Fix Fitbit tz inference from phone data
JulioV
parent
636b64c61a
commit
46f5e24814
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@ -1,42 +1,50 @@
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library(tibble)
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library(dplyr)
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library(tidyr)
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library(purrr)
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library(yaml)
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library(glue)
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library(lubridate)
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options(scipen = 999)
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buils_tz_intervals <- function(tz_codes){
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buils_tz_intervals <- function(tz_codes, device_type){
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tz_codes <- tz_codes %>%
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group_by(device_id) %>%
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arrange(timestamp)
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if(device_type == "fitbit" )
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tz_codes <- tz_codes %>%
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mutate(end_timestamp = lead(timestamp), end_local_date_time = lead(local_date_time)) %>%
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ungroup() %>%
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replace_na(list(end_timestamp = as.numeric(Sys.time())*1000, end_local_date_time = format(Sys.time(), format="%Y-%m-%d %H:%M:%S") )) %>%
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mutate(local_date_time = lubridate::ymd_hms(local_date_time), end_local_date_time = lubridate::ymd_hms(end_local_date_time))
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else
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tz_codes <- tz_codes %>%
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mutate(end_timestamp = lead(timestamp)) %>%
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ungroup() %>%
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replace_na(list(end_timestamp = as.numeric(Sys.time())*1000 ))
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return(tz_codes)
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}
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filter_tz_per_device <- function(device_id, tz_codes, default, IF_MISSING_TZCODE){
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device_tz_codes <- tz_codes %>% filter(device_id == !!device_id) %>% select(-device_id)
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if(nrow(device_tz_codes) > 0)
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return(device_tz_codes)
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else if(IF_MISSING_TZCODE == "STOP")
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stop(paste("The device id '", device_id, "' does not have any time zone codes in your [MULTIPLE][TZCODES_FILE], add one or set IF_MISSING_TZCODE to 'USE_DEFAULT'"))
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else if(IF_MISSING_TZCODE == "USE_DEFAULT")
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return(data.frame(timestamp = c(0), tzcode = default, end_timestamp = as.numeric(Sys.time())*1000))
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assign_tz_code <- function(data, device_id, tz_codes, device_type){
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tz_codes <- tz_codes %>% filter(device_id == !!device_id) %>% select(-device_id)
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stop("We should have obtained the time zones for a device, stop the execution or use the default tz but this didn't happen. Create an issue on Github")
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}
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assign_tz_code <- function(data, tz_codes){
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if(device_type == "fitbit" && all(data$timestamp == 0) && "local_date_time" %in% colnames(data)){
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# Only do this for Fitbit raw data, other devices and Fitbit sleep episodes can use timestamps
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column <- "local_date_time"
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data <- data %>% mutate(local_date_time=lubridate::ymd_hms(local_date_time))
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} else
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column <- "timestamp"
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for(i in 1:nrow(tz_codes)) {
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start_timestamp <- tz_codes[[i, "timestamp"]]
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end_timestamp <- tz_codes[[i, "end_timestamp"]]
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start <- tz_codes[[i, column]]
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end <- tz_codes[[i, paste0("end_", column)]]
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time_zone <- trimws(tz_codes[[i, "tzcode"]], which="both")
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data$local_timezone <- if_else(start_timestamp <= data$timestamp & data$timestamp < end_timestamp, time_zone, data$local_timezone)
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data$local_timezone <- if_else(start <= data[[column]] & data[[column]] < end, time_zone, data$local_timezone)
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}
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return(data %>% filter(!is.na(local_timezone)))
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}
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@ -47,59 +55,84 @@ validate_single_tz_per_fitbit_device <- function(tz_codes, INFER_FROM_SMARTPHONE
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stop("If [TIMEZONE][MULTIPLE][FITBIT][INFER_FROM_SMARTPHONE_TZ] is True (you want to infer Fitbit time zones with smartphone data), you need to set ALLOW_MULTIPLE_TZ_PER_DEVICE to True. However, read the docs to understand why this can be innacurate")
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tz_per_device <- tz_codes %>% group_by(device_id) %>% summarise(n = n(), .groups = "drop_last") %>% filter(n > 1)
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if(nrow(tz_per_device) > 0)
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stop(paste("The following Fitbit device ids have more than one time zone change which is not allowed if [TIMEZONE][MULTIPLE][FITBIT][ALLOW_MULTIPLE_TZ_PER_DEVICE] is False:", paste(tz_per_device %>% pull(device_id), collapse = ",")))
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stop("If [TIMEZONE][MULTIPLE][FITBIT][ALLOW_MULTIPLE_TZ_PER_DEVICE] is False, every fitbit device id in [MULTIPLE][TZCODES_FILE] must have only one timezone with a timestamp equal to 0. The following device ids do not comply:", paste(tz_per_device %>% pull(device_id), collapse = ","))
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zero_ts <- tz_codes %>% filter(timestamp > 0)
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if(nrow(zero_ts) > 0)
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stop(paste("The following Fitbit device ids have a time zone change with a timestamp bigger than 0 which is not allowed if [TIMEZONE][MULTIPLE][FITBIT][ALLOW_MULTIPLE_TZ_PER_DEVICE] is False: ", paste(zero_ts %>% pull(device_id), collapse = ",")))
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stop("If [TIMEZONE][MULTIPLE][FITBIT][ALLOW_MULTIPLE_TZ_PER_DEVICE] is False, every fitbit device id in [MULTIPLE][TZCODES_FILE] must have only one timezone with a timestamp equal to 0. The following device ids do not comply:", paste(zero_ts %>% pull(device_id), collapse = ","))
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}
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validate_devies_exist_in_participant_file <- function(devices, device_type, pid, participant_file){
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if(length(devices) == 0)
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stop("[TIMEZONE][MULTIPLE][FITBIT][ALLOW_MULTIPLE_TZ_PER_DEVICE] is True (you want to infer Fitbit time zones with smartphone data), however participant ", pid," does not have any [",device_type,"][DEVICE_IDS] in ", participant_file)
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infer_tz_codes_from_phones <- function(data_device_ids, tz_codes, participant_file){
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participant_data <- read_yaml(participant_file)
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phone_device_ids <- participant_data$PHONE$DEVICE_IDS
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phone_tz_codes <- tz_codes %>% filter(device_id %in% phone_device_ids)
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if(nrow(phone_tz_codes) == 0)
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warning("The PHONE device ids that we were supposed to use to infer fitbit devices timezones do not have timezone data in [MULTIPLE][TZCODES_FILE]. ",
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" Problematic phone devices ids: ", paste0(phone_device_ids, collapse = ", "))
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data_tz_codes <- NULL
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for(data_device_id in data_device_ids)
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data_tz_codes <- bind_rows(data_tz_codes, phone_tz_codes %>% mutate(device_id = data_device_id) %>% arrange(timestamp))
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data_tz_codes
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}
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# TODO include CSV timezone file in rule
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multiple_time_zone_assignment <- function(sensor_data, timezone_parameters, device_type, pid, participant_file){
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if(nrow(sensor_data) == 0)
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return(sensor_data %>% mutate(local_timezone = NA_character_))
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tz_codes <- read.csv(timezone_parameters$MULTIPLE$TZCODES_FILE)
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default <- timezone_parameters$MULTIPLE$DEFAULT_TZCODE
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IF_MISSING_TZCODE <- timezone_parameters$MULTIPLE$IF_MISSING_TZCODE
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ALLOW_MULTIPLE_TZ_PER_DEVICE <- timezone_parameters$MULTIPLE$FITBIT$ALLOW_MULTIPLE_TZ_PER_DEVICE
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INFER_FROM_SMARTPHONE_TZ <- timezone_parameters$MULTIPLE$FITBIT$INFER_FROM_SMARTPHONE_TZ
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data_device_ids <- sensor_data %>% distinct(device_id) %>% pull(device_id)
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participant_data <- read_yaml(participant_file)
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phone_ids <- participant_data$PHONE$DEVICE_IDS
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fitbit_ids <- participant_data$FITBIT$DEVICE_IDS
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if(INFER_FROM_SMARTPHONE_TZ && device_type == "fitbit")
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data_tz_codes <- infer_tz_codes_from_phones(data_device_ids, tz_codes, participant_file)
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else
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data_tz_codes <- tz_codes %>% filter(device_id %in% data_device_ids)
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# Check if we have timezones for all device ids
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if(length(unique(data_tz_codes$device_id)) < length(data_device_ids)){
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if(IF_MISSING_TZCODE == "STOP")
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stop(glue("One or more device ids do not have any time zone codes in your [MULTIPLE][TZCODES_FILE].",
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"You can add one or set [MULTIPLE][IF_MISSING_TZCODE] to 'USE_DEFAULT'. The missing device ids are [{ids}]",
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ids=paste0(setdiff(data_device_ids, data_tz_codes %>% pull(device_id)), collapse = ",")))
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else if(IF_MISSING_TZCODE == "USE_DEFAULT"){
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warning("Using DEFAULT time zone for ", paste0(setdiff(data_device_ids, data_tz_codes %>% pull(device_id)), collapse = ","))
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default_tz_codes <- data.frame(timestamp = rep_along(c(data_device_ids),0), tzcode = rep_along(c(data_device_ids),default), device_id=data_device_ids) %>%
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filter(!device_id %in% data_tz_codes$device_id)
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data_tz_codes <- bind_rows(data_tz_codes, default_tz_codes)
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}
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}
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if(device_type == "fitbit"){
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if(!ALLOW_MULTIPLE_TZ_PER_DEVICE){
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validate_single_tz_per_fitbit_device(tz_codes, INFER_FROM_SMARTPHONE_TZ)
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} else if(INFER_FROM_SMARTPHONE_TZ){
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validate_devies_exist_in_participant_file(phone_ids, "PHONE", pid, participant_file)
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validate_devies_exist_in_participant_file(fitbit_ids, "FITBIT", pid, participant_file)
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unified_device_id <- paste0("unified_device_id", pid)
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sensor_data <- sensor_data %>% mutate(device_id = if_else(device_id %in% phone_ids, unified_device_id, device_id))
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tz_codes <- tz_codes %>% mutate(device_id = if_else(device_id %in% fitbit_ids, unified_device_id, device_id))
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}
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if(!ALLOW_MULTIPLE_TZ_PER_DEVICE)
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validate_single_tz_per_fitbit_device(data_tz_codes, INFER_FROM_SMARTPHONE_TZ)
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# We only use datetimes for raw Fitbit data
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data_tz_codes <- data_tz_codes %>%
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group_by(tzcode) %>%
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nest() %>%
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mutate(data = map2(data, tzcode, function(nested_data, tz){
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nested_data %>% mutate(local_date_time = format(as_datetime(timestamp / 1000, tz=tz), format="%Y-%m-%d %H:%M:%S"))
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})) %>%
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unnest(cols=everything())
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}
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tz_intervals <- buils_tz_intervals(tz_codes)
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tz_intervals <- buils_tz_intervals(data_tz_codes, device_type)
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sensor_data <- sensor_data %>% mutate(local_timezone = NA_character_)
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if(nrow(sensor_data) > 0){
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sensor_data <- sensor_data %>%
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group_by(device_id) %>%
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nest() %>%
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mutate(tz_codes_per_device = map(device_id, filter_tz_per_device, tz_intervals, default, IF_MISSING_TZCODE)) %>%
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mutate(data = map2(data, tz_codes_per_device, assign_tz_code )) %>%
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select(-tz_codes_per_device) %>%
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mutate(data = map2(data, device_id, assign_tz_code, tz_intervals, device_type)) %>%
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unnest(cols = data)
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}
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return(sensor_data)
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}
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