Software for Assisted Habitat Modeling Package for VisTrails
(SAHM: VisTrails)

Version 1.0

Release Date: March 2012

Contact: Jeff Morisette and Colin Talbert

The Software for Assisted Habitat Modeling (SAHM) has been created to both expedite habitat modeling and help maintain a record of the various input data, pre- and post- processing steps, and modeling options incorporated in the construction of a species distribution model. It is constructed as a package of modules to be utilized within the VisTrails system. 

VisTrails is an open-source management and scientific workflow system designed to integrate the best of both scientific workflow and scientific visualization systems.  Developers can extend VisTrails by creating custom modules that are bundled into a user "package." 

The SAHM package was created to extend VisTrails to assist with habitat suitability modeling. SAHM works by combining environmental predictor layers of the study area, such as climate and remote sensing data, with field sampling measurements for a particular species. The program then runs statistical models using these data to analyze habitat requirements of the species of interest and predict its potential distribution based on habitat suitability. Model outputs can help users, such as land and natural resource managers, generate maps to aid in predicting and managing species of concern.

The modules within the SAHM package can be divided into five main components:

• Input data (both field observations and predictor layers)
• Preprocessing
• Preliminary model analysis and decision
• Correlative models
• Output routines

Figure 1: These five components are highlighted in the representative model workflow.

 

The SAHM: VisTrails modules employ a suite of open-source or freely available libraries including GDAL, Proj.4, Maxent, NumPy, Matplotlib, and R.

The SAHM: VisTrails package,documentation, and tutorial can be downloaded from:

• https://my.usgs.gov/catalog/RAM/SAHM

Note: SAHM: VisTrails v. 1.0, released March 2012, replaces the previous SAHM 1.0.7 (released in October 2010) as a stand-alone package separate from VisTrails. With the release of SAHM: VisTrails 1.0, the USGS will no longer maintain the stand-alone SAHM software.

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System Requirements

• Windows XP
• VisTrails 2.0
• R (developed under version 2.14.0)
• Maxent (developed under version 3.3.3k)
• GDAL (developed under version 1.8.0)
• GDAL Python bindings for Python 2.7

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Contact

Catherine Jarnevich	Jeff Morisette	Tracy Holcombe	Colin Talbert
U.S. Geological Survey Fort Collins Science Center 2150 Centre Ave. Building C Fort Collins, CO 80526-8118 Tel. 970.226.9439 Fax 970.226.9230	U.S. Geological Survey North Central Climate Science Center 2150 Centre Ave. Building C Fort Collins, CO 80526-8118 Tel. 970.226.9144 Fax 970.226.9230	U.S. Geological Survey Fort Collins Science Center 2150 Centre Ave. Building C Fort Collins, CO 80526-8118 Tel. 970.226.9380 Fax 970.226.9230	U.S. Geological Survey Fort Collins Science Center 2150 Centre Ave. Building C Fort Collins, CO 80526-8118 Tel. 970.226.9380 Fax 970.226.9230

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