ScienceBase R Tools
Tools for interfacing R with ScienceBase data services.
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
(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
Current CRAN information
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To install the
sbtools package, you must be using R 3.0 or greater and
run the following command:
To get cutting-edge changes, install from GitHub using the
Please consider reporting bugs and asking questions on the Issues page:
library(sbtools) # Query ScienceBase for data about Antarctica query_sb_text('Antarctica', limit=1) #> [] #> <ScienceBase Item> #> Title: Tectonics of Antarctica #> Creator/LastUpdatedBy: / #> Provenance (Created / Updated): / #> Children: #> Item ID: 505ba488e4b08c986b3203fa #> Parent ID: 4f4e4771e4b07f02db47e1e4 # Query for a specific DOI query_sb_doi('10.5066/F7M043G7') #> list() # Inspect the contents of the above item children <- item_list_children('557f0367e4b023124e8ef621') #> Request failed . Retrying in 1 seconds... #> Request failed . Retrying in 2.2 seconds... #> Item not found for ID=557f0367e4b023124e8ef621. Either the item does not exist or the item is secured and requires authentication to access.FALSE #> Request failed . Retrying in 1.7 seconds... #> Request failed . Retrying in 1 seconds... sapply(children, function(child) child$title) #> list() # Log in (requires a ScienceBase account) and create an item authenticate_sb(Sys.getenv("sb_user")) # type in password my_home_item <- user_id() new_item <- item_create(title = 'new test item', parent_id = my_home_item) test.txt <- file.path(tempdir(), 'test.txt') writeLines(c('this is','my data file'), "test.txt") item_append_files(new_item, "test.txt") #> <ScienceBase Item> #> Title: new test item #> Creator/LastUpdatedBy: firstname.lastname@example.org / email@example.com #> Provenance (Created / Updated): 2022-11-03T19:47:46Z / 2022-11-03T19:47:48Z #> Children: FALSE #> Item ID: 63641ae2d34ebe4425074d93 #> Parent ID: 4f7afec1e4b0b2f259355f30 item_list_files(new_item)$fname #>  "test.txt" item_rm(new_item) #> Response [https://www.sciencebase.gov/catalog/item/63641ae2d34ebe4425074d93?format=json] #> Date: 2022-11-03 19:47 #> Status: 200 #> Content-Type: <unknown> #> <EMPTY BODY> unlink("test.txt")
For release of the sbtools package, a number of steps are required.
- Ensure all checks pass and code coverage is adequate.
NEWS.mdreflects updates in version.
DESCRIPTIONto reflect release version.
- Build source package and upload to CRAN.
- Once accepted to CRAN, convert
DISCLAIMER.mdto approved language.
- Change references to main branch in
code.jsonto release version.
- Commit changes and tag repository at release version. Push tag.
DISCLAIMER.mdback to development mode.
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