extractMed | R Documentation |
This function is an interface to the medExtractR
function
within the medExtractR package, and allows drug dosing information to be extracted
from free-text sources, e.g., clinical notes.
extractMed(note_fn, drugnames, drgunit, windowlength, max_edit_dist = 0, ...)
note_fn |
File name(s) for the text file(s) containing the clinical notes. Can be a character string for an individual note, or a vector or list of file names for multiple notes. |
drugnames |
Vector of drug names for which dosing information should be extracted. Can include various forms (e.g., generic, brand name) as well as abbreviations. |
drgunit |
Unit of the drug being extracted, e.g., 'mg' |
windowlength |
Length of the search window (in characters) around the drug name in which to search for dosing entities |
max_edit_dist |
Maximum edit distance allowed when attempting to extract |
... |
Additional arguments to |
Medication information, including dosing data, is often stored in free-text sources such as
clinical notes. The extractMed
function serves as a convenient wrapper for the
medExtractR package, a natural language processing system written in R for extracting
medication data. Within extractMed
, the medExtractR
function
identifies dosing data for drug(s) of interest, specified by the drugnames
argument,
using rule-based and dictionary-based approaches. Relevant dosing entities include medication
strength (identified using the unit
argument), dose amount, dose given intake, intake
time or frequency of dose, dose change keywords (e.g., 'increase' or 'decrease'), and time of
last dose. After applying medExtractR
to extract drug dosing information, extractMed
appends the file name to results to ensure
they are appropriately labeled.
See EHR Vignette for for Extract-Med and Pro-Med-NLP. For more details, see Weeks, et al. 2020.
A data.frame with the extracted dosing information, labeled with file name as an identifier
Sample output:
filename | entity | expr | pos |
note_file1.txt | DoseChange | decrease | 66:74 |
note_file1.txt | DrugName | Prograf | 78:85 |
note_file1.txt | Strength | 2 mg | 86:90 |
note_file1.txt | DoseAmt | 1 | 91:92 |
note_file1.txt | Frequency | bid | 101:104 |
note_file1.txt | LastDose | 2100 | 121:125 |
tac_fn <- list(system.file("examples", "tacpid1_2008-06-26_note1_1.txt", package = "EHR"), system.file("examples", "tacpid1_2008-06-26_note2_1.txt", package = "EHR"), system.file("examples", "tacpid1_2008-12-16_note3_1.txt", package = "EHR")) extractMed(tac_fn, drugnames = c("tacrolimus", "prograf", "tac", "tacro", "fk", "fk506"), drgunit = "mg", windowlength = 60, max_edit_dist = 2, lastdose=TRUE)
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