),\nperson(given = 'Ben',\nfamily = 'Marwick',\nemail = 'benmarwick@gmail.com',\nrole = 'ctb'))","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) .","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] (),\nBelay Birlie Yimer [ctb],\nBen Marwick [ctb]","Maintainer":"David Selby ","Repository":"CRAN","Date/Publication":"2021-07-19 10:40:05 UTC","repoType":"cran","tarballUrl":"ftp://cran.r-project.org/pub/R/src/contrib/doseminer_0.1.2.tar.gz","jsonAuthors":[{"name":"David Selby","email":"david.selby@manchester.ac.uk","maintainer":true},{"name":"Belay Birlie Yimer","email":"belaybirlie.yimer@manchester.ac.uk","maintainer":false},{"name":"Ben Marwick","email":"benmarwick@gmail.com","maintainer":false}],"readme":"R package doseminer\n================\nDavid Selby and Belay Birlie\n\n\n\n\nAn R implementation of the text mining algorithm of [Karystianis et\nal. (2015)](https://doi.org/10.1186/s12911-016-0255-x) for extracting\ndrug dosage information from electronic prescription data (especially\nfrom CPRD). The aim of this project is to provide a complete replacement\nfor the algorithm, entirely written in R with no external dependencies\n(unlike the original implementation, which depended on Python and Java).\nThis should make the tool more portable, extensible and suitable for use\nacross different platforms (Windows, Mac, Unix).\n\n## Installation\n\nYou can install **doseminer** from CRAN using\n\n``` r\ninstall.packages('doseminer')\n```\n\nor get the latest development version via GitHub:\n\n``` r\n# install.packages('remotes')\nremotes::install_github('Selbosh/doseminer')\n```\n\n## Usage\n\nThe workhorse function is called `extract_from_prescription`. Pass it a\ncharacter vector of freetext prescriptions and it will try to extract\nthe following variables:\n\n- Dose frequency (the number of times per day a dose is administered)\n- Dose interval (the number of days between doses)\n- Dose unit (how individual doses are measured, e.g. millilitres,\n tablets)\n- Dose number (how many of those units comprise a single dose, e.g. 2\n tablets)\n- Optional (should the dose only be taken ‘if required’ / ‘as\n needed’?)\n\n``` r\nlibrary(doseminer)\nextract_from_prescription('take two and a half tablets every two to three days as needed')\n```\n\n

\n\n| raw | output | freq | itvl | dose | unit | optional |\n|:--------------------------------------------------------------|:--------|:-----|:-----|:-----|:-----|---------:|\n| take two and a half tablets every two to three days as needed | 2.5 tab | 1 | 2-3 | 2.5 | tab | 1 |\n\n

\n\nAnything not matched is returned as `NA`, though some inferences are\nalso made. For instance: if a dosage is specified as multiple times per\nday, with no explicit interval between days, it’s inferred the interval\nis one day. Similarly, if an interval is specified (e.g. every 3 days)\nbut not a daily frequency, it’s presumed the dose is taken only once\nduring the day.\n\nTo see the package in action, a small vector of example prescriptions is\nincluded in the variable `example_prescriptions`.\n\n``` r\nextract_from_prescription(example_prescriptions)\n```\n\n

\n\n| raw | output | freq | itvl | dose | unit | optional |\n|:--------------------------------------------------------------|:-----------------------------------------|:-----|:-----|:-----|:------------|---------:|\n| 1 tablet to be taken daily | 1 tab to be taken | 1 | 1 | 1 | tab | 0 |\n| 2.5ml four times a day when required | 2.5 ml | 4 | 1 | 2.5 | ml | 1 |\n| 1.25mls three times a day | 1.25 ml | 3 | 1 | 1.25 | ml | 0 |\n| take 10mls q.d.s. p.r.n. | 10 ml | 1 | 1 | 10 | ml | 1 |\n| take 1 or 2 4 times/day | 1 - 2 | 4 | 1 | 1-2 | NA | 0 |\n| 2x5ml spoon 4 times/day | 2 x 5 ml spoonful | 4 | 1 | 10 | ml spoonful | 0 |\n| take 2 tablets every six hours max eight in twenty four hours | 2 tab 0 - 8 in 24 hours | 4 | 1 | 2 | tab | 0 |\n| 1 tab nocte twenty eight tablets | 1 tab 28 tab | 1 | 1 | 1 | tab | 0 |\n| 1-2 four times a day when required | 1 - 2 | 4 | 1 | 1-2 | NA | 1 |\n| take one twice daily | 1 | 2 | 1 | 1 | NA | 0 |\n| 1 q4h prn | 1 | 6 | 1 | 1 | NA | 1 |\n| take two every three days | 2 | 1 | 3 | 2 | NA | 0 |\n| five every week | 5 | 1 | 7 | 5 | NA | 0 |\n| every 72 hours | | 1 | 3 | NA | NA | 0 |\n| 1 x 5 ml spoon 4 / day for 10 days | 1 x 5 ml spoonful for 10 days | 4 | 1 | 5 | ml spoonful | 0 |\n| two to three times a day | | 2-3 | 1 | NA | NA | 0 |\n| three times a week | | 1 | 2-3 | NA | NA | 0 |\n| three 5ml spoonsful to be taken four times a day after food | 3 x 5 ml spoonful to be taken after food | 4 | 1 | 15 | ml spoonful | 0 |\n| take one or two every 4-6 hrs | 1 - 2 | 4-6 | 1 | 1-2 | NA | 0 |\n| 5ml 3 hrly when required | 5 ml | 8 | 1 | 5 | ml | 1 |\n| one every morning to reduce bp | 1 to reduce bp | 1 | 1 | 1 | NA | 0 |\n| take 1 or 2 6hrly when required | 1 - 2 | 4 | 1 | 1-2 | NA | 1 |\n| take 1 or 2 four times a day as required for pain | 1 - 2 for pain | 4 | 1 | 1-2 | NA | 1 |\n| take 1 or 2 4 times/day if needed for pain | 1 - 2 for pain | 4 | 1 | 1-2 | NA | 1 |\n| 1-2 tablets up to four times daily | 1 - 2 tab | 0-4 | 1 | 1-2 | tab | 1 |\n| take one or two tablets 6-8 hrly every 2-3 days | 1 - 2 tab | 3-4 | 2-3 | 1-2 | tab | 0 |\n| one and a half tablets every three hours | 1.5 tab | 8 | 1 | 1.5 | tab | 0 |\n\n

\n\nThe column `output` represents the ‘residual’ text after other features\nhave been extracted. It can be ignored for most applications, but is\nuseful for debugging prescriptions that have not been parsed as\nexpected.\n\n## English words to numbers\n\nBuilt into this package is a series of functions for extracting and\nparsing natural language English numbers into their digit-based numeric\nform. This could be spun out into its own package for more general use.\n\n``` r\nreplace_numbers(c('Thirty seven bottles of beer on the wall',\n 'Take one down, pass it around',\n 'Thirty-six bottles of beer on the wall!',\n 'One MILLION dollars.',\n 'We do not take any half measures'))\n```\n\n ## [1] \"37 bottles of beer on the wall\" \"Take 1 down, pass it around\" \n ## [3] \"36 bottles of beer on the wall!\" \"1e+06 dollars.\" \n ## [5] \"We do not take any 0.5 measures\"\n\nInspired by Ben Marwick’s `words2number`\n().\n\n## Contributors\n\nMaintained by David Selby (`david.selby@manchester.ac.uk`) and Belay\nBirlie.\n\n## References\n\nKarystianis, G., Sheppard, T., Dixon, W.G. *et al.* Modelling and\nextraction of variability in free-text medication prescriptions from an\nanonymised primary care electronic medical record research database.\n*BMC Med Inform Decis Mak* **16**, 18 (2015). \n","jobInfo":{"package":"doseminer","version":"0.1.2","parsingStatus":"success","parserVersion":1,"parsedAt":"2021-07-19T13:30:42+0000"}}

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