Tools for interacting with U.S. Geological Survey ScienceBase < https://www.sciencebase.gov> interfaces. ScienceBase is a data cataloging and collaborative data management platform. Functions included for querying ScienceBase, and creating and fetching datasets.
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. See
citation('sbtools') for how to cite the package.
To install the
sbtools package, you must be using R 3.0 or greater and run the following command:
To get inter-CRAN release updates, use the command:
To get cutting-edge changes, install from GitHub using the
Please consider reporting bugs and asking questions on the Issues page:
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library(sbtools)# Query ScienceBase for data about Antarcticaquery_sb_text('Antarctica', limit=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 DOIquery_sb_doi('10.5066/F7M043G7')## []## <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 itemchildren <- item_list_children('557f0367e4b023124e8ef621')sapply(children, function(child) child$title)##  "Raw Ground Penetrating Radar Data, Valdez Glacier, Alaska; 2013"##  "Raw Ground Penetrating Radar Data, Gulkana Glacier, Alaska; 2013"##  "Raw Ground Penetrating Radar Data, Eklutna Glacier, Alaska; 2013"##  "Raw Ground Penetrating Radar Data, Eureka Glacier, Alaska; 2013"##  "Raw Ground Penetrating Radar Data, Taku Glacier, Alaska; 2013"##  "Raw Ground Penetrating Radar Data, Scott Glacier, Alaska; 2013"##  "Raw Ground Penetrating Radar Data, Wolverine Glacier, Alaska; 2013"# Log in (requires a ScienceBase account) and create an itemauthenticate_sb() # type in username and passwordmy_home_item <- user_id()new_item <- item_create(title = 'new test item', parent_id = my_home_item)test.txt <- file.path(tempdir(), 'test.txt')writeLines(c('this is','my data file'), test.txt)item_append_files(new_item, test.txt)item_list_files(new_item)$fname##  "test.txt"
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
Although this software program has been used by the U.S. Geological Survey (USGS), no warranty, expressed or implied, is made by the USGS or the U.S. Government as to the accuracy and functioning of the program and related program material nor shall the fact of distribution constitute any such warranty, and no responsibility is assumed by the USGS in connection therewith.
This software is provided "AS IS."
Fix items_create to properly handle cases creating one item
Add sbtools to user agent string
item_list_children to use
query_sb so item return limit can be > 1000.
raw option removed to support this functionality.
Bunch of changes from reviews
item_get_parent now returns
sbitem, not just ID
fixed probablem with
query_sb_spatial no longer has awkard bounding box specification,
just uses lat/long arrays and determines box from those
sb_ping returns boolean TRUE/FALSE for success/fail
set_endpoint no longer includes verbose message and properly uses
item_list_children now returns list of
sbitem to be uniform with rest of
Lots of documentation updates and new demos
Fixed issue with
New and improved
item_get_wfs. Better performance and
no longer requires hard-to-install external dependencies.
Improved version of
query_sb() now requests useful metadata so
sbitem list has key metadata
query_item_identifier() now returns an
sbitem list instead of a
*_item_identifier() funcitons now have unified
item_replace_files() changed default on
all flag to FALSE
so it doesn't delete files by default.
item_rename_files() to enable user to easily
rename files attached to items directly.