Modify HR zone boundaries for existing Garmin activity (export .fit file from Garmin Connect and convert it to .csv file using fitcsvtool)

hr.R

#!/usr/bin/env Rscript

library(data.table)
library(stringr)

# run example:
# Rscript --vanilla hr.R 99,119,139,158,178,198 ACTIVITY.csv

# params:

# new upper boundaries for HR zones
# it should be a vector of 6 integers separated by commas, e.g.
# "99,119,139,158,178,198"

# input csv file as exported by fitcsvtool,
# e.g. ACTIVITY.csv generated by:
# java -jar FitCSVTool.jar ACTIVITY.fit ACTIVITY.csv

# (optional) output filename, if not specified, it will use original file name
# with ".mod" suffix, e.g. ACTIVITY.mod.csv

# Returns the new csv file whch you can then convert to fit binary file
# using fitcsvtool, e.g.
# java -jar FitCSVTool.jar -c ACTIVITY.mod.csv ACTIVITY.mod.fit

# test if there is at least two arguments
args <- commandArgs(trailingOnly = TRUE)
if (length(args) < 2) {
  stop(
    "At least two arguments must be supplied:
    upper HR zone boundaries and input csv file\n",
    call. = FALSE
)
}
if (length(args) == 2) {
  # default output file file
  args[3] <- stringr::str_replace(args[1], ".csv", ".mod.csv")
}
hv <- args[1]
fn <- args[2]
fo <- args[3]

# import csv file
dt <- fread(fn, fill = TRUE)

# set new boundaries
hr_bounds_v <- as.integer(strsplit(hv, split = ",")[[1]])
hr_bounds <- paste(hv, collapse = "|")
dt[Type == "Data" & Message == "time_in_zone", `Value 5` := hr_bounds]

# get time stamps
ts <- dt[Type == "Data"][Message == "time_in_zone"]$`Value 1`

# update time in zones per timestamps
for (i in seq_along(ts)[-length(ts)]) {
    message(i)
    tst <- ts[i]
    ten <- ts[i + 1]
    x <- dt[Type == "Data"][Message == "record"][`Field 1` == "timestamp"][
        `Value 1` >= tst & `Value 1` <= ten
    ]$`Value 1`
    t <- as.integer(x[-1]) - as.integer(x[-length(x)])
    h <- dt[Type == "Data"][Message == "record"][`Field 1` == "timestamp"][
        `Value 1` >= tst & `Value 1` < ten
    ]$`Value 8`
    z <- cut(h, c(0, hv, Inf))
    s <- tapply(c(t, rep(1, pmax(0, length(z) - length(t)))), z, sum)
    s[is.na(s)] <- 0
    dt[Type == "Data" & Message == "time_in_zone" & `Value 1` == tst,
        `Value 2` := paste(s, collapse = "|")
    ]
}

# uppdate total time in zones
zs <- dt[Type == "Data" & Message == "time_in_zone"]$`Value 2`
zm <- sapply(zs, function(x) {
    sapply(strsplit(x, split = "\\|")[[1]], as.integer)
}, USE.NAMES = FALSE)
rownames(zm) <- NULL
zt <- paste(apply(zm, 1, sum), collapse = "|")
dt[Type == "Data" & Message == "time_in_zone" & `Value 1` == ts[length(ts)],
    `Value 2` := paste(s, collapse = "|")
]

# save new csv file
fwrite(dt, fo, sep = ",", col.names = TRUE)

message("Done, saved file ", fo)