The goal of SummarizedActigraphy is to provide functions for reading
Actigraphy data and turn it into SummarizedExperiments.
You can install SummarizedActigraphy from GitHub with:
# install.packages("remotes")
remotes::install_github("muschellij2/SummarizedActigraphy")library(SummarizedActigraphy)
url = paste0("https://github.com/THLfi/read.gt3x/files/",
"3522749/GT3X%2B.01.day.gt3x.zip")
destfile = tempfile(fileext = ".zip")
dl = utils::download.file(url, destfile = destfile)
gt3x_file = utils::unzip(destfile, exdir = tempdir())
gt3x_file = gt3x_file[!grepl("__MACOSX", gt3x_file)]
path = gt3x_file
result = summarize_actigraphy(path)
#> Running Daily Actigraphy
#> Input is a .gt3x file, unzipping to a temporary location first...
#> Unzipping gt3x data to /var/folders/1s/wrtqcpxn685_zk570bnx9_rr0000gr/T//RtmpanwnsY
#> 1/1
#> Unzipping /var/folders/1s/wrtqcpxn685_zk570bnx9_rr0000gr/T//RtmpanwnsY/GT3X+ (01 day).gt3x
#> === info.txt, activity.bin, lux.bin extracted to /var/folders/1s/wrtqcpxn685_zk570bnx9_rr0000gr/T//RtmpanwnsY/GT3X+(01day)
#> GT3X information
#> $ Serial Number :"NEO1DXXXXXXXX"
#> $ Device Type :"GT3XPlus"
#> $ Firmware :"2.5.0"
#> $ Battery Voltage :"4.22"
#> $ Sample Rate :30
#> $ Start Date : POSIXct, format: "2012-06-27 10:54:00"
#> $ Stop Date : POSIXct, format: "2012-06-28 11:54:00"
#> $ Download Date : POSIXct, format: "2012-06-28 16:25:52"
#> $ Board Revision :"4"
#> $ Unexpected Resets :"0"
#> $ Sex :"Male"
#> $ Height :"172.72"
#> $ Mass :"69.8532249799612"
#> $ Age :"43"
#> $ Race :"White / Caucasian"
#> $ Limb :"Ankle"
#> $ Side :"Left"
#> $ Dominance :"Non-Dominant"
#> $ DateOfBirth :"621132192000000000"
#> $ Subject Name :"GT3XPlus"
#> $ Serial Prefix :"NEO"
#> $ Last Sample Time : 'POSIXct' num(0)
#> - attr(*, "tzone")= chr "GMT"
#> $ Acceleration Scale:341
#> Parsing GT3X data via CPP.. expected sample size: 2700000
#> Using NHANES-GT3X format - older format
#> Sample size: 2700000
#> Scaling...
#> Done (in 0.588511943817139 seconds)
#> Joining, by = "HEADER_TIME_STAMP"
#> Getting the First Day
#> Summarizing Data
result
#> # A tsibble: 1,440 x 11 [1m]
#> time AI_mean AI_median SD_mean SD_median MAD_mean MAD_median MEDAD_mean
#> <time> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 00'00" 0.266 0.177 0.00646 0.00507 0.00373 0.00317 0.00221
#> 2 01'00" 0.323 0.230 0.0150 0.00644 0.00578 0.00448 0.00271
#> 3 02'00" 0.144 0.142 0.00402 0.00447 0.00252 0.00276 0.00132
#> 4 03'00" 0.947 0.643 0.0310 0.0145 0.0108 0.00640 0.00516
#> 5 04'00" 1.11 1.48 0.0324 0.0224 0.0130 0.0120 0.00428
#> 6 05'00" 0.536 0.214 0.00836 0.00615 0.00498 0.00294 0.00274
#> 7 06'00" 0.0921 0.122 0.00511 0.00641 0.00441 0.00460 0.00372
#> 8 07'00" 0.179 0.130 0.00979 0.00834 0.00587 0.00566 0.00380
#> 9 08'00" 0.572 0.139 0.0289 0.00503 0.00769 0.00301 0.00240
#> 10 09'00" 0.387 0.427 0.0167 0.0208 0.00580 0.00593 0.00254
#> # … with 1,430 more rows, and 3 more variables: MEDAD_median <dbl>,
#> # mean_r_mean <dbl>, mean_r_median <dbl>hms_times = structure(seq(0, 86340, by = 60), class = c("hms", "difftime"),
units = "secs")
hms_times = tibble::tibble(time = hms_times)
measure = "AI_mean"
tmeasure = c("time", measure)
x = result[, tmeasure, drop = FALSE]
x = tibble::as_tibble(x)
x = dplyr::left_join(hms_times, x)
#> Joining, by = "time"
head(x)
#> # A tibble: 6 x 2
#> time AI_mean
#> <time> <dbl>
#> 1 00'00" 0.266
#> 2 01'00" 0.323
#> 3 02'00" 0.144
#> 4 03'00" 0.947
#> 5 04'00" 1.11
#> 6 05'00" 0.536
x1440 = tidyr::spread(x, time, value = measure)
x1440
#> # A tibble: 1 x 1,440
#> `00:00:00` `00:01:00` `00:02:00` `00:03:00` `00:04:00` `00:05:00` `00:06:00`
#> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 0.266 0.323 0.144 0.947 1.11 0.536 0.0921
#> # … with 1,433 more variables: `00:07:00` <dbl>, `00:08:00` <dbl>,
#> # `00:09:00` <dbl>, `00:10:00` <dbl>, `00:11:00` <dbl>, `00:12:00` <dbl>,
#> # `00:13:00` <dbl>, `00:14:00` <dbl>, `00:15:00` <dbl>, `00:16:00` <dbl>,
#> # `00:17:00` <dbl>, `00:18:00` <dbl>, `00:19:00` <dbl>, `00:20:00` <dbl>,
#> # `00:21:00` <dbl>, `00:22:00` <dbl>, `00:23:00` <dbl>, `00:24:00` <dbl>,
#> # `00:25:00` <dbl>, `00:26:00` <dbl>, `00:27:00` <dbl>, `00:28:00` <dbl>,
#> # `00:29:00` <dbl>, `00:30:00` <dbl>, `00:31:00` <dbl>, `00:32:00` <dbl>,
#> # `00:33:00` <dbl>, `00:34:00` <dbl>, `00:35:00` <dbl>, `00:36:00` <dbl>,
#> # `00:37:00` <dbl>, `00:38:00` <dbl>, `00:39:00` <dbl>, `00:40:00` <dbl>,
#> # `00:41:00` <dbl>, `00:42:00` <dbl>, `00:43:00` <dbl>, `00:44:00` <dbl>,
#> # `00:45:00` <dbl>, `00:46:00` <dbl>, `00:47:00` <dbl>, `00:48:00` <dbl>,
#> # `00:49:00` <dbl>, `00:50:00` <dbl>, `00:51:00` <dbl>, `00:52:00` <dbl>,
#> # `00:53:00` <dbl>, `00:54:00` <dbl>, `00:55:00` <dbl>, `00:56:00` <dbl>,
#> # `00:57:00` <dbl>, `00:58:00` <dbl>, `00:59:00` <dbl>, `01:00:00` <dbl>,
#> # `01:01:00` <dbl>, `01:02:00` <dbl>, `01:03:00` <dbl>, `01:04:00` <dbl>,
#> # `01:05:00` <dbl>, `01:06:00` <dbl>, `01:07:00` <dbl>, `01:08:00` <dbl>,
#> # `01:09:00` <dbl>, `01:10:00` <dbl>, `01:11:00` <dbl>, `01:12:00` <dbl>,
#> # `01:13:00` <dbl>, `01:14:00` <dbl>, `01:15:00` <dbl>, `01:16:00` <dbl>,
#> # `01:17:00` <dbl>, `01:18:00` <dbl>, `01:19:00` <dbl>, `01:20:00` <dbl>,
#> # `01:21:00` <dbl>, `01:22:00` <dbl>, `01:23:00` <dbl>, `01:24:00` <dbl>,
#> # `01:25:00` <dbl>, `01:26:00` <dbl>, `01:27:00` <dbl>, `01:28:00` <dbl>,
#> # `01:29:00` <dbl>, `01:30:00` <dbl>, `01:31:00` <dbl>, `01:32:00` <dbl>,
#> # `01:33:00` <dbl>, `01:34:00` <dbl>, `01:35:00` <dbl>, `01:36:00` <dbl>,
#> # `01:37:00` <dbl>, `01:38:00` <dbl>, `01:39:00` <dbl>, `01:40:00` <dbl>,
#> # `01:41:00` <dbl>, `01:42:00` <dbl>, `01:43:00` <dbl>, `01:44:00` <dbl>,
#> # `01:45:00` <dbl>, `01:46:00` <dbl>, …