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Download and read data and metadata from repositories in the DataONE network.
Irene Steves, Mitchell Maier and Julien Brun; NCEAS
The metajam
package can be installed from GitHub using
the devtools
package:
#install.packages("devtools")
devtools::install_github('NCEAS/metajam')
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
xmlFrom 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
The 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
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.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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