This is a package aimed at converting .agd files from Actigraph into data.frames.

Installation

library("devtools")
install_github("masalmon/convertagd")

Converting a single file

read_agd is the function for reading a agd file and getting two tables out of it.

library("convertagd")
file <- system.file("extdata", "dummyCHAI.agd", package = "convertagd")
testRes <- read_agd(file, tz = "GMT")
kable(testRes[["settings"]])

settingID	settingName	settingValue
1	softwarename	ActiLife
2	softwareversion	5.10.0
3	osversion	Microsoft Windows NT 6.1.7601 Service Pack 1
4	machinename	THINKCENTRE
5	datetimeformat	dd-MM-yyyy
6	decimal	.
7	grouping	,
8	culturename	English (India)
9	finished	true
10	devicename	GT3XPlus
11	filter	Normal
12	deviceserial	NEO1D31110533
13	deviceversion	2.5.0
14	modenumber	61
15	epochlength	10
16	startdatetime	635670972000000000
17	stopdatetime	635672088000000000
18	downloaddatetime	635672179164562010
19	batteryvoltage	4.22
20	original sample rate	30
21	subjectname	11
22	sex	Male
23	race	Asian / Pacific Islander
24	limb	Other
25	epochcount	11159
26	sleepscorealgorithmname	Sadeh
27	customsleepparameters
28	notes

kable(head(testRes[["raw.data"]]))

timedate	axis1	axis2	axis3	steps	lux	incline
2015-05-13 07:00:00	7	1	64	1	0	3
2015-05-13 07:00:10	5	0	44	0	0	3
2015-05-13 07:00:20	0	0	17	0	0	3
2015-05-13 07:00:30	0	0	0	0	0	3
2015-05-13 07:00:40	0	0	6	0	0	3
2015-05-13 07:00:50	0	0	1	0	0	3

Converting all files in a directory

Suppose you have a lot of agd files in one directory. You can convert all of them at the same time, outside of memory, using the batch_read_agd function.

It takes the path to the directory as input and will save the results in the current working directory.

You will get two csv files for all agd files (all_in_one = TRUE) :

• settings.csv which is a table with 28 columns (the 28 settings names) and as many rows as there are agd files in the directory.

• raw_data.csv which is a table with all measurements for all files, with a column "file_name" for identifying the individual sets of measurements.

This is how a call to the function looks like:

path_to_directory <- system.file("extdata", package = "convertagd")
batch_read_agd(path_to_directory, tz="GMT")