How to create an apply function to calculate time difference between samples?

Question

I am trying to calculate the average sampling frequency grouped by variable_units and sitename, and I want to use apply function instead of for loop for the calculations.

The first section of the code groups data by variable and site. Then, in the second section, I wrote a for loop to calculate the time difference between the first sampling time and the next sampling time and repeat it over each sampling event. I am not sure how to re-write it using apply and put the output as a new column (time_diff) in the original data frame.

After calculating the time differences, I plan to calculate the mean of these sampling frequencies to get an average time sampled per variable and site.

#First section

data <- data %>%
      group_by(variable_units, site_name)
    

#Second section

test <- data.frame()
for (i in 1:data$valuedatetime) {
  
  diff_time <- difftime(i+1, i, units = "min")
  
  test <- rbind(test, diff_time)
}
    

Below is my sample data:

structure(list(valuedatetime = structure(c(584830800, 584830860, 
588891600, 588891660, 591483600, 994712400, 998514000, 1000846800, 
1002747600, 1005166800, 994712400, 998514000, 1000846800, 1002747600, 
1005166800, 584830800, 584830860, 588891600, 588891660, 591483600, 
994712400, 998514000, 1000846800, 1002747600, 1005166800, 994712400, 
998514000, 1000846800, 1002747600, 1005166800, 1041379200, 1041381000, 
1041382800, 1041384600, 1041386400, 1050507000, 1050508800, 1050510600, 
1050512400, 1050514200), tzone = "UTC", class = c("POSIXct", 
"POSIXt")), datavalue = c(90.27497, 87.49935, 85.32486, 109.56417, 
112.45021, 101.2, 101.7, 145.4, 86.2, 144, 107.8, 90.2, 117, 
121.4, 123.8, 6.82727, 6.41, 6.61, 8.425, 9.89, 8.99, 8.2, 12.48, 
7.29, 13.75, 8.4, 6.7, 9.3, 10.6, 12.1, 1, 0.9, 2.1, 1.4, 1.3, 
5, 3, 14, 34, 37), variable_units = c("Dissolved Oxygen Saturation_%", 
"Dissolved Oxygen Saturation_%", "Dissolved Oxygen Saturation_%", 
"Dissolved Oxygen Saturation_%", "Dissolved Oxygen Saturation_%", 
"Dissolved Oxygen Saturation_%", "Dissolved Oxygen Saturation_%", 
"Dissolved Oxygen Saturation_%", "Dissolved Oxygen Saturation_%", 
"Dissolved Oxygen Saturation_%", "Dissolved Oxygen Saturation_%", 
"Dissolved Oxygen Saturation_%", "Dissolved Oxygen Saturation_%", 
"Dissolved Oxygen Saturation_%", "Dissolved Oxygen Saturation_%", 
"Dissolved Oxygen_mg/l", "Dissolved Oxygen_mg/l", "Dissolved Oxygen_mg/l", 
"Dissolved Oxygen_mg/l", "Dissolved Oxygen_mg/l", "Dissolved Oxygen_mg/l", 
"Dissolved Oxygen_mg/l", "Dissolved Oxygen_mg/l", "Dissolved Oxygen_mg/l", 
"Dissolved Oxygen_mg/l", "Dissolved Oxygen_mg/l", "Dissolved Oxygen_mg/l", 
"Dissolved Oxygen_mg/l", "Dissolved Oxygen_mg/l", "Dissolved Oxygen_mg/l", 
"Turbidity_ntu", "Turbidity_ntu", "Turbidity_ntu", "Turbidity_ntu", 
"Turbidity_ntu", "Turbidity_ntu", "Turbidity_ntu", "Turbidity_ntu", 
"Turbidity_ntu", "Turbidity_ntu"), sitename = c("GREAT BAY ESTUARY - ADAMS POINT", 
"GREAT BAY ESTUARY - ADAMS POINT", "GREAT BAY ESTUARY - ADAMS POINT", 
"GREAT BAY ESTUARY - ADAMS POINT", "GREAT BAY ESTUARY - ADAMS POINT", 
"GREAT BAY ESTUARY - COASTAL MARINE LABORATORY", "GREAT BAY ESTUARY - COASTAL MARINE LABORATORY", 
"GREAT BAY ESTUARY - COASTAL MARINE LABORATORY", "GREAT BAY ESTUARY - COASTAL MARINE LABORATORY", 
"GREAT BAY ESTUARY - COASTAL MARINE LABORATORY", "GREAT BAY ESTUARY - GREAT BAY", 
"GREAT BAY ESTUARY - GREAT BAY", "GREAT BAY ESTUARY - GREAT BAY", 
"GREAT BAY ESTUARY - GREAT BAY", "GREAT BAY ESTUARY - GREAT BAY", 
"GREAT BAY ESTUARY - ADAMS POINT", "GREAT BAY ESTUARY - ADAMS POINT", 
"GREAT BAY ESTUARY - ADAMS POINT", "GREAT BAY ESTUARY - ADAMS POINT", 
"GREAT BAY ESTUARY - ADAMS POINT", "GREAT BAY ESTUARY - COASTAL MARINE LABORATORY", 
"GREAT BAY ESTUARY - COASTAL MARINE LABORATORY", "GREAT BAY ESTUARY - COASTAL MARINE LABORATORY", 
"GREAT BAY ESTUARY - COASTAL MARINE LABORATORY", "GREAT BAY ESTUARY - COASTAL MARINE LABORATORY", 
"GREAT BAY ESTUARY - GREAT BAY", "GREAT BAY ESTUARY - GREAT BAY", 
"GREAT BAY ESTUARY - GREAT BAY", "GREAT BAY ESTUARY - GREAT BAY", 
"GREAT BAY ESTUARY - GREAT BAY", "GREAT BAY ESTUARY - COASTAL MARINE LABORATORY", 
"GREAT BAY ESTUARY - COASTAL MARINE LABORATORY", "GREAT BAY ESTUARY - COASTAL MARINE LABORATORY", 
"GREAT BAY ESTUARY - COASTAL MARINE LABORATORY", "GREAT BAY ESTUARY - COASTAL MARINE LABORATORY", 
"GREAT BAY ESTUARY - GREAT BAY", "GREAT BAY ESTUARY - GREAT BAY", 
"GREAT BAY ESTUARY - GREAT BAY", "GREAT BAY ESTUARY - GREAT BAY", 
"GREAT BAY ESTUARY - GREAT BAY")), class = c("grouped_df", "tbl_df", 
"tbl", "data.frame"), row.names = c(NA, -40L), groups = structure(list(
    variable_units = c("Dissolved Oxygen Saturation_%", "Dissolved Oxygen Saturation_%", 
    "Dissolved Oxygen Saturation_%", "Dissolved Oxygen_mg/l", 
    "Dissolved Oxygen_mg/l", "Dissolved Oxygen_mg/l", "Turbidity_ntu", 
    "Turbidity_ntu"), sitename = c("GREAT BAY ESTUARY - ADAMS POINT", 
    "GREAT BAY ESTUARY - COASTAL MARINE LABORATORY", "GREAT BAY ESTUARY - GREAT BAY", 
    "GREAT BAY ESTUARY - ADAMS POINT", "GREAT BAY ESTUARY - COASTAL MARINE LABORATORY", 
    "GREAT BAY ESTUARY - GREAT BAY", "GREAT BAY ESTUARY - COASTAL MARINE LABORATORY", 
    "GREAT BAY ESTUARY - GREAT BAY"), .rows = structure(list(
        1:5, 6:10, 11:15, 16:20, 21:25, 26:30, 31:35, 36:40), ptype = integer(0), class = c("vctrs_list_of", 
    "vctrs_vctr", "list"))), row.names = c(NA, -8L), .drop = TRUE, class = c("tbl_df", 
"tbl", "data.frame")))

Answer 1

I figured out a way to do this without using for loop or apply.

data_timediff <- data %>%
  group_by(variable_units, sitename) %>%
  arrange(valuedatetime) %>%
  mutate(time_diff = c(NA, difftime(valuedatetime[-1], valuedatetime[-n()], units = "min"))) 
# Creates a vector of time differences. NA is added as the first element because the time difference for the first row is not defined. 'difftime' calculates the time difference in minutes between each row and the previous row within each group. [-1] and [-n()] exclude the first and last elements, respectively, to align the differences correctly.