tac_mxr_parsed

The output after running <code>parseMedExtractR</code> on 3 example clinical notes.

datasets

Process and analyze electronic health record (EHR) data. The 'EHR'
package provides modules to perform diverse medication-related studies using
data from EHR databases. Especially, the package includes modules to perform
pharmacokinetic/pharmacodynamic (PK/PD) analyses using EHRs, as outlined in
Choi, Beck, McNeer, Weeks, Williams, James, Niu, Abou-Khalil, Birdwell, Roden,
Stein, Bejan, Denny, and Van Driest (2020) <doi:10.1002/cpt.1787>. Additional
modules will be added in future. In addition, this package provides various
functions useful to perform Phenome Wide Association Study (PheWAS) to explore
associations between drug exposure and phenotypes obtained from EHR data, as
outlined in Choi, Carroll, Beck, Mosley, Roden, Denny, and Van Driest (2018)
<doi:10.1093/bioinformatics/bty306>.

Leena Choi

Electronic Health Record (EHR) Data Processing and Analysis Tool

Cole Beck

Hannah Weeks

Elizabeth McNeer

Nathan James

Michael Williams

tac_mxr_parsed function

A data frame with 7 observations on the following variables.<dl>
 <dt>filename</dt>
<dd>A character vector, filename for the clinical note</dd> <dt>drugname</dt>
<dd>A character vector, drug name extracted from the clinical note along with start and stop positions</dd> <dt>strength</dt>
<dd>A character vector, strengths extracted from the clinical note along with start and stop positions</dd> <dt>dose</dt>
<dd>A character vector, dose amounts extracted from the clinical note along with start and stop positions</dd> <dt>route</dt>
<dd>A character vector, routes extracted from the clinical note along with start and stop positions</dd> <dt>freq</dt>
<dd>A character vector, frequencies extracted from the clinical note along with start and stop positions</dd> <dt>dosestr</dt>
<dd>A character vector, dose intakes extracted from the clinical note along with start and stop positions</dd> <dt>dosechange</dt>
<dd>A character vector, dose change keywords extracted from the clinical note along with start and stop positions</dd> <dt>lastdose</dt>
<dd>A character vector, last dose times extracted from the clinical note along with start and stop positions</dd>
</dl>

Format

Example of Tacrolimus Output from `parseMedExtractR` — tac_mxr_parsed

A data frame with 7 observations on the following variables.<dl>
 <dt>filename</dt>
<dd>A character vector, filename for the clinical note</dd>

 <dt>drugname</dt>
<dd>A character vector, drug name extracted from the clinical note along with start and stop positions</dd>

 <dt>strength</dt>
<dd>A character vector, strengths extracted from the clinical note along with start and stop positions</dd>

 <dt>dose</dt>
<dd>A character vector, dose amounts extracted from the clinical note along with start and stop positions</dd>

 <dt>route</dt>
<dd>A character vector, routes extracted from the clinical note along with start and stop positions</dd>

 <dt>freq</dt>
<dd>A character vector, frequencies extracted from the clinical note along with start and stop positions</dd>

 <dt>dosestr</dt>
<dd>A character vector, dose intakes extracted from the clinical note along with start and stop positions</dd>

 <dt>dosechange</dt>
<dd>A character vector, dose change keywords extracted from the clinical note along with start and stop positions</dd>

 <dt>lastdose</dt>
<dd>A character vector, last dose times extracted from the clinical note along with start and stop positions</dd>


</dl>

tac_mxr_parsed: Example of Tacrolimus Output from `parseMedExtractR`

Description

Usage

Arguments

Format

Examples