README.md

In masalmon/convertagd: Read agd Files From Actigraph

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")

masalmon/convertagd documentation built on May 21, 2019, 12:40 p.m.