metajam v0.2.3

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Easily Download Data and Metadata from 'DataONE'

A set of tools to foster the development of reproducible analytical workflow by simplifying the download of data and metadata from 'DataONE' (<https://www.dataone.org>) and easily importing this information into R.

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metajam

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Download and read data and metadata from repositories in the DataONE network.

Authors

Irene Steves, Mitchell Maier and Julien Brun; NCEAS

Installation

The metajam package can be installed from GitHub using the devtools package:

#install.packages("devtools")
devtools::install_github('NCEAS/metajam')

Download data

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 xml

How to get the URL to your dataset of interest ?

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



Read data

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")



Quick Overview of metajam

Acknowledgements

Work on this package was supported by:

  • NSF-PLR grant #1546024 to M. B. Jones, S. Baker-Yeboah, J. Dozier, M. Schildhauer, and A. Budden
  • 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

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.

NCEAS logo

Functions in metajam

Name Description
metajam metajam package
download_d1_data_pkg Download all data and metadata of a data package from DataONE
read_d1_files Read data and metadata based on download_d1_data() file structure
tabularize_eml Get tabular metadata
download_d1_data Download data and metadata from DataONE
check_version Check PID version
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Vignettes of metajam

Name
dataset-batch-processing.Rmd
dataset-single.Rmd
package-download.Rmd
reading-raster.Rmd
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Last month downloads

Details

Type Package
Date 2020-10-14
License Apache License (== 2.0)
URL https://github.com/nceas/metajam
BugReports https://github.com/nceas/metajam/issues
Encoding UTF-8
VignetteBuilder knitr
RoxygenNote 7.1.1
NeedsCompilation no
Packaged 2020-10-24 15:06:06 UTC; brun
Repository CRAN
Date/Publication 2020-11-03 11:40:02 UTC

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