medExtractR_tapering {medExtractR}

Extract Medication Entities From Clinical Note - Extension of medExtractR for Tapering applications

Description

This function identifies medication entities of interest and returns found expressions with start and stop positions.

Usage

medExtractR_tapering(
  note,
  drug_names,
  unit,
  max_dist = 0,
  drug_list = "rxnorm",
  lastdose = FALSE,
  strength_sep = NULL,
  ...
)

Arguments

note

Text to search.

drug_names

Vector of drug names of interest to locate.

unit

Strength unit to look for (e.g., ‘mg’).

max_dist

Numeric - edit distance to use when searching for drug_names.

drug_list

Vector of known drugs that may end search window. By default calls rxnorm_druglist. Can be supplemented with expressions in addl_expr.

lastdose

Logical - whether or not last dose time entity should be extracted. See ‘Details’ section below for more information.

strength_sep

Delimiter for contiguous medication strengths (e.g., ‘-’ for “LTG 200-300”).

...

Parameter settings used in dictionary-based entities. For each dictionary-based entity, the user can supply the optional arguments <entity>_fun and <entity>_dict to provide custom extraction functions and dictionaries, respectively. If no additional arguments are provided, medExtractR_tapering will use extract_generic and the default dictionary for each entity. See extract_entities_tapering documentation for details.

Details

This function uses a combination of regular expressions, rule-based approaches, and dictionaries to identify various drug entities of interest, with a particular focus on drugs administered with a tapering schedule. Specific medications to be found are specified with drug_names, which is not case-sensitive or space-sensitive (e.g., ‘lamotrigine XR’ is treated the same as ‘lamotrigineXR’). Entities to be extracted include drug name, strength, dose amount, dose strength, frequency, intake time, route, duration, dose schedule, time keyword, preposition, transition, dispense amount, refill, and time of last dose. While it is still an optional entity in medExtractR_tapering, if lastdose=TRUE then medExtractR_tapering will search for time of last dose in the same search window used for all other entities. As a result, there is no need for the lastdose_window_ext argument. See extract_entities_tapering and extract_lastdose for more details.

When searching for medication names of interest, fuzzy matching may be used. The max_dist argument determines the maximum edit distance allowed for such matches. If using fuzzy matching, any drug name with less than 7 characters will force an exact match, regardless of the value of max_dist. The default value of 7 was selected based on a set of training notes for the drug prednisone, and differs slightly from the default values of 5 for medExtractR. The tapering extension does not use the window_length argument to define the search window, since tapering schedules can be much longer than a static regimens. Instead, medExtractR_tapering dynamically generates the search window based on competing drug names or phrases, and the distance between consecutive entities. The stength_sep argument is NULL by default, and operates in the same manner as it does in medExtractR.

By default, the drug_list argument is “rxnorm” which calls data(rxnorm_druglist). A custom drug list in the form of a character string can be supplied instead, or can be appended to rxnorm_druglist by specifying drug_list = c("rxnorm", custom_drug_list). This uses publicly available data courtesy of the U.S. National Library of Medicine (NLM), National Institutes of Health, Department of Health and Human Services; NLM is not responsible for the product and does not endorse or recommend this or any other product. See rxnorm_druglist documentation for details.

Value

data.frame with entity information. If no dosing information for the drug of interest is found, the following output will be returned:

entity	expr	pos
NA	NA	NA

The “entity” column of the output contains the formatted label for that entity, according to the following mapping.
drug name: “DrugName”
strength: “Strength”
dose amount: “DoseAmt”
dose strength: “DoseStrength”
frequency: “Frequency”
intake time: “IntakeTime”
duration: “Duration”
route: “Route”
dose change: “DoseChange”
dose schedule: “DoseScheule”
time keyword: “TimeKeyword”
transition: “Transition”
preposition: “Preposition”
dispense amount: “DispenseAmt”
refill: “Refill”
time of last dose: “LastDose”
Sample output:

entity	expr	pos
DoseChange	decrease	66:74
DrugName	Prograf	78:85
Strength	2 mg	86:90
DoseAmt	1	91:92
Frequency	bid	101:104
LastDose	2100	121:125

References

Nelson SJ, Zeng K, Kilbourne J, Powell T, Moore R. Normalized names for clinical drugs: RxNorm at 6 years. J Am Med Inform Assoc. 2011 Jul-Aug;18(4)441-8. doi: 10.1136/amiajnl-2011-000116. Epub 2011 Apr 21. PubMed PMID: 21515544; PubMed Central PMCID: PMC3128404.