{"Type":"Package","Package":"nsrr","Title":"Interface to National Sleep Research Resource","Version":"0.2.0","Authors@R":"\nperson(given = \"John\",\nfamily = \"Muschelli\",\nrole = c(\"aut\", \"cre\"),\nemail = \"muschellij2@gmail.com\",\ncomment = c(ORCID = \"0000-0001-6469-1750\"))","Description":"Allows users to access data from the National Sleep\nResearch Resource ('NSRR') .","License":"GPL-3","Imports":"httr, jsonlite, tools, digest, stats, utils","Suggests":"covr, DT, knitr, rmarkdown, testthat, xml2, rvest, readr","Encoding":"UTF-8","LazyData":"true","VignetteBuilder":"knitr","URL":"https://github.com/muschellij2/nsrr","BugReports":"https://github.com/muschellij2/nsrr/issues","RoxygenNote":"7.1.0","NeedsCompilation":"no","Packaged":"2020-06-24 16:51:21 UTC; johnmuschelli","Author":"John Muschelli [aut, cre] ()","Maintainer":"John Muschelli ","Repository":"CRAN","Date/Publication":"2020-06-24 18:40:03 UTC","repoType":"cran","tarballUrl":"ftp://cran.r-project.org/pub/R/src/contrib/nsrr_0.2.0.tar.gz","jsonAuthors":[{"name":"John Muschelli","email":"muschellij2@gmail.com","maintainer":true}],"readme":"\n\n\n# nsrr\n\n\n\n[![Travis build\nstatus](https://travis-ci.com/muschellij2/nsrr.svg?branch=master)](https://travis-ci.com/muschellij2/nsrr)\n[![AppVeyor Build\nStatus](https://ci.appveyor.com/api/projects/status/github/muschellij2/nsrr?branch=master&svg=true)](https://ci.appveyor.com/project/muschellij2/nsrr)\n[![Codecov test\ncoverage](https://codecov.io/gh/muschellij2/nsrr/branch/master/graph/badge.svg)](https://codecov.io/gh/muschellij2/nsrr?branch=master)\n\n\nThe goal of nsrr is to allow users to access data from the National\nSleep Research Resource (’NSRR’) () through an\n`R` interface.\n\nWhy `R`? Many packages in `R` can read and process accelerometry, such\nas the [`GGIR`](https://cran.r-project.org/package=GGIR),\n[`ActivityIndex`](https://cran.r-project.org/package=ActivityIndex), and\n[`accelerometry`](https://cran.r-project.org/package=accelerometry);\nother packages such as\n[`edfReader`](https://cran.r-project.org/package=edfReader) can read in\nEDF data for polysomnography data. Also, the\n[`xml2`](https://cran.r-project.org/package=xml2) package can easily\nread in XML annotations into `R`. We believe the interplay with these\npackages, amongst others, allow for a flexible framework to download,\nprocess, and visualize data. The `nsrr` package is simply the entry\npoint into navigating the files available and downloading the data.\n\n## Installation\n\nYou can install the released version of nsrr from\n[CRAN](https://CRAN.R-project.org) with:\n\n``` r\ninstall.packages(\"nsrr\")\n```\n\n## Token\n\nTo retrieve your NSRR token, go to ,\nand sign in. This token will allow you access to any data sets you have\nrequested access to. If you do not have access, then it will allow you\nto download files that are publicly available.\n\nSet the token by adding this to your `~/.Renviron` file:\n\n``` r\nNSRR_TOKEN=\"YOUR TOKEN GOES HERE\"\n```\n\nThe token is accessible via `token = Sys.getenv(\"NSRR_TOKEN\")`. Each\n`nsrr` function also has the argument `token` to pass through if you do\nnot wish to set it.\n\nTo determine if you are authenticated, you can use:\n\n``` r\nlibrary(nsrr)\nnsrr_auth()\n$authenticated\n[1] TRUE\n\n$username\n[1] \"muschellij2\"\n\n$full_name\n[1] \"\"\n\n$first_name\nNULL\n\n$last_name\nNULL\n\n$email\n[1] \"muschellij2@gmail.com\"\n```\n\n## Examples\n\n### NSRR data sets\n\nHere is how you can access the NSRR datasets list:\n\n``` r\nlibrary(nsrr)\ndf = nsrr_datasets()\nDT::datatable(df)\n```\n\n

\n\n### NSRR data set files\n\nHere we first get a list of the files in the `datasets` sub-directory\nfrom the `shhs` data set:\n\n``` r\ndf = nsrr_dataset_files(\"shhs\", path = \"datasets\")\nhead(df)\n dataset full_path folder\n1 shhs datasets/archive datasets/\n2 shhs datasets/hrv-analysis datasets/\n3 shhs datasets/CHANGELOG.md datasets/\n4 shhs datasets/KNOWNISSUES.md datasets/\n5 shhs datasets/shhs1-dataset-0.15.0.csv datasets/\n6 shhs datasets/shhs2-dataset-0.15.0.csv datasets/\n file_name is_file file_size\n1 archive FALSE 0\n2 hrv-analysis FALSE 0\n3 CHANGELOG.md TRUE 11010\n4 KNOWNISSUES.md TRUE 11421\n5 shhs1-dataset-0.15.0.csv TRUE 24322962\n6 shhs2-dataset-0.15.0.csv TRUE 11897377\n file_checksum_md5 archived\n1 FALSE\n2 FALSE\n3 69bb54a32cdfc7bdddc13276b7c858c1 FALSE\n4 8598129123baa60e16977dc24aa780af FALSE\n5 3f26d37ec97e2bc88776850a31715398 FALSE\n6 21807d854010f036fd0d4f006eeed49d FALSE\n```\n\n### Downloading NSRR data set files\n\nWe can then download the `CHANGELOG.md` file as it’s publicly\naccessible.\n\n``` r\nurl = nsrr_download_url(\"shhs\", path = \"datasets/CHANGELOG.md\")\n# print URL\ndl = nsrr_download_file(\"shhs\", path = \"datasets/CHANGELOG.md\")\ndl$outfile\n[1] \"/var/folders/1s/wrtqcpxn685_zk570bnx9_rr0000gr/T//RtmpJUlkmk/filea17e12cd407.md\"\ncat(head(readLines(dl$outfile)), sep = \"\\n\")\n## 0.15.0 (November 18, 2019)\n\n- Remove EEG spectral summary variables\n- Add notes to height and weight varibles about top and bottom coding\n- The CSV datasets generated from a SAS export are located here:\n - `\\\\rfawin\\bwh-sleepepi-shhs\\nsrr-prep\\_releases\\0.15.0\\`\n```\n\n### Listing All NSRR data set files\n\nTo list all the files, recursively, you would run:\n\n``` r\nnsrr_all_dataset_files(\"shhs\")\n```\n\nbut it may take some time.\n\n### EDF files\n\nThe [`edfReader`](https://cran.r-project.org/package=edfReader) can read\nin EDF fields for polysomnography data. **Work in Progress - need access\nto EDF data**.\n\n``` r\nfiles = nsrr_dataset_files(\"shhs\", path= \"polysomnography/edfs/shhs1\")\ndl = nsrr_download_file(\"shhs\", path = \"polysomnography/edfs/shhs1/shhs1-200001.edf\")\n```","jobInfo":{"package":"nsrr","version":"0.2.0","parsingStatus":"success","parserVersion":1,"parsedAt":"2020-06-24T19:30:10+0000"}}

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Examples