processLastDose {EHR}

Process and standardize extracted last dose times

Description

This function takes last dose times extracted using the medExtractR system and processes the times into standardized datetime objects using recorded lab data where necessary. The raw output from extractMed is filtered to just the LastDose extractions. Time expressions are standardized into HH:MM:SS format based on what category they fall into (e.g., a time represented with AM/PM, 24-hour military time, etc.). When the last dose time is after 12pm, it is assumed to have been taken one day previous to the note's date. For any duration extractions (e.g. "14 hour level"), the last dose time is calculated from the labtime by extracting the appropriate number of hours. The final dataset is returned with last dose time formatted into a POSIXct variable.

Usage

processLastDose(mxrData, noteMetaData, labData)

Arguments

mxrData

data.frame containing output from the medExtractR system

noteMetaData

data.frame with meta data (pid (patient ID) and date) for the file names contained within mxrData

labData

data.frame that contains lab dates and times associated with the file names within mxrData. Must contain columns pid and date, as well as labtime. The date column must be in the same format as date in noteMetaData, and labtime must be a POSIXct

Details

See EHR Vignette for Extract-Med and Pro-Med-NLP for details.

Value

data.frame with identifying information (e.g., filename, etc) as well as processed and standardized last dose times as a POSIXct column

Examples

tac_mxr <- read.csv(system.file("examples", "tac_mxr.csv", package = "EHR"))
data(tac_metadata)
data(tac_lab)

processLastDose(mxrData = tac_mxr, noteMetaData = tac_metadata, labData = tac_lab)