{"Package":"metajam","Type":"Package","Title":"Easily Download Data and Metadata from 'DataONE'","Version":"0.2.3","Date":"2020-10-14","Authors@R":"c(\nperson(\"Julien\", \"Brun\",\nemail = \"brun@nceas.ucsb.edu\",\ncomment = c(ORCID = \"0000-0002-7751-6238\"),\nrole = c(\"cre\", \"aut\")),\nperson(\"Irene\", \"Steves\",\ncomment = c(ORCID = \"0000-0002-5511-9717\",\n\"https://github.com/isteves\"),\nrole = \"aut\"),\nperson(\"Mitchell\", \"Maier\",\ncomment= c(ORCID = \"0000-0001-6955-0535\"),\nrole = \"aut\"),\nperson(\"Nathan\", \"Hwangbo\",\nemail = \"nathanhwangbo@gmail.com\",\ncomment= c(ORCID = \"0000-0002-3777-0821\"),\nrole = \"ctb\"),\nperson(\"Derek\", \"Strong\",\nemail = \"dstrong@nceas.ucsb.edu\",\ncomment= c(ORCID = \"0000-0002-0347-8574\"),\nrole = \"ctb\"),\nperson(\"Colin\", \"Smith\",\nemail = \"colin.smith@wisc.edu\",\ncomment = c(ORCID = \"0000-0003-2261-9931\"),\nrole = \"ctb\"),\nperson(\"Kristen\", \"Peach\",\nemail = \"peach@nceas.ucsb.edu\",\ncomment = c(ORCID = \"0000-0002-6388-0901\"),\nrole = \"ctb\")\n)","Maintainer":"Julien Brun ","Description":"A set of tools to foster the development of reproducible analytical workflow by simplifying the download of data and\nmetadata from 'DataONE' () and easily importing this information into R.","License":"Apache License (== 2.0)","URL":"https://github.com/nceas/metajam","BugReports":"https://github.com/nceas/metajam/issues","Imports":"dataone, dplyr, EML, emld, lubridate, purrr, readr, stats,\nstringr, tibble, tidyr, rlang","Suggests":"testthat, knitr, rmarkdown, udunits2","Encoding":"UTF-8","VignetteBuilder":"knitr","RoxygenNote":"7.1.1","NeedsCompilation":"no","Packaged":"2020-10-24 15:06:06 UTC; brun","Author":"Julien Brun [cre, aut] (),\nIrene Steves [aut] (,\nhttps://github.com/isteves),\nMitchell Maier [aut] (),\nNathan Hwangbo [ctb] (),\nDerek Strong [ctb] (),\nColin Smith [ctb] (),\nKristen Peach [ctb] ()","Repository":"CRAN","Date/Publication":"2020-11-03 11:40:02 UTC","repoType":"cran","tarballUrl":"ftp://cran.r-project.org/pub/R/src/contrib/metajam_0.2.3.tar.gz","jsonAuthors":[{"name":"Julien Brun","email":"brun@nceas.ucsb.edu","maintainer":true},{"name":"Irene Steves","email":null,"maintainer":false},{"name":"Mitchell Maier","email":null,"maintainer":false},{"name":"Nathan Hwangbo","email":"nathanhwangbo@gmail.com","maintainer":false},{"name":"Derek Strong","email":"dstrong@nceas.ucsb.edu","maintainer":false},{"name":"Colin Smith","email":"colin.smith@wisc.edu","maintainer":false},{"name":"Kristen Peach","email":"peach@nceas.ucsb.edu","maintainer":false}],"readme":"

\n\n# metajam\n\n[![Travis-CI Build Status](https://travis-ci.org/NCEAS/metajam.svg?branch=master)](https://travis-ci.org/NCEAS/metajam)\n\n\nDownload and read data and metadata from repositories in the DataONE network. \n\n## Authors\n\nIrene Steves, Mitchell Maier and Julien Brun; NCEAS\n\n## Installation\n\nThe `metajam` package can be installed from GitHub using the `devtools` package:\n\n```\n#install.packages(\"devtools\")\ndevtools::install_github('NCEAS/metajam')\n```\n\n## Download data\n\nTo download a data object, specify the data object URL and local download path in the `download_d1_data` function:\n\n```\nlibrary(metajam)\n\ndownload_d1_data(\"https://arcticdata.io/metacat/d1/mn/v2/object/urn%3Auuid%3A9e123f84-ce0d-4094-b898-c9e73680eafa\", path = \".\")\n```\n
\n

\n
\n
\n

\n
\n\nThe output is saved in a folder with the name `{metadata_id}__{file_name}`, which contains the data file and its associated metadata. The metadata follows these conventions:\n\n- `{file_name}__summary_metadata.csv` - summary metadata in a tabular format, which includes date downloaded, data file name, file/metadata URLs, etc.\n- `{file_name}__full_metadata.xml` - metadata xml file, if it could be downloaded\n- `{file_name}__attribute_metadata.csv` - attribute metadata in a tabular format, if included in the metadata xml\n- `{file_name}__attribute_factor_metadata.csv` - attribute factor metadata in a tabular format, if included in the metadata xml\n\n## How to get the URL to your dataset of interest ?\n\nFrom DataONE or any currently supported data repository ([KNB](https://knb.ecoinformatics.org/), [Arctic Data Center](https://arcticdata.io/), or [EDI/LTER](https://portal.edirepository.org/nis/home.jsp)), you can right-click on the `Download` button of a specific dataset and choose `Copy Link Address` to copy the URL to your clipboard\n\n
\n

\n
\n\n## Read data\n\nThe `read_d1_files` function allows you to read the downloaded data and metadata directly into your R environment. Simply run the function with the folder path to the downloaded objects, and all data and metadata files will be returned as data frames stored in a list. Use `{object_name}$data` to access the data, and `{object_name}${metadata_type}_metadata` to access its associated metadata.\n\n```\nschools <- read_d1_files(\"./doi_10.18739_A2DP3X__Alaska_Schools_Rentention2009_15\")\n```\n\n
\n

\n
\n\n## Quick Overview of `metajam`\n\n- Recent presentation on `metajam` and its functionalities: [Click here](https://brunj7.github.io/metajam-presentations/metajam-nceas-roundtable18.html)\n- Package website: https://nceas.github.io/metajam/\n\n## Acknowledgements\n\nWork on this package was supported by:\n\n- NSF-PLR grant #1546024 to M. B. Jones, S. Baker-Yeboah, J. Dozier, M. Schildhauer, and A. Budden\n- Long Term Ecological Research (LTER) National Communications Office (LNCO), NSF grant #1545288 to F. Davis, M. Schildhauer, S. Rebich Hespanha, J. Caselle and C. Blanchette\n\nThanks also go to NCEAS computing team members Mark Schildhauer, Peter Slaughter, Dominic Muellen, Steven Chong, Jesse Goldstein and Matt Jones for their inputs on this package.\n\n![NCEAS logo](https://www.nceas.ucsb.edu/files/logos/NCEAS/NCEAS-full%20logo-4C.jpg)","jobInfo":{"package":"metajam","version":"0.2.3","parsingStatus":"success","parserVersion":1,"parsedAt":"2020-11-03T12:29:47+0000"}}

Description

Arguments

Details