In rickeycarter/easyRecg: Simple tools to facilitate reading and writing digital ECG files

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

R and RStudio Installation

If you do not already have an environment ready to run R code, we recommend installing it along with RStudio. For more information on this process, please see here.

Project Setup

Once you have RStudio up and running, we suggest creating a new R project and placing all ECG XML files in a sub-directory. The file structure may look something like this:

The RStudio file panel may look something like this:

Installing easyRecg

You can run the following lines of code to install easyRecg. Depending on what dependencies you already have in your compute environment, this could take several minutes:

install.packages("devtools")
devtools::install_github("rickeycarter/easyRecg")

Extracting Data

Once you have your environment configured, you can start using the package to extract your data. We recommend including all the code below in a single R script that can be saved and shared.

Load the easyRecg package:

devtools::load_all(".")

library(easyRecg)

dir.create('ecg_files')
from <- system.file("extdata", path = "muse", package = "easyRecg")
to <- "ecg_files"
files <- list.files(from, full.names = TRUE)
file.copy(files, to, recursive = TRUE)

Extract and save the ECG 12-lead data

all_muse <- read_muse_xml_directory("ecg_files")
save(all_muse, file = "ecg_lead_data.Rda")

Extract and save meta data

For more info on whitelisting, blacklisting, or mixed filtering, please see the readme.

# Get list of files to read
all_files <- list.files("ecg_files", full.names = TRUE)

# Decide what meta data to share - this can be changes
exclude <- list(
  patient_demographics = c("patient_last_name", "patient_first_name")
)

meta_data <- read_muse_xml_meta(all_files, exclude = exclude)

# Inspect data - ensure it only contains appropriate data
meta_data

# save data
save(meta_data, file = "ecg_meta_data.Rda")

file.remove("ecg_meta_data.Rda")
file.remove("ecg_lead_data.Rda")
unlink("ecg_files", recursive=TRUE)

rickeycarter/easyRecg documentation built on Dec. 22, 2021, 4:09 p.m.