Garmin FIT files for RHRV analysis

1. Read Garmin FIT file and extract the necessary data for the RHRV analysis

Garmin’s cycle computers Edge series and smart-watches record activity information every second in real time. For example, heart rate, breathing rate and ride speed and so on. As they are equipped with GPS, information such as the latitude, longitude and altitude of the ride is also recorded.

The data is stored in a file called FIT. FIT is a binary file format developed by Garmin. It is a format that can be read by the FIT SDK provided by Garmin. The FIT SDK is available in C, C++, C#, Java, and Python. In addition, there are libraries that can be used in R. However, the libraries are not easy to use, and it is difficult to read the FIT file in R.

This section provides instructions on how to load a FIT file in R and extract the necessary data for the RHRV analysis.

1. Install devtools package fist before installing ReadFit package from GitHub.

Code

if(!requireNamespace("remotes")) {
  install.packages("remotes")
}
remotes::install_github("grimbough/FITfileR")
library("FITfileR")
library(tidyverse)

2.1 Read the Garmin FIT file.

2.1.1. Select the fit file from data folder

Code

TargetDir <- paste(as.character(tkchooseDirectory(title = "Select the fit data folder"),sep = "", collapse =""))

setwd(TargetDir)

2.2. Read the Garmin FIT file.

2.2.1. Get .fit files in the folder.

FIT files stored in the folder are read into FitNameList.

Code

FitNameList <- list.files(path = TargetDir) %>%
   str_extract("^.*fit*$") %>%
   na.omit()

head(FitNameList, 4) # check

[1] "12509331867_ACTIVITY 2.fit" "12509331867_ACTIVITY.fit"  

2.2.2 Read fit to ReadFit

If the FIT file is the third, give 3 to FileNo. FileNo <- 65

Code

setwd(TargetDir)
FileNo <- 2
ReadFit <- readFitFile(FitNameList[FileNo])
ReadFit # check

Fit File
├╴File created: 2023-10-29 00:00:05
├╴Device: garmin fenix7x_apac
└╴Number of data messages: 40789

2.2.3. Check the message type

Code

listMessageTypes(ReadFit) # check

 [1] "file_id"         "device_settings" "user_profile"    "zones_target"   
 [5] "sport"           "session"         "lap"             "record"         
 [9] "event"           "device_info"     "activity"        "file_creator"   
[13] "training_file"   "hrv"             "gps_metadata"   

“records” often contain data such as heart rat, speed, etc.

Code

#Read the record message
RecodeData <- getMessagesByType(ReadFit,
                                message_type = "record")
#RecodeData #check

#データ格納用引数
MasterRecord <- NULL

#RecodeData分の繰り返し処理
for(i in seq(RecodeData)){
  
  Recode <- bind_cols("id" = i, RecodeData[[i]])
  MasterRecord <- bind_rows(MasterRecord, Recode)
}

#日付けデータを変換する
MasterRecord <-
  MasterRecord %>%
  mutate_if(is.POSIXt, ~with_tz(., tz = "Asia/Tokyo"))

#MasterRecordを時間で並び替え
MasterRecord <- MasterRecord %>%
  arrange(timestamp)

3. Load openxlsx package to read and write CSV, Excel, and other spreadsheet files.

Code

if(!require("openxlsx", quietly = TRUE)){
  install.packages("openxlsx");require("openxlsx")
}

5. Extract timestamp and HR data

Code

# Extract heart_rate
df <- MasterRecord %>%
  select(timestamp, heart_rate) %>%
  na.omit()

6. Write to a csv file to csv_xls folder the name is time_HR_xx.csv. xx: readed file number.

Code

setwd("~/Documents/brevet")
FileName <- paste0("time_hr_", FileNo, ".csv")

write.csv(df, file.path("csv_xls", file = FileName), row.names = FALSE)