The goal of nsrr is to allow users to access data from the National
Sleep Research Resource (’NSRR’) (https://sleepdata.org/) through an
R interface.
Why R? Many packages in R can read and process accelerometry, such
as the GGIR,
ActivityIndex, and
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.
You can install the released version of nsrr from CRAN with:
install.packages("nsrr")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 ~/.Renviron file:
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:
library(nsrr)
nsrr_auth()
$authenticated
[1] TRUE
$username
[1] "muschellij2"
$full_name
[1] ""
$first_name
NULL
$last_name
NULL
$email
[1] "[email protected]"Here is how you can access the NSRR datasets list:
library(nsrr)
df = nsrr_datasets()
DT::datatable(df)
Here we first get a list of the files in the datasets sub-directory
from the shhs data set:
df = nsrr_dataset_files("shhs", path = "datasets")
head(df)
dataset full_path folder
1 shhs datasets/archive datasets/
2 shhs datasets/hrv-analysis datasets/
3 shhs datasets/CHANGELOG.md datasets/
4 shhs datasets/KNOWNISSUES.md datasets/
5 shhs datasets/shhs1-dataset-0.15.0.csv datasets/
6 shhs datasets/shhs2-dataset-0.15.0.csv datasets/
file_name is_file file_size
1 archive FALSE 0
2 hrv-analysis FALSE 0
3 CHANGELOG.md TRUE 11010
4 KNOWNISSUES.md TRUE 11421
5 shhs1-dataset-0.15.0.csv TRUE 24322962
6 shhs2-dataset-0.15.0.csv TRUE 11897377
file_checksum_md5 archived
1 <NA> FALSE
2 <NA> FALSE
3 69bb54a32cdfc7bdddc13276b7c858c1 FALSE
4 8598129123baa60e16977dc24aa780af FALSE
5 3f26d37ec97e2bc88776850a31715398 FALSE
6 21807d854010f036fd0d4f006eeed49d FALSEWe can then download the CHANGELOG.md file as it’s publicly
accessible.
url = nsrr_download_url("shhs", path = "datasets/CHANGELOG.md")
# print URL
dl = nsrr_download_file("shhs", path = "datasets/CHANGELOG.md")
dl$outfile
[1] "/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:
nsrr_all_dataset_files("shhs")but it may take some time.
The edfReader can read
in EDF fields for polysomnography data. Work in Progress - need access
to EDF data.
files = nsrr_dataset_files("shhs", path= "polysomnography/edfs/shhs1")
dl = nsrr_download_file("shhs", path = "polysomnography/edfs/shhs1/shhs1-200001.edf")
React
Typescript
Django
Laravel
Facebook
Microsoft
Google
Alibaba
D3
Tencent