Download and read data and metadata from repositories in the DataONE network.
Julien Brun, Irene Steves, Mitchell Maier, Kristen Peach and Nick Lyon as main contributors; with special thanks to Colin Smith, Derek Strong and Nathan Hwangbo for their contributions to this package.
The metajam
package can be installed from CRAN:
install.packages("metajam")
The development version of metajam
package can also be installed from GitHub using the devtools
package:
#install.packages("devtools")
devtools::install_github('NCEAS/metajam')
The process of using metajam
is as follows:
metajam::download_d1_data
)metajam::read_d1_files
)These steps are described in greater detail--with included examples--below.
From DataONE or any currently supported data repository (KNB, Arctic Data Center, or EDI/LTER), you can right-click on the Download
button of a specific dataset and choose Copy Link Address
to copy the URL to your clipboard
To download a data object, specify the data object URL and local download path in the download_d1_data
function:
library(metajam)
download_d1_data("https://arcticdata.io/metacat/d1/mn/v2/object/urn%3Auuid%3A9e123f84-ce0d-4094-b898-c9e73680eafa", path = ".")
The 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:
{file_name}__summary_metadata.csv
- summary metadata in a tabular format, which includes date downloaded, data file name, file/metadata URLs, etc.{file_name}__full_metadata.xml
- metadata xml file, if it could be downloaded{file_name}__attribute_metadata.csv
- attribute metadata in a tabular format, if included in the metadata xml{file_name}__attribute_factor_metadata.csv
- attribute factor metadata in a tabular format, if included in the metadata xmlThe 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.
schools <- read_d1_files("./doi_10.18739_A2DP3X__Alaska_Schools_Rentention2009_15")
metajam
metajam
and its functionalities: Click heremetajam
demo: Click hereWork on this package was supported by:
Thanks 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.