The goal of nsrr is to allow users to access data from the National Sleep Research Resource (’NSRR’) (https://sleepdata.org/) through an
R? Many packages in
R can read and process accelerometry, such as the
accelerometry; other packages such as
edfReader can read in EDF data for polysomnography data. Also, the
xml2 package can easily read in XML annotations into
R. We believe the interplay with these packages, amongst others, allow for a flexible framework to download, process, and visualize data. The
nsrr package is simply the entry point into navigating the files available and downloading the data.
To retrieve your NSRR token, go to https://sleepdata.org/dashboard, and sign in. This token will allow you access to any data sets you have requested access to. If you do not have access, then it will allow you to download files that are publicly available.
Set the token by adding this to your
NSRR_TOKEN="YOUR TOKEN GOES HERE"
The token is accessible via
token = Sys.getenv("NSRR_TOKEN"). Each
nsrr function also has the argument
token to pass through if you do not wish to set it.
To determine if you are authenticated, you can use:
Here is how you can access the NSRR datasets list:
Here we first get a list of the files in the
datasets sub-directory from the
shhs data set:
df = nsrr_dataset_files("shhs", path = "datasets") head(df) dataset full_path folder 1 shhs datasets/archive datasets/ 2 shhs datasets/hrv-analysis datasets/ 3 shhs datasets/CHANGELOG.md datasets/ 4 shhs datasets/KNOWNISSUES.md datasets/ 5 shhs datasets/shhs1-dataset-0.15.0.csv datasets/ 6 shhs datasets/shhs2-dataset-0.15.0.csv datasets/ file_name is_file file_size 1 archive FALSE 0 2 hrv-analysis FALSE 0 3 CHANGELOG.md TRUE 11010 4 KNOWNISSUES.md TRUE 11421 5 shhs1-dataset-0.15.0.csv TRUE 24322962 6 shhs2-dataset-0.15.0.csv TRUE 11897377 file_checksum_md5 archived 1 <NA> FALSE 2 <NA> FALSE 3 69bb54a32cdfc7bdddc13276b7c858c1 FALSE 4 8598129123baa60e16977dc24aa780af FALSE 5 3f26d37ec97e2bc88776850a31715398 FALSE 6 21807d854010f036fd0d4f006eeed49d FALSE
We can then download the
CHANGELOG.md file as it’s publicly accessible.
url = nsrr_download_url("shhs", path = "datasets/CHANGELOG.md") # print URL dl = nsrr_download_file("shhs", path = "datasets/CHANGELOG.md") dl$outfile  "/var/folders/1s/wrtqcpxn685_zk570bnx9_rr0000gr/T//RtmpJUlkmk/filea17e12cd407.md" cat(head(readLines(dl$outfile)), sep = "\n") ## 0.15.0 (November 18, 2019) - Remove EEG spectral summary variables - Add notes to height and weight varibles about top and bottom coding - The CSV datasets generated from a SAS export are located here: - `\\rfawin\bwh-sleepepi-shhs\nsrr-prep\_releases\0.15.0\`
To list all the files, recursively, you would run:
but it may take some time.