In Lightbridge-KS/labChartHRV: LabChart's HRV Data Import and Manipulation

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

Tutorial

• How to import LabChart's HRV report file (.txt) into a tidy tibble with 1 subject per rows.

Export HRV report file

After you've analysed the HRV data in LabChart, follow these steps to export HRV report:

Go to menu HRV -> Export Report... -> save file as .txt

Open that file, it should look like this:

{width="700"}

As you can see, the text file is slightly formatted and store data in key-value pairs (mostly).

How to transform it so that a data analysis can be performed?

To process this data for further analysis, one approach is to convert it to a table-like data structure which, in R, is a data frame (or tibble). The design of this data frame should be tidy, meaning column names are variables, and each rows represent a single subject. (As in this example, it should be converted to a 1 row data frame.)

It takes time and effort to manually transforms this into a table which can be even harder when the number of subject grows.

That's why I've build this package!

Read HRV report file

read_HRV_reports() read and transform LabChart's HRV report file (.txt) to a tidy tibble.

The first argument (file) is a path to either single HRV report file or folder containing multiple HRV report file, the latter case should be more useful to you.

library(labChartHRV)

# Path to a folder containing example HRV report text files
path_hrv <- labChartHRV_example("HRV")
path_hrv

There are r length(dir(path_hrv)) HRV report .txt files in this folder.

dir(path_hrv)

Now, just supply the path to the folder to import it.

# Read In
hrv_tbl <- read_HRV_reports(path_hrv)
hrv_tbl

(Note: Internally read_HRV_reports() use readtext::readtext() to read textual data. I've set the text encoding to UTF-16LE. If you found that the output looks abnormal try changing text encoding via argument encoding.)

hrv_tbl has r ncol(hrv_tbl) columns and r nrow(hrv_tbl) rows. Column names correspond to each fields of the HRV report, and each rows correspond to each HRV report files.

# Column Names
names(hrv_tbl)

The description of each columns is stored in HRV_vars_desc data frame.

HRV_vars_desc

Parse HRV report

parse_HRV_reports() is a lower-level function that parse HRV report from character vector to a data frame.

Read Manually

First, you need to read HRV report in to character vector using any text reading engine of your choice.

# Path to an HRV report text file
path_hrv1 <- labChartHRV_example("HRV/file1.txt")

# Read into character vector, I use `{readtext}`
hrv_chr <- readtext::readtext(path_hrv1, 
                              encoding = "UTF-16LE")$text
# For nice printing
glue::as_glue(hrv_chr) 

Parse to Data Frame

Now parse the character vector to a data frame.

parse_HRV_reports(hrv_chr)

Since I've import only 1 HRV report into a character vector of length 1, the resulting data frame has only 1 row.

However, you can supply HRV report character vector which has > 1 length, and the resulting data frame would have multiple rows corresponding to each HRV reports.

Selection Helper

{labChartHRV} comes with a helper for select HRV time-and frequency-domain variables.

HRV_vars_domain is a list with 2 elements:

• time: contains character vector of time-domain variables.

• freq: contains character vector of frequency-domain variables.

For example

library(dplyr)

vars <- HRV_vars_domain
str(vars)

Select HRV time-domain variables.

hrv_tbl %>% 
  select(Name, vars$time)

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Last updated: r Sys.Date()

Lightbridge-KS/labChartHRV documentation built on June 12, 2022, 3:21 p.m.