Update iFitbit to v 0.1.8

NAMESPACE

@@ -13,6 +13,7 @@ import(ggplot2)
 import(magrittr)
 importFrom(DBI,dbConnect)
 importFrom(DBI,dbDisconnect)
+importFrom(DBI,dbExecute)
 importFrom(DBI,dbExistsTable)
 importFrom(DBI,dbReadTable)
 importFrom(DBI,dbRemoveTable)

NEWS.md

@@ -1,3 +1,11 @@
+# iFitbit 0.1.8
+* Added `.adjustDates` and an overwrite argument to make continuous data collection easier and less memory intensive
+* Added a database command within `DBI::dbExecute` to remove duplicate entries when writing to SQL database
+* Updated `.readTables` to only include first 12 columns of sleep data as everyone in a study may not have sleep stages
+* Updated `get_fitbit_device` to append last synced information to SQL database to provide a sync history
+* Updated `get_fitbit_report` to include sleep data when exporting to the .xlsx format
+
+
 # iFitbit 0.1.7
 * Add `.readTables` database function.
 * Add parallel processing to the `fitbit_heart_intraday` function.

R/activity.R

@@ -10,6 +10,7 @@
 #' @param end.date The end date specified in the format YYYY-MM-DD or today, Default: Sys.Date()
 #' @param returnData Return the data to the user's R environment, Default: TRUE
 #' @param toSQL Write the data to a SQL database, Default: FALSE
+#' @param overwrite Data extraction should be continued from the most recent date in the SQL database, Default: FALSE
 #' @return Writes the activities to a SQL database stored in the data folder.
 #' @details Extract calories, distance, elevation, physical activity, and steps from the Fitbit API.
 #' @seealso
@@ -22,10 +23,14 @@
 
 get_fitbit_activities <- function(token.pathname, resource = "All Resources",
                                   start.date = Sys.Date(), end.date = Sys.Date(),
-                                  returnData = TRUE, toSQL = FALSE){
+                                  returnData = TRUE, toSQL = FALSE, overwrite = FALSE){
 
   tkn <- .extract_token(token.pathname)
 
+  start.date <- .adjustDates(token.pathname, database = "activities", overwrite, start.date, end.date)$start.date
+
+  end.date <- .adjustDates(token.pathname, database = "activities", overwrite, start.date, end.date)$end.date
+
   url_activity <- paste0("https://api.fitbit.com/1/", "user/", tkn$user, "/", "activities/")
 
   # Check to see if data is greater than 100 days
@@ -125,7 +130,10 @@ get_fitbit_activities <- function(token.pathname, resource = "All Resources",
   if(toSQL){
     database <- .checkDatabase(tkn$directory, tkn$user)
     con <- DBI::dbConnect(RSQLite::SQLite(), database)
-    DBI::dbWriteTable(con, "activities", data, overwrite = TRUE)
+    if(nrow(data) != 0){
+      DBI::dbExecute(con, sprintf("DELETE FROM %s WHERE date BETWEEN '%s' AND '%s'", "activities", data$date[1], data$date[nrow(data)]))
+    }
+    DBI::dbWriteTable(con, "activities", data, overwrite = overwrite, append = !overwrite)
     DBI::dbDisconnect(con)
   }
 

R/database.R

@@ -113,7 +113,8 @@
     con <- DBI::dbConnect(RSQLite::SQLite(), file)
     if(tableName %in% DBI::dbListTables(con)){
       data <- DBI::dbReadTable(con, tableName)
-      main_data <- plyr::rbind.fill(main_data, data.frame(user_id, data))
+      if(tableName == "sleep") data <- data[, 1:12]
+      if(nrow(data) != 0) main_data <- plyr::rbind.fill(main_data, data.frame(user_id, data))
     }
     DBI::dbDisconnect(con)
   }

R/device.R

@@ -36,7 +36,8 @@ get_fitbit_device <- function(token.pathname, returnData = TRUE, toSQL = FALSE){
   if(toSQL){
     database <- .checkDatabase(tkn$directory, tkn$user)
     con <- DBI::dbConnect(RSQLite::SQLite(), database)
-    DBI::dbWriteTable(con, "device", data, overwrite = TRUE)
+    DBI::dbExecute(con, sprintf("DELETE FROM %s WHERE DATE(lastSyncTime) = '%s'", "device", as.Date(data$lastSyncTime)))
+    DBI::dbWriteTable(con, "device", data, overwrite = FALSE, append = TRUE)
     DBI::dbDisconnect(con)
   }
 

R/exercise.R

@@ -98,7 +98,10 @@ get_fitbit_exercise_log <- function(token.pathname, after.date = Sys.Date(),
 
 
   data <- data.frame(cbind(date, time, type, duration, steps, calories, hr, distance, distanceUnit, logType, activityLevel, heartZones))
-  data <- data[data$duration >= 1 & !is.na(data$duration), ]
+
+  # data <- data[data$duration >= 1 & !is.na(data$duration), ] # Removed this filter for now as I am not sure the best option
+
+  data <- dplyr::arrange(data, date, time)
 
   if(toSQL){
     database <- .checkDatabase(tkn$directory, tkn$user)

R/heart.R

@@ -24,6 +24,7 @@
 #'  rate data, Default: FALSE
 #' @param returnData Return a summary of the intensity minutes to the user's R environment, Default: TRUE
 #' @param toSQL Write a summary of the intensity minutes to a SQL database, Default: FALSE
+#' @param overwrite Data extraction should be continued from the most recent date in the SQL database, Default: FALSE
 #' @param verbose Print the progress of the Fitbit API heart rate data extraction and calculation of intensity minutes, Default: FALSE
 #' @return A measure of day-level non-wear, sleep, sedentary time, and physical activity
 #' @details This function retrieves a continuous measure of heart rate from the Fitbit API. The user has access to a variety of
@@ -51,18 +52,17 @@ get_fitbit_heart_intraday <- function(token.pathname, start.date = Sys.Date(),
                                       intensity = NULL, intensity_labels = NULL,
                                       heart_rate_method = 1, rest.hr = NULL, do.parallel = FALSE,
                                       returnData = TRUE, returnRawData = FALSE,
-                                      toSQL = FALSE, verbose = FALSE){
+                                      toSQL = FALSE, overwrite = FALSE, verbose = FALSE){
 
   if(!equals(length(intensity), length(intensity_labels))) {
     stop("Heart intensities and their labels must be the same length")
   }
 
   tkn <- .extract_token(token.pathname)
 
-  # Device
-  device <- get_fitbit_device(token.pathname, returnData = TRUE)
-  lastSync <- as.POSIXct(device$lastSyncTime, format = "%Y-%m-%dT%H:%M:%OS")
-  if(end.date > Sys.Date()) end.date <- Sys.Date()
+  start.date <- .adjustDates(token.pathname, database = "heart", overwrite, start.date, end.date)$start.date
+
+  end.date <- .adjustDates(token.pathname, database = "heart", overwrite, start.date, end.date)$end.date
 
   # Age
   if(is.null(age)) age <- get_fitbit_profile(token.pathname)$user$age
@@ -83,7 +83,10 @@ get_fitbit_heart_intraday <- function(token.pathname, start.date = Sys.Date(),
   if(toSQL){
     database <- .checkDatabase(directory, tkn$user)
     con <- DBI::dbConnect(RSQLite::SQLite(), database)
-    DBI::dbWriteTable(con, "heart", heart_data, overwrite = TRUE)
+    if(nrow(heart_data) != 0){
+      DBI::dbExecute(con, sprintf("DELETE FROM %s WHERE date BETWEEN '%s' AND '%s'", "heart", heart_data$date[1], heart_data$date[nrow(heart_data)]))
+    }
+    DBI::dbWriteTable(con, "heart", heart_data, overwrite = overwrite, append = !overwrite)
     DBI::dbDisconnect(con)
   }
 
@@ -191,6 +194,7 @@ calculate_heart_intensities <- function(heart_raw_data = NULL, sleep_data = NULL
   if(heart_rate_method %in% 1:2 & is.null(intensity)) {
     intensities <- c(0, 0.20, 0.30, 0.40, 0.60, 0.90, 1) # Heart Rate Reserve
     heart_categories <- do.call("c", lapply(intensities, function(x) ((max.hr - rest.hr) * x) + rest.hr))
+    heart_categories[1] <- 0
   }
 
   if(heart_rate_method == 3 & is.null(intensity)) {
@@ -218,7 +222,7 @@ calculate_heart_intensities <- function(heart_raw_data = NULL, sleep_data = NULL
   }
 
   # Add Nonwear and Intensity
-  heart_raw_data$hrr.percent <- cut(heart_raw_data$hr, breaks = heart_categories, labels = intensity_labels, include.lowest = TRUE, right = FALSE)
+  heart_raw_data$hrr.percent <- cut(heart_raw_data$hr, breaks = heart_categories, labels = intensity_labels, include.lowest = TRUE, right = TRUE)
   heart_raw_data$nonwear <- ifelse(heart_raw_data$hr == 0, 1, 0)
   if(!is.null(sleep_data)) {
     heart_raw_data$sleep <- ifelse(heart_raw_data$sleep == 1 & heart_raw_data$nonwear == 0, 1, 0)

R/helpers.R

@@ -92,5 +92,30 @@
 }
 
 
+#' @title .adjustHeartDates
+#' @description Adjusts the start and end date for the `get_fitbit_heart_intraday` function
+#' @param token.pathname Full pathname to the location of the access token
+#' @param database Name of the database to retrieve the last date value (Choices: activity, heart, and sleep)
+#' @param overwrite Data extraction should be continued from the most recent date in the heart SQL database
+#' @param start.date The start date specified in the format YYYY-MM-DD or today, Default: Sys.Date()
+#' @param end.date The end date specified in the format YYYY-MM-DD or today, Default: Sys.Date()
+#' @return An updated start and end date for the `get_fitbit_heart_intraday` function
+#' @details Adjusts the start and end date for the `get_fitbit_heart_intraday` function
+#' @noRd
+#' @keywords internal
+
+.adjustDates <- function(token.pathname, database, overwrite = FALSE, start.date, end.date){
+  tkn <- .extract_token(token.pathname)
+  device <- get_fitbit_device(token.pathname, returnData = TRUE)
+  lastSync <- as.POSIXct(device$lastSyncTime, format = "%Y-%m-%dT%H:%M:%OS")
+  if(end.date > lastSync) end.date <- as.Date(lastSync) - 1
+  if(!overwrite){
+    con <- DBI::dbConnect(RSQLite::SQLite(), .checkDatabase(directory, tkn$user))
+    lastDate <- tail(DBI::dbReadTable(con, database)$date, 1)
+    DBI::dbDisconnect(con)
+    if(length(lastDate) != 0) start.date <- as.Date(lastDate) - 1
+  }
+  return(list(start.date = start.date, end.date = end.date))
+}
 
 

R/iFitbit.R

@@ -30,7 +30,7 @@
 #' @import ggplot2
 #' @importFrom jsonlite fromJSON
 #' @importFrom httr content GET POST add_headers content_type oauth_endpoint oauth_app oauth2.0_token
-#' @importFrom DBI dbConnect dbWriteTable dbReadTable dbExistsTable dbRemoveTable dbDisconnect
+#' @importFrom DBI dbConnect dbWriteTable dbReadTable dbExistsTable dbExecute dbRemoveTable dbDisconnect
 #' @importFrom RSQLite SQLite
 #' @importFrom RCurl base64Encode
 #' @importFrom utils modifyList tail menu

R/report.R

@@ -49,6 +49,7 @@ get_fitbit_report <- function(
   con <- DBI::dbConnect(RSQLite::SQLite(), database_pathname)
   table_names <- DBI::dbListTables(con)
   activities <- if("activities" %in% table_names) DBI::dbReadTable(con, "activities")
+  sleep <- if("sleep" %in% table_names) DBI::dbReadTable(con, "sleep")
   exercise_log <- if("exercise_log" %in% table_names) DBI::dbReadTable(con, "exercise_log")
   heart <- if("heart" %in% table_names) DBI::dbReadTable(con, "heart")
   device <- if("device" %in% table_names) DBI::dbReadTable(con, "device")
@@ -63,14 +64,15 @@ get_fitbit_report <- function(
   # Create a list from the data
   if(toXLSX | returnData){
     names(exercise_log)[2:ncol(exercise_log)] <- paste0("exercise_", names(exercise_log)[2:ncol(exercise_log)])
-    data <- list(device = device, activities = activities, exercise_log = exercise_log, heart = heart)
+    data <- list(device = device, activities = activities, sleep = sleep, exercise_log = exercise_log, heart = heart)
   }
 
   if(toXLSX){
     wb <- openxlsx::createWorkbook()
-    sapply(c("Device", "Activities", "Exercise Log", "Heart"), function(x) openxlsx::addWorksheet(wb, sheetName = x))
+    sapply(c("Device", "Activities", "Sleep", "Exercise Log", "Heart"), function(x) openxlsx::addWorksheet(wb, sheetName = x))
     openxlsx::writeData(wb, sheet = "Device", x = device)
     openxlsx::writeData(wb, sheet = "Activities", x = activities)
+    openxlsx::writeData(wb, sheet = "Sleep", x = sleep)
     openxlsx::writeData(wb, sheet = "Exercise Log", x = exercise_log)
     openxlsx::writeData(wb, sheet = "Heart", x = heart)
     openxlsx::saveWorkbook(wb, paste0(reports_pathname, "/", user, ".xlsx"), overwrite = TRUE, ...)

R/sleep.R

@@ -10,6 +10,7 @@
 #' @param end.date The end date specified in the format YYYY-MM-DD or today, Default: Sys.Date()
 #' @param returnData Return the data to the user's R environment, Default: TRUE
 #' @param toSQL Write the data to a SQL database, Default: FALSE
+#' @param overwrite Data extraction should be continued from the most recent date in the SQL database, Default: FALSE
 #' @return Output is either written to a SQL database or returned as a dataframe
 #' @details Extract sleep outcomes including duration, efficiency, time
 #'     asleep, time awake, minutes to fall asleep, and time in bed.
@@ -23,14 +24,17 @@
 #' @export
 
 get_fitbit_sleep <- function(token.pathname, start.date = Sys.Date(),
-                             end.date = Sys.Date(), returnData = TRUE, toSQL = FALSE){
+                             end.date = Sys.Date(), returnData = TRUE,
+                             toSQL = FALSE, overwrite = FALSE){
 
-  directory <- dirname(dirname(token.pathname))
-  token <- readRDS(token.pathname)
-  token <- token[[2]]
-  user <- token$credentials$user_id
-  sleep.url <- paste0("https://api.fitbit.com/1.2/user/", user, sprintf("/sleep/date/%s/%s.json", start.date, end.date))
-  sleep <- jsonlite::fromJSON(httr::content(httr::GET(sleep.url, token), as = "text"))
+  tkn <- .extract_token(token.pathname)
+
+  start.date <- .adjustDates(token.pathname, database = "sleep", overwrite, start.date, end.date)$start.date
+
+  end.date <- .adjustDates(token.pathname, database = "sleep", overwrite, start.date, end.date)$end.date
+
+  sleep.url <- paste0("https://api.fitbit.com/1.2/user/", tkn$user, sprintf("/sleep/date/%s/%s.json", start.date, end.date))
+  sleep <- jsonlite::fromJSON(httr::content(httr::GET(sleep.url, tkn$token), as = "text"))
   data <- data.frame(matrix(ncol = 12, nrow = 0))
   cols <- c("dateOfSleep", "startTime", "endTime", "isMainSleep", "duration", "efficiency", "minutesAfterWakeup", "minutesAsleep", "minutesAwake", "minutesToFallAsleep", "timeInBed", "type")
   colnames(data) <- cols
@@ -52,21 +56,18 @@ get_fitbit_sleep <- function(token.pathname, start.date = Sys.Date(),
     stages[, grep("thirtyDayAvg", colnames(stages))] <- NULL
 
     data <- cbind(data, stages)
+
+    data <- dplyr::arrange(data, "dateOfSleep")
+
   }
 
   if(toSQL){
-    database <- grep(user, list.files(paste0(directory, "/data"), full.names = TRUE), value = TRUE)
+    database <- .checkDatabase(tkn$directory, tkn$user)
     con <- DBI::dbConnect(RSQLite::SQLite(), database)
-    if(length(sleep$sleep)!=0){
-      DBI::dbWriteTable(con, "sleep", data, overwrite = TRUE)
-    }
-    if(length(sleep$sleep)==0 & DBI::dbExistsTable(con, "sleep")){
-      DBI::dbRemoveTable(con, "sleep")
+    if(nrow(data) != 0){
+      DBI::dbExecute(con, sprintf("DELETE FROM %s WHERE dateOfSleep BETWEEN '%s' AND '%s'", "sleep", data$dateOfSleep[1], data$dateOfSleep[nrow(data)]))
     }
-    if(length(sleep$sleep)==0 & !DBI::dbExistsTable(con, "sleep")){
-      DBI::dbWriteTable(con, "sleep", data, overwrite = TRUE)
-    }
-
+    DBI::dbWriteTable(con, "sleep", data, overwrite = overwrite, append = !overwrite)
     DBI::dbDisconnect(con)
   }
 

inst/rmd/BriefReport.Rmd

@@ -88,7 +88,7 @@ hr.light {
 ```{r load libraries, include=FALSE}
 
 library(ggplot2)
-lastSynced <- as.POSIXct(device$lastSyncTime, format = "%Y-%m-%dT%H:%M:%OS", tz = "America/Chicago")
+lastSynced <- as.POSIXct(device$lastSyncTime[nrow(device)], format = "%Y-%m-%dT%H:%M:%OS", tz = "America/Chicago")
 
 ```
 

inst/rmd/FitbitReport.Rmd

@@ -100,13 +100,14 @@ library(ggplot2)
 
 ```{r deviceData, fig.height=1, fig.width=4, fig.align='center'}
 
+deviceInfo <- device[nrow(device), ]
 
-batteryColor <- dplyr::case_when(as.numeric(device$batteryLevel) >= 50 ~ "#39ff14",
-                          as.numeric(device$batteryLevel) >= 20 & as.numeric(device$batteryLevel) <= 49 ~ "#ff6700",
-                          as.numeric(device$batteryLevel) <= 19 ~ "#de1738")
+batteryColor <- dplyr::case_when(as.numeric(deviceInfo$batteryLevel) >= 50 ~ "#39ff14",
+                          as.numeric(deviceInfo$batteryLevel) >= 20 & as.numeric(deviceInfo$batteryLevel) <= 49 ~ "#ff6700",
+                          as.numeric(deviceInfo$batteryLevel) <= 19 ~ "#de1738")
 
 
-ggplot(data = device, aes(y="Battery Level")) +
+ggplot(data = deviceInfo, aes(y="Battery Level")) +
   geom_col(aes(x=as.numeric(batteryLevel)), fill = batteryColor) +
   geom_col(aes(x = 100), alpha = 0.1, color = "black", fill = "white") +
     geom_text(
@@ -124,7 +125,7 @@ ggplot(data = device, aes(y="Battery Level")) +
           panel.background = element_blank())
 
   
-lastSynced <- as.POSIXct(device$lastSyncTime, format = "%Y-%m-%dT%H:%M:%OS", tz = "America/Chicago")
+lastSynced <- as.POSIXct(deviceInfo$lastSyncTime, format = "%Y-%m-%dT%H:%M:%OS", tz = "America/Chicago")
 
 ```
 
@@ -301,8 +302,10 @@ activities %>%
 
 heart.img <-  magick::image_read(system.file("images/heart.jpeg", package = "iFitbit"))
 
+lastThree <- c((nrow(exercise_log) - 2):nrow(exercise_log))
+
 # Most recent session is equal to 1
-exercise_log_plot <- function(session=1){
+exercise_log_plot <- function(session){
   ggplot() +
   geom_rect(aes(xmin = 0, xmax = 500, ymin = 0, ymax = 500), fill = "white", color = "black", size = 2) +
   annotation_raster(heart.img, xmin = 300, xmax = 450, ymin = 150, ymax = 400) +
@@ -316,9 +319,9 @@ exercise_log_plot <- function(session=1){
 }
    
 gridExtra::grid.arrange(
-  exercise_log_plot(1),
-  exercise_log_plot(2),
-  exercise_log_plot(3),
+  exercise_log_plot(lastThree[1]),
+  exercise_log_plot(lastThree[2]),
+  exercise_log_plot(lastThree[3]),
   nrow = 1
 )