sbtools
USGS ScienceBase Tools
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.
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 Journal. See citation('sbtools') for how to cite the package.
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 inter-CRAN release updates, use the command:
install.packages("sbtools",repos="https://owi.usgs.gov/R")To get cutting-edge changes, install from GitHub using the devtools packages:
library(devtools)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
Current CRAN information
| Version | Monthly Downloads | Total Downloads |
|---|---|---|
Examples
library(sbtools) # Query ScienceBase for data about Antarcticaquery_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 DOIquery_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 itemchildren <- item_list_children('557f0367e4b023124e8ef621')sapply(children, function(child) child$title)## [1] "Raw Ground Penetrating Radar Data, Valdez Glacier, Alaska; 2013" ## [2] "Raw Ground Penetrating Radar Data, Gulkana Glacier, Alaska; 2013" ## [3] "Raw Ground Penetrating Radar Data, Eklutna Glacier, Alaska; 2013" ## [4] "Raw Ground Penetrating Radar Data, Eureka Glacier, Alaska; 2013" ## [5] "Raw Ground Penetrating Radar Data, Taku Glacier, Alaska; 2013" ## [6] "Raw Ground Penetrating Radar Data, Scott Glacier, Alaska; 2013" ## [7] "Raw Ground Penetrating Radar Data, Wolverine Glacier, Alaska; 2013" # Log in (requires a ScienceBase account) and create an itemauthenticate_sb() # type in username and passwordmy_home_item <- user_id()new_item <- item_create(title = 'new test item', parent_id = my_home_item)test.txt <- file.path(tempdir(), 'test.txt')writeLines(c('this is','my data file'), test.txt)item_append_files(new_item, test.txt)item_list_files(new_item)$fname## [1] "test.txt"Disclaimer
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."
News
Version 1.1.3 (2016-08-18)
-
Fix items_create to properly handle cases creating one item
-
Add sbtools to user agent string
-
Alter
item_list_childrento usequery_sbso item return limit can be > 1000.rawoption removed to support this functionality.
Version 1.0.3 (2016-06-30)
- Fix item_rm bug
Version 1.0.2 (2016-06-22)
- Cleanup for CRAN release
Version 0.19.3 (2016-06-17)
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Bunch of changes from reviews
-
item_get_parentnow returnssbitem, not just ID -
fixed probablem with
query_sb_doi -
query_sb_spatialno longer has awkard bounding box specification, just uses lat/long arrays and determines box from those -
sb_pingreturns boolean TRUE/FALSE for success/fail -
set_endpointno longer includes verbose message and properly usesmatch.arg -
item_list_childrennow returns list ofsbitemto be uniform with rest ofsbtools -
Lots of documentation updates and new demos
Version 0.18.5 (2016-06-01)
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Fixed issue with
query_sb_datatype -
New and improved
item_get_wfs. Better performance and no longer requires hard-to-install external dependencies.
Version 0.18.0 (2016-04-10)
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Improved version of
query_sb()now requests useful metadata sosbitemlist has key metadata -
query_item_identifier()now returns ansbitemlist instead of a data.frame. Also,*_item_identifier()funcitons now have unified parameter order
Version 0.17.0 (2016-04-10)
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On
item_replace_files()changed default onallflag to FALSE so it doesn't delete files by default. -
Added
item_rename_files()to enable user to easily rename files attached to items directly.