ScienceBase R Tools

Tools for interfacing R with ScienceBase data services.

Package Description

This package provides a rich interface to USGS’s ScienceBase, a data cataloging and collaborative data management platform. For further information, see the sbtools manuscript in The R Journal (USGS IP-075498). See citation('sbtools') for how to cite the package.

  Winslow, LA, S Chamberlain, AP Appling, and JS Read. 2016. sbtools: 
  A package connecting R to cloud-based data for collaborative online 
  research. The R Journal 8:387-398.

Package source code DOI: https://doi.org/10.5066/P912NGFV

Linux Test Coverage
R-CMD-check codecov.io

Current CRAN information

Version Monthly Downloads Total Downloads
CRAN version

Package Installation

To install the sbtools package, you must be using R 3.0 or greater and run the following command:

install.packages("sbtools")

To get cutting-edge changes, install from GitHub using the devtools packages:

remotes::install_github("USGS-R/sbtools")

Reporting bugs

Please consider reporting bugs and asking questions on the Issues page:

https://github.com/USGS-R/sbtools/issues

Follow @USGS_R on Twitter for updates on USGS R packages:

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Examples

library(sbtools)

# Query ScienceBase for data about Antarctica
query_sb_text('Antarctica', limit=1)
## [[1]]
## <ScienceBase Item>
##   Title: Antarctica. Unnamed peak in the Nunataks near camp 18. January 21, 1978.
##   Creator/LastUpdatedBy:      /
##   Provenance (Created / Updated):   /
##   Children:
##   Item ID: 51dc2e89e4b0f81004b79cf6
##   Parent ID: 519ba0a3e4b0e4e151ef5dd9

# Query for a specific DOI
query_sb_doi('10.5066/F7M043G7')
## [[1]]
## <ScienceBase Item>
##   Title: 2013 Raw Ground Penetrating Radar Data on Alaska's Glaciers
##   Creator/LastUpdatedBy: /
##   Provenance (Created / Updated): 2015-06-15T16:55:03Z / 2015-12-15T20:39:06Z
##   Children: TRUE
##   Item ID: 557f0367e4b023124e8ef621
##   Parent ID: 5474ec49e4b04d7459a7eab2

# Inspect the contents of the above item
children <- item_list_children('557f0367e4b023124e8ef621')
sapply(children, function(child) child$title)
## [1] "Raw Ground Penetrating Radar Data, Valdez Glacier, Alaska; 2013"   
## [2] "Raw Ground Penetrating Radar Data, Gulkana Glacier, Alaska; 2013"  
## [3] "Raw Ground Penetrating Radar Data, Eklutna Glacier, Alaska; 2013"  
## [4] "Raw Ground Penetrating Radar Data, Eureka Glacier, Alaska; 2013"   
## [5] "Raw Ground Penetrating Radar Data, Taku Glacier, Alaska; 2013"     
## [6] "Raw Ground Penetrating Radar Data, Scott Glacier, Alaska; 2013"    
## [7] "Raw Ground Penetrating Radar Data, Wolverine Glacier, Alaska; 2013"

# Log in (requires a ScienceBase account) and create an item
authenticate_sb() # type in username and password
my_home_item <- user_id()
new_item <- item_create(title = 'new test item', parent_id = my_home_item)
test.txt <- file.path(tempdir(), 'test.txt')
writeLines(c('this is','my data file'), test.txt)
item_append_files(new_item, test.txt)
item_list_files(new_item)$fname
## [1] "test.txt"

Release Procedure

For release of the sbtools package, a number of steps are required.

  1. Ensure all checks pass and code coverage is adequate.
  2. Ensure NEWS.md reflects updates in version.
  3. Update DESCRIPTION to reflect release version.
  4. Build source package and upload to CRAN.
  5. Once accepted to CRAN, convert DISCLAIMER.md to approved language.
  6. Change references to main branch in code.json to release version.
  7. Commit changes and tag repository at release version. Push tag.
  8. Change code.json and DISCLAIMER.md back to development mode.

Disclaimer

This software has been approved for release by the U.S. Geological Survey (USGS). Although the software has been subjected to rigorous review, the USGS reserves the right to update the software as needed pursuant to further analysis and review. No warranty, expressed or implied, is made by the USGS or the U.S. Government as to the functionality of the software and related material nor shall the fact of release constitute any such warranty. Furthermore, the software is released on condition that neither the USGS nor the U.S. Government shall be held liable for any damages resulting from its authorized or unauthorized use.

This software is in the public domain because it contains materials that originally came from the U.S. Geological Survey, an agency of the United States Department of Interior. For more information, see the official USGS copyright policy

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