read_gt3x null activity?

[edmundseto]

Thanks for developing this package. I'm a new user.

When I call read_gt3x on an Actigraph wGT3X-BT raw gt3x file, the result contains useful metadata, parameters, battery, capsense info. But, the activity in the result is null. Is this expected?

The gt3x file seems OK, as I can export it to csv in Actilife, and obtain the time-series of activity that way.

Best,

Edmund

[paulhibbing]

Hi Edmund,

Thanks for reaching out. I'm happy to try diagnosing what's going on. It's been awhile since I wrote the current version of the code, but here are a few clarifying questions based on what I remember:

• Do you get any errors or warnings?
• Does your output include a RAW element, or is that what you're saying is NULL? (Most packet types get saved under their original names [PARAMETERS, CAPSENSE, etc.], but I think acceleration data get saved as RAW in most or all cases -- If you see that in your output, it should match what you get out of ActiLife)
• Was your data collected through CentrePoint? (I don't think that's applicable for wGT3X-BT, but if it is, that's a very likely culprit -- my current code often generalizes poorly to output from CentrePoint)
• Is the output from ActiLife all 0's? (If there's no acceleration data in the file, AGread might return NULL, whereas ActiLife might fill in 0's)
• Is there a chance the data were collected using a hardware/firmware scheme that is not yet supported (see #10 and #19)? (This might be hard to tell, which is fine -- basically there are some monitors that collect data in a different way than I currently support, which could be the issue)

If those questions don't help us solve the issue, I can try to take a more careful look. But I will probably need you to provide a sample file if we go that route, and I know that can be an issue with research data. Hopefully it won't be necessary. Just let me know!

[edmundseto]

Hi Paul,

Your response was helpful. I think it's related to issue #19.

• I turned on verbose=T, and yes there were warnings/errors (in bold below):

---

Processing file.gt3x

Parsing info.txt ............. COMPLETE

Will parse the following packet types, if available: METADATA, PARAMETERS, SENSOR_SCHEMA, BATTERY EVENT, TAG, ACTIVITY, HEART_RATE_BPM HEART_RATE_ANT, HEART_RATE_BLE, LUX, CAPSENSE EPOCH, EPOCH2, EPOCH3, EPOCH4 ACTIVITY2, SENSOR_DATA

Reading log.bin ............. COMPLETE Getting record headers ............... COMPLETE Parsing PARAMETERS packet(s) ............. COMPLETE
Parsing EVENT packet(s) ............. COMPLETE
Parsing METADATA packet(s) ............. COMPLETE
Parsing BATTERY packet(s) ............. COMPLETE
Parsing ACTIVITY packet(s)No method exists yet for parsing ACTIVITY packets -- returning NULL. Parsing LUX packet(s)No method exists yet for parsing LUX packets -- returning NULL. Parsing CAPSENSE packet(s) ............. COMPLETE

---

• I don't see a "RAW" element. I get a result list with METADATA, BATTERY, ACTIVITY(this is null), LUX (this is also null), CAPSENSE, PARAMETERS, and EVENT.
• I don't think this went through Centrepoint. I believe the study coordinator downloaded this file directly from a participant's device and provided to me.
• Looking at the code in issue #19, I also tried running the file through the read.gt3x package. Following the vignette for that package, I was able to see the X,Y,Z data and plot a subset of the data. The accelerometry seems to exist, and is non-zero.
• If it helps, read.gt3x reported that my devices are running firmware v1.9.2. I did read at the bottom of issue #19 that there's a way, using parser = "dev" in AGread to parse the ACTIVITY packets that apparently my Actigraphs are saving in the gt3x files. I'll try that soon. But, in the meantime, the read.gt3x package seems to be a good complement to AGread for working with the files. So if you want to close this issue, that'd be OK for me.

Thanks again, Edmund

[paulhibbing]

Ah, I think this may be a version issue. I have made updates on GitHub that are not yet available on CRAN. I always forget about that (not the first time).

Can you try running remotes::install_github(“paulhibbing/AGread”) ? After the installation completes, you may want to restart your session before trying your file again.

Hope that does the trick!

[paulhibbing]

Hi @edmundseto, just checking back to see if the above suggestion helped. I will probably close this issue in a week or so if there's no further discussion.