Preparing file for IBI extraction

We are going to use the physioscripts suite of functions to use peak signal detection and compute the IBI series. In order to use the built-in signal detection utilities in this suite of functions, each participant needs a few additional files to tell the program how to handle the raw data. The phys_file() and phys_info() functions helper functions I wrote to put the raw ECG signal into a format that the automatic R peak detection algorithm (from the physioscripts package) is expecting.

source('R/hrv_tutorial/physio_functions.R')

df <- readRDS(data, file = 'data/hrv_tutorial/sub1101a.RDS')

# create and write each new ecg file and event file
phys_file(df, c('time','ecg'), 'data/hrv_tutorial/sub1101')
phys_info('sub1101', 'data/hrv_tutorial/', fs = 1000, origin = NA)

Now, we can pass the .phys.csv file to the process and extract functions.

files <- list.files('data/hrv_tutorial/', pattern = 'phys.csv', full.names = TRUE)

process.ecg(in.file.list = files, processing.mode = "batch")

extract.ibi(in.file.list = files, processing.mode = "batch")

Let’s take a look at the ibi file that was created:

head(read.csv('data/hrv_tutorial/sub1101.phys.csv'))

##    time        ecg  r
## 1 0.000 0.01647949 NA
## 2 0.001 0.01647949 NA
## 3 0.002 0.01861572 NA
## 4 0.003 0.02227783 NA
## 5 0.004 0.02593994 NA
## 6 0.005 0.02929688 NA

head(read.csv('data/hrv_tutorial/sub1101.ibi.gz'))

##    time ibi
## 1 1.323 887
## 2 2.195 872
## 3 3.064 869
## 4 3.898 834
## 5 4.643 745
## 6 5.375 732