updated sleep diary data cleaning scripts

R/act_fit_sleep_stats_merge.R

@@ -0,0 +1,100 @@
+
+data_dir <- '~/Box/CogNeuroLab/Wearables/data/'
+fit <- read_csv(paste0(data_dir, "fitbit/sleep_stats_fitabase_beiwe_all.csv")) #paste0(data_dir, 'fitbit/fitbitSleepStatsGroup.csv'))
+actiware <- read_csv(paste0(data_dir, 'actiwatch/wa_act_combined.csv'))
+actiware_cl <- read_csv(paste0(data_dir, 'actiwatch/actiware_manual_clean/wa_act_combined.csv'))
+
+# n subjects
+length(unique(fit$subject))
+length(unique(actiware$subject_id))
+
+#clean actiware datasets
+
+clean_actiware_combined_df <- function(df, suffix) {
+  TimeInBed <- df %>%
+    filter(interval_type == 'REST') %>%
+    select(subject_id, start_date, interval_number, duration) %>%
+    rename(time_in_bed = duration)
+
+  dfnew <- df %>%
+    dplyr::filter(interval_type == 'SLEEP') %>%
+    merge(TimeInBed, by = c('subject_id', 'start_date', 'interval_number')) %>%
+    select(where(function(x) all(!is.na(x)))) %>%
+    rename(
+      subject = subject_id,
+      sleep_duration = duration) %>%
+    mutate(
+      bed_time = ymd_hms(as_datetime(paste(start_date, start_time), format = '%m/%d/%Y %I:%M:%S %p')),
+      wake_time = ymd_hms(as_datetime(paste(end_date, end_time), format = '%m/%d/%Y %I:%M:%S %p'))) %>%
+    select(-interval_type) %>%
+    mutate(join_date = format(ymd_hms(wake_time), '%Y-%m-%d'),
+           redcap_id = str_pad(str_sub(subject, -3, -1), width = 3, pad = "0")) %>%
+    rename_at(vars(-subject, -redcap_id, -join_date), ~ paste0(., suffix))
+
+
+  return(dfnew)
+}
+
+act <- clean_actiware_combined_df(actiware, "_act")
+act_cl <- clean_actiware_combined_df(actiware_cl, "_cl")
+
+
+#fitbit subject numbers are different for subjects who used Beiwe, so need to match them with their full subject number from Actiware
+
+# match date formats between fitbit and actiwatch datasets
+act_cl <- act_cl %>%
+  mutate(cleaned = ifelse(analysis_name_cl == "Manual", 1, 0))
+
+
+fitnew <- fit %>% 
+  mutate(redcap_id = str_pad(str_sub(subject, -3, -1), width = 3, pad = "0"), 
+         join_date = format(ymd_hms(WakeTime), '%Y-%m-%d')) %>%
+  rename(sleep_duration = MinutesAsleep, 
+         time_in_bed = TimeInBed, 
+         efficiency = Efficiency, 
+         onset_latency = MinutesToFallAsleep, 
+         awake_duration = AwakeDuration,
+         wake_time = WakeTime,
+         bed_time = BedTime) %>%
+  select(-X1, -Duration) %>%
+  rename_at(vars(-subject, -redcap_id, -join_date), ~ paste0(., '_fit')) %>%
+  filter(rowSums(is.na(.)) != ncol(.)-1)
+
+
+df <- merge(act, fitnew, by = c('redcap_id', 'join_date'), all = T) %>%
+  rename(subject = subject.x) %>%
+  select(-subject.y)
+
+redcap <- read.csv(paste0(data_dir, "WearableAssessment-Validation_DATA_2021-01-29_1236.csv"))
+
+rc <- redcap %>%
+  filter(grepl("arm_1", redcap_event_name)) %>%
+  mutate(fitbit_device = ifelse((selected_devices___3 == 1),
+                                 "Fitbit Inspire HR", "Fitbit Charge 2 HR")) %>%
+  select(record_id, age_group, handedness, actiwatch_arm, fitbit_device) %>%
+  mutate(redcap_id = str_pad(str_sub(record_id, -3, -1), width = 3, pad = "0")) %>%
+  group_by(redcap_id) %>%
+  fill(age_group, handedness, .direction = "down") %>%
+  drop_na(actiwatch_arm) %>%
+  mutate(age_group = recode(age_group, "Young Adults", "Older Adults")) %>%
+  mutate(handedness = recode(handedness, "Left", "Right", "Both")) %>%
+  mutate(actiwatch_arm = recode(actiwatch_arm, "Left", "Right")) %>%
+  mutate(dominant = ifelse(handedness == actiwatch_arm, 1, 0)) %>%
+  ungroup() 
+
+write.csv(rc, paste0(data_dir, 'demographics_condition_assignments.csv'))
+
+df <- merge(rc, df, by = 'redcap_id', all = T) %>%
+  select(subject, everything(), -record_id) %>%
+  group_by(redcap_id) %>%
+  fill(subject, .direction = "down") %>%
+  ungroup()
+
+length(unique(df$subject))
+
+check<- df %>%
+  select(subject, redcap_id, interval_number_act, bed_time_act, bed_time_fit)
+
+unique(df$subject)
+
+write.csv(df, file = paste0(data_dir, 'sleep_stats.csv'), row.names = F)

R/fitabase_beiwe_sleep_stats_merge.R

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+
+data_dir <- "~/Box/CogNeuroLab/Wearables/data/"
+fitabase <- read.csv(paste0(data_dir, "fitbit/Fitabase_sleep_all.csv"))
+beiwe <- read.csv(paste0(data_dir, "fitbit/Beiwe/Beiwe_sleep_all.csv"))
+
+length(unique(c(beiwe$subject, fitabase$subject)))
+
+colnames(fitabase)[! colnames(fitabase) %in% colnames(beiwe)]
+
+head(fitabase)
+head(beiwe)
+
+fitabase <- fitabase %>%
+  mutate(BedTime = ymd_hms(mdy_hms(BedTime)),
+         WakeTime = ymd_hms(WakeTime))
+
+beiwe <- beiwe %>%
+  mutate(BedTime = ymd_hms(BedTime),
+         WakeTime = ymd_hms(WakeTime)) 
+
+d <- fitabase %>%
+  select(colnames(fitabase)[colnames(fitabase) %in% colnames(beiwe)]) %>%
+  arrange() %>%
+  rbind(arrange(beiwe[colnames(beiwe) %in% colnames(fitabase)])) %>%
+  select(subject, everything(), -X) 
+
+check <- d %>%
+  select(subject, BedTime, WakeTime)
+
+length(unique(d$subject))
+
+head(d)
+tail(d)
+
+write.csv(d, paste0(data_dir, "fitbit/sleep_stats_fitabase_beiwe_all.csv"))
+
+

R/fitabase_sleep_stats.R

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+
+library(tidyverse)
+
+data_dir <- "~/Box/CogNeuroLab/Wearables/data/"
+fitabase_files <- list.files(path = paste0(data_dir, "fitbit/"), pattern = "*sleepLogInfo*", full.names = T)
+
+length(unique(substring(str_split_fixed(fitabase_files, pattern = "WA_", 2)[,2], 0, 5)))
+
+d <- c()
+for (file in fitabase_files){
+  data <- read.csv(file)
+  data <- data %>%
+    rename(BedTime = StartTime) %>%
+    mutate(subject = substring(str_split_fixed(file, pattern = "WA_", 2)[,2], 0, 5),
+           WakeTime = mdy_hms(BedTime) + minutes(MinutesAsleep))
+
+  d <- rbind(d, data)
+
+}
+head(d)
+write.csv(d, paste0(data_dir, "fitbit/Fitabase_sleep_all.csv"))