Confluence Retirement

Due to the feedback from stakeholders and our commitment to not adversely impact USGS science activities that Confluence supports, we are extending the migration deadline to January 2023.

In an effort to consolidate USGS hosted Wikis, myUSGS’ Confluence service is targeted for retirement. The official USGS Wiki and collaboration space is now SharePoint. Please migrate existing spaces and content to the SharePoint platform and remove it from Confluence at your earliest convenience. If you need any additional information or have any concerns about this change, please contact myusgs@usgs.gov. Thank you for your prompt attention to this matter.
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Scientific Computing Topics

Scientific Computing Environments

Statistical environments

S-Plus

USGS holds a license for a version of the S-Plus statistical package, and the USGS internal distribution includes USGS-developed statistical and graphics tools.

R

R is an open-source statistical analysis system built to be functionally equivalent to S. It is gaining in popularity, and has a body of GUI's (such as RCommander) and interfaces available for it. Since R has a command-line interface, it is fairly easy to connect with other software, for example, ArcGIS. and Java Python ("Jython"). Some have described R as a "statistical scripting language."

Although the user community is very good at answering questions, the volume of questions and answers may be overwhelming.

Python

Python, an interpreted, interactive, object-oriented, extensible programming language, supported on numerous computing platforms.

  • Python is distributed with a large standard library of modules that support various tasks, but many more are available online. An extensive collection of pre-compiled libraries are available in this collection posted by Christoph Gohlke. Key libraries of interest to scientific computing include NumPy, SciPy, matplotlib, and netCDF4.

Python and ArcGIS

  • Python, aside from being a standalone general scripting language, has become the main scripting language for the ArcGIS platform. Versions of Python 2.x and Python libraries that are included in different versions of ArcGIS are as follows:

    ArcGIS

    9.3

    10.0

    10.1 (beta)

    Python

    2.5.1

    2.6.2

    2.7

    NumPy

    1.0.3

    1.3

    1.5

    matplotlib

    1.0.1

  • The netCDF4 module compiled for ArcGIS 10.0, 10.1 allows fairly straightforward access of netCDF and OPeNDAP data from ArcGIS Python scripts. Thanks to Rich Signell and, most of all, Christoph Gohlke (who compiled the module so it will work with Arc). Rich and Curtis Price provided these test python scripts.
    • The image below shows an example of a raster that has been loaded into ArcMap from a remote dataset using a Python script tool that accesses data using the netCDF4 library and the OPeNDAP access protocol. (Click it for a full-resolution view.)

MATLAB

MATLAB is commonly used for data and compute-intensive scientific analysis.

Known USGS MATLAB users: Rich Signell, Ashley Van Beusekom

Microsoft Office

Although Microsoft Office is very useful for general-purpose computing widely used in science, it has also been also widely criticized by the scientific community (especially by statisticians). The largest problem by far is data import/export, and the misuse of the tools, for example the (far too common) use of Excel as a database, and errors in worksheet cell references.

USGS holds a site license for MS Office, through the Bureau Windows Technical Support Team (BWTST).

Geographic Information Systems (GIS)

Since much of USGS scientific computing involves spatial data, it is no suprise that more than half of the attendees of the 2011 CDI meeting were polled identified themselves as users of Esri's ArcGIS product.

USGS Core Science Systems supports the Enterprise GIS (EGIS) team, who supports GIS activities in the Bureau. EGIS supports USGS-wide site licenses for Esri's ArcGIS suite, and Global Mapper.

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