Use Case 1 - Processing a Single Dataset from Arctic Data Center

Summary

This vignette aims to showcase a use case using the 2 main functions of metajam - download_d1_data and read_d1_files to download one dataset from the Arctic Data Center data repository.

As example, we are using permafrost data from the Polaris Project 2017: Sarah Ludwig, Robert M Holmes, Susan Natali, Paul Mann, John Schade, et al. 2018. Polaris Project 2017: Permafrost carbon and nitrogen, Yukon-Kuskokwim Delta, Alaska. Arctic Data Center. doi:10.18739/A2KK3F.

Libraries and constants

# devtools::install_github("NCEAS/metajam")
library(metajam)  

# Directory to save the data set
path_folder <- "Data_polaris"

# URL to download the dataset from DataONE
data_url <- "https://arcticdata.io/metacat/d1/mn/v2/object/urn%3Auuid%3Aec704da8-f174-49db-b993-bae479cdc5d9"

Download the dataset

# Create the local directory to download the datasets
dir.create(path_folder, showWarnings = FALSE)

# Download the dataset and associated metdata 
data_folder <- metajam::download_d1_data(data_url, path_folder)
# data_folder
# "Data_polaris/doi_10.18739_A2KK3F__Polaris_2017_Permafrost"

At this point, you should have the data and the metadata downloaded inside your main directory; Data_polaris in this example. metajam organize the files as follow:

• Each dataset is stored a sub-directory named after the package DOI and the file name
• Inside this sub-directory, you will find
  • the data: my_data.csv
  • the raw EML with the naming convention file name + __full_metadata.xml: my_data__full_metadata.xml
  • the package level metadata summary with the naming convention file name + __summary_metadata.csv: my_data__summary_metadata.csv
  • If relevant, the attribute level metadata with the naming convention file name + __attribute_metadata.csv: my_data__attribute_metadata.csv
  • If relevant, the factor level metadata with the naming convention file name + __attribute_factor_metadata.csv: my_data__attribute_factor_metadata.csv

Local file structure of a dataset downloaded by metajam

Read the data and metadata in your R environment

# Read all the datasets and their associated metadata in as a named list
polaris17_permafrost <- metajam::read_d1_files(data_folder)

Structure of the named list object

You have now loaded in your R environment one named list object that contains the data polaris17_permafrost$data, the general (summary) metadata polaris17_permafrost$summary_metadata - such as title, creators, dates, locations - and the attribute level metadata information polaris17_permafrost$attribute_metadata, allowing user to get more information, such as units and definitions of your attributes.

Structure of the named list object containing tabular metadata and data as loaded by metajam