Type:	Package
Title:	Easily Download Data and Metadata from 'DataONE'
Version:	0.3.1
Date:	2024-08-06
Maintainer:	Julien Brun <julien.brun@alumni.duke.edu>
Description:	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.
License:	Apache License (== 2.0)
Encoding:	UTF-8
Language:	en-US
RoxygenNote:	7.3.2
SystemRequirements:	Mac OSX: redland (>= 1.0.14) ; Linux: librdf0 (>= 1.0.14), librdf0-dev (>= 1.0.14)
URL:	https://nceas.github.io/metajam/, https://github.com/NCEAS/metajam
BugReports:	https://github.com/NCEAS/metajam/issues
Depends:	R (≥ 3.6.0)
Imports:	dataone, dplyr, EML, emld, lubridate, purrr, readr, stats, stringr, tibble, tidyr, XML
Suggests:	knitr, rmarkdown, testthat
VignetteBuilder:	knitr
NeedsCompilation:	no
Packaged:	2024-08-16 17:28:05 UTC; jb160-local
Author:	Julien Brun [cre, aut], Irene Steves [aut] (https://github.com/isteves), Mitchell Maier [aut], Kristen Peach [aut], Nicholas Lyon [aut] (https://njlyon0.github.io/), Nathan Hwangbo [ctb], Derek Strong [ctb], Colin Smith [ctb], Regents of the University of California [cph]
Repository:	CRAN
Date/Publication:	2024-08-16 17:50:02 UTC

metajam: Easily Download Data and Metadata from 'DataONE'

Description

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.

Author(s)

Maintainer: Julien Brun julien.brun@alumni.duke.edu (ORCID)

Authors:

• Irene Steves (ORCID) (https://github.com/isteves)

• Mitchell Maier (ORCID)

• Kristen Peach peach@nceas.ucsb.edu (ORCID)

• Nicholas Lyon lyon@nceas.ucsb.edu (ORCID) (https://njlyon0.github.io/)

Other contributors:

• Nathan Hwangbo nathanhwangbo@gmail.com (ORCID) [contributor]

• Derek Strong dstrong@nceas.ucsb.edu (ORCID) [contributor]

• Colin Smith colin.smith@wisc.edu (ORCID) [contributor]

• Regents of the University of California [copyright holder]

See Also

Useful links:

• https://nceas.github.io/metajam/

• https://github.com/NCEAS/metajam

• Report bugs at https://github.com/NCEAS/metajam/issues

Check PID version

Description

This function takes an identifier and checks to see if it has been obsoleted.

Usage

check_version(pid, formatType = NULL)

Arguments

Value

(data.frame) A data frame of object version PIDs and related information.

Examples

## Not run: 
# Most data URLs and identifiers work
check_version("https://cn.dataone.org/cn/v2/resolve/urn:uuid:a2834e3e-f453-4c2b-8343-99477662b570")
check_version("doi:10.18739/A2ZF6M")

# Specify a formatType (data, metadata, or resource)
check_version("doi:10.18739/A2ZF6M", formatType = "metadata")

# Returns a warning if the identifier has been obsoleted
check_version("doi:10.18739/A2HF7Z", formatType = "metadata")

# Returns an error if no matching identifiers are found
check_version("a_test_pid")

# Returns a warning if several identifiers are returned
check_version("10.18739/A2057CR99")

## End(Not run)

Download data and metadata from a dataset that uses EML metadata.

Description

This is an internal function called by the download_d1_data.R function. Not to be exported

Usage

download_EML_data(data_url, meta_obj, meta_id, data_id, metadata_nodes, path)

Arguments

Download data and metadata from a dataset that uses ISO metadata.

Description

This is an internal function called by the download_d1_data.R function. Not to be exported

Usage

download_ISO_data(meta_raw, meta_obj, meta_id, data_id, metadata_nodes, path)

Arguments

Download data and metadata from DataONE

Description

Downloads a data object from DataONE along with metadata.

Usage

download_d1_data(data_url, path)

Arguments

Value

(character) Path where data is downloaded to.

See Also

[read_d1_files()] [download_d1_data_pkg()]

Examples

## Not run: 
download_d1_data("urn:uuid:a2834e3e-f453-4c2b-8343-99477662b570", path = file.path("."))
download_d1_data(
   "https://cn.dataone.org/cn/v2/resolve/urn:uuid:a2834e3e-f453-4c2b-8343-99477662b570",
    path = file.path(".")
    )

## End(Not run)

Download all data and metadata of a data package from DataONE

Description

Downloads all the data objects of a data package from DataONE along with metadata.

Usage

download_d1_data_pkg(meta_obj, path)

Arguments

Value

(list) Paths where data are downloaded to.

See Also

[read_d1_files()] [download_d1_data()]

Examples

## Not run: 
download_d1_data_pkg("doi:10.18739/A2028W", ".")
download_d1_data_pkg("https://doi.org/10.18739/A2028W", ".")

## End(Not run)

Read data and metadata based on 'download_d1_data()' file structure

Description

Reads data along with metadata into your R environment based on [download_d1_data()] file structure.

Usage

read_d1_files(folder_path, fnc = "read_csv", ...)

Arguments

Value

(list) Named list containing data and metadata as data frames.

See Also

[download_d1_data()] [download_d1_data_pkg()]

Examples

data_folder <- system.file(file.path("extdata", "test_data"), package = "metajam")
soil_moist_data <- read_d1_files(data_folder)

# You can specify the function you would like to use to read the file and pass parameters
soil_moist_data_skipped <- read_d1_files(data_folder, "read.csv",
                                         skip = 8, stringsAsFactors = FALSE)

Get tabular metadata

Description

This function takes a path to an EML (.xml) metadata file and returns a data frame.

Usage

tabularize_eml(eml, full = FALSE)

Arguments

Value

(data.frame) A data frame of selected EML values.

Examples

   eml <- system.file("extdata", "test_data", "SoilMois2012_2017__full_metadata.xml",
                  package = "metajam")
   tabularize_eml(eml)