NSRR staff
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Winda,
Dr. Quan does have the files, but he does not have permission to disseminate those data. We are arranging an NSRR Stakeholders meeting for this month and this may be one of the topics at hand. The option open to both of us at this point in time is to reach back out to the parent cohorts to (re)seek access to these specialized data points and to obtain permission for analyzing such data. I think the purpose of our internal discussion will be to see whether it is worthwhile to try and invest the time and effort to obtain additional data (e.g. physical activity) to somehow bring under the more "open" umbrella here at sleepdata.org. If we make any progress I will provide updates.
Stephany,
As an update -- we have regenerated most of the "NSRR XML" files for our datasets (only MrOS is still pending). We fixed the two issues you brought to our attention. Remo's suggested changes/fixes from above were both incorporated into the translation tool.
It looks as if these are B/C variables that were available in select cohorts, but were not compiled and published with the main SHHS data sources and A variables.
From S. Quan:
In any event, these data are SHHS cohort specific and need to be requested from individual cohorts if they are available. Not every cohort has the data.
Your question spurred an additional question about whether we (the NSRR group) should attempt to compile some of these additional data domains from the SHHS cohorts in order to share these out to our users. That would obviously take awhile, but I will try to revisit this thread if anything ever come of it!
Thanks,
Mike
I see the Table you are referencing. Nothing comes to mind for me regarding those domains, and I can't find anything of much use in the SHHS data dictionary. I went ahead and emailed a couple of the paper authors to see if they could provide any guidance.
I'll get back in touch when I hear back.
Thanks for inquiring about this on the forum! It appears you have discovered a bug with the NSRR-translated XML files. The bug exists in the EDF Editor and Translator tool, which appears to not be counting the first epoch (30 seconds) of the recording in the duration of the first staging element (typically Wake).
To answer your questions:
Yes, the staging information appears different between the files, which is incorrect. Your best bet is to use staging information from the Profusion XML files until we implement a fix in the tool and regenerate the NSRR-translated XMLs.
As for your second question about total lengths of sleep staging, I believe the NSRR-translated XMLs drop the last staging group in the file. Hence, if you had two hours of wake (Profusion XML staging = 0) at the end of the recording, this wouldn't be output to the NSRR-translated XML file. I gather this was done for "cropping" purposes to eliminate lots of not-that-useful data from the end of the file and make the hypnogram display better in the accompanying EDF Viewer. That said, I am going to follow-up with the developers of the tool to confirm and ask whether it might be more appropriate to have the total lengths of sleep staging match 1:1 between the two XML files (i.e. output the last staging group).
Thanks again for bringing this to our attention!
Good question. SHHS is, at times, difficult to understand! I pored over the original documentation from the SHHS Coordinating Center and here's my take:
'weight20' was collected at the time of the blood pressure collection (clinic visit) that was specifically geared toward SHHS (i.e. not a regular visit for the parent cohort study).
'weight' was likely collected from a time period before 'weight20'. 'weight' is listed in the documentation as an "A-variable", which were not collected as part of the SHHS clinic visit, but were reported otherwise by the parent cohort. The A-variable, in this case, would be used to compute BMI in instances where 'weight20' was not available.
To conclude, it looks like 'weight20' would be the preferred weight variable to use for SHHS1 since it happened closest to the SHHS clinic visit. We don't know how much earlier 'weight' was collected because the corresponding 'weightdt' (date of weight data collection) was stripped out of the final dataset.
'weight20' was collected at the SHHS1 clinic visit, which corresponds with the initial round of home sleep testing. Weight was collected on a form alongside blood pressure and neck circumference at this clinic visit.
Thanks for pointing this out -- it is rather confusing. We will add it to our Known Issues list. We'll also add more context on the variable page itself.
We have released the 0.7.0 dataset for the Sleep Heart Health Study. This dataset adds new dataset files pertaining to EEG spectral analysis and cardiovascular events.
Release summary:
Yes, you can view the CHANGELOG to see the changes. For this release we added new datasets (EEG spectral analysis and CVD Events); the existing datasets should have stayed the same (save for some data dictionary corrections/fixes).
I will make a post for the new release. Thanks!