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projects > development of selected model components of an across-trophic-level system simulation (atlss) for the wetland systems of south florida > project summary

Project Summary Sheet

U.S. Geological Survey, Greater Everglades Priority Ecosystems Science (GE PES) Initiative

Fiscal Year 2007 Study Summary Report

Study Title: Development of Selected Model Components of an Across-Trophic-Level System Simulation (ATLSS) for the Wetland Systems of South Florida
Study Start Date: 1997 Study End Date: 12/31/2008
Web Sites: ATLSS.ORG
Location: The Greater Everglades ecosystem
Funding Source: ENP Critical Ecosystems Studies Initiative (CESI) and USGS Greater Everglades Priority Ecosystems Science (GE PES) Initiative
Annual Costs: PES FY07
Principal Investigators: Louis J. Gross, The Institute for Environmental Modeling (TIEM), University of Tennessee, Knoxville, TN 37996-1610 Phone: 865-974-4295 e-mail:
Study Personnel: Donald L. DeAngelis, Phone: 305-284-1690 e-mail:
Other Supporting Organizations: USGS Greater Everglades PES Funding, NPS, ACE, EPA
Associated Projects: Component of ATLSS Program, SFWMD Hydrology and Environmental Modeling; USGS National Wetlands Research Center

Overview & Objectives: The ongoing goals in this project have been the following: 1) As part of the ATLSS Program combine biological and physical models using multiple approaches, including trophic system components at differing spatial and temporal scales, to estimate landscape-level responses of biotic systems to environmental changes. 2) Produce models capable of using detailed behavioral and physiological data and dynamically linking these with spatially-explicit abiotic information. 3) Produce models capable of generating testable hypotheses about trophic component responses to alternative possible anthropogenic influences. ATLSS provides a mechanism to evaluate the relative impacts of alternative hydrologic scenarios on various trophic components. The methodology to integrate components involves: i) a landscape structure for dynamic communication between models; ii) a high resolution topography to estimate high resolution water depth across the landscape; and, iii) a variety of visualization tools to aid model development, validation, and comparison to field data.

The current objectives shifted somewhat during FY2006 to accommodate the need by DOI agencies to have ATLSS models working in South Florida on PCs. Currently the USGS's Across Trophic Level System Simulation (ATLSS) models are run at the University of Tennessee using 2 x 2 mile hydrology provided by the South Florida Water Management Model (SFWMM). The initial step in this process is converting SFWMM topography and hydrology to the 500 x 500 meter scale of resolution used by the ATLSS models. The 500-m hydrology is used in the ATLSS models, which include Spatially Explicit Species Index (SESI) models for wading birds, snail kites, white-tailed deer, American alligator, Cape Sable seaside sparrow, crayfish, Florida panthers, and apple snails, as well as population demographic models of the American alligator and the forage fish functional group (ALFISH model). In order to transfer these functions to DOI agencies, the University of Tennessee will cooperate in training between two and four persons from these agencies during a series of visits to the University of Tennessee beginning in early 2006. In addition, source code and documentation of the models and procedures will be transferred to the involved agencies.

Recent Progress: The progress made objectives of the proposed work during late FY2006 was the following,

  • A series of two visits to the University of Tennessee (UT) by a team from DOI in South Florida has been started, with the first two visits occurring in April and June 2006. A final version of the SOW was developed and the team learned the process of developing ATLSS's high resolution topography (HRT) and hydrology (HRH). The UT staff started the documentation of the process of developed HRT and HRH, and also of converting ATLSS SESI models from UNIX work stations to LINUX boxes.
  • The source code for a suite of the ATLSS models was provided to the DOI agencies by UT. This included ALFISH, and the wading bird, alligator, Cape Sable seaside sparrow, and snail kite SESI models. The source code will be the versions of ATLSS which utilize Version 2 of the ATLSS Landscape classes built for Sun Microsystems Solaris Forte C++ compiler. These will be provided by March 31, 2006.
  • As part of the preparation for the third meeting, UT staff delivered to Everglades National Park and the JEM lab in July, 2006, the following handbooks:
    • ATLSS High Resolution Topography (HRT) Manual
    • ATLSS High Resolution Multi-Source Topography (HRMST) Implementation Manual
    • ATLSS HydroSuite (HS) Implementation Manual
  • These draft versions of instruction manuals cover the complete ATLSS hydrology creation process from SFWMM Calibration/Verification to generation of ATLSS hydrology from Scenario runs. In the draft version, separate manuals are provided for HRT, HMDT, and HydroSuite. In addition, a copy of the Linux version of the ATLSS white-tailed SESI has been delivered to Everglades National Park and the JEM lab.

The above work was largely completed by the end of August, 2006. However, problems remained in the implementation of the ATLSS hydrology (HydroSuite) in South Florida, which produces high resolution hydrology for the ATLSS simulation models. This implementation was delayed because of the difficulty in transferring the High Resolution Multi-Data Source Topography (HMDT), which provides needed input. Part of this was due to initial uncertainty about whether PV-WAVE code, which is an essential part of the HydroSuite at the University of Tennessee should be replaced or that software purchased by agencies in South Florida. It was decided to purchase a version of PV WAVE and not try to rewrite the code. A second problem was the difficulty in accessing essential information from the South Florida Water Management District (SFWMD) for the creation of the latest version, HMDT 5.4.

This second problem has been eliminated with the help of Jennifer Barnes of SFWMD, who facilitated obtaining the Calibration/Verification (Cal/Ver) runs from the South Florida Water Management Model (SFWMM), 5.4. This is now being used to construct HMDT 5.4.

The Cal/Ver for SFWMM version 5.4 is the most recent calibration run. Although the current model version is up to 5.6, the District has indicated that no changes have been made that would trigger the creation of a new Cal/Ver. No future CalVer is currently on the District's schedule and Cal/Ver 5.4 will apparently be the reference point for future SFWMM versions. An update was also obtained on the current topography used by the SFWMM 5.4. This is essential for knowing what has to be incorporated into HMDT 5.4. Finally, information is being sought (it is still not obtained) on the soils water storage coefficients (STC) used in SFWMM 5.4. This information is essential. HRT uses the soil storage coefficient to conserve water while it adjusts elevation at he 500m level to find the appropriate hydroperiod for that vegetation type. STC values used by the SFWMM 5.4 have changed, due to land use changes.

Because of the availability of new information from the SFWMD, the following workplan has been underway since the end of August, 2007. The schedule being followed is the following

Examination of New Information. A new HMDT must begin with an examination of the Cal/Ver that it is based on. This evaluation is necessary in order to understand any changes from previous versions that could impact HRT/HMDT/HRH or the ATLSS SESI models. In particular, the process involves:

Find what topographic changes have been made in the SFWMM.
Find what Soil Storage Coefficient changes have been made in the SFWMM.
Initiate Cal/Ver 5.4 analysis.

Implement Baseline Out-of-Box Build of HRT - This will utilize no changes other than files used (the objective is to rebuild the demo HRT from one year ago, as part of QA/QC).

Modification of HRT - Implement needed STC changes in the HRT inputs, as well as any associated code changes; Analysis of changes to 5.4 baseline (the demo distributed last year) and the last HRT produced for 5.0; Recreate HRT for 5.4.; Certify HRT_5.4.

HMDT creation - Check topo source mask changes from SFWMM elevation input changes and compare location averages in cases; when some HAED values are not used; Implement topo source mask changes; Combine HRT, LIDAR, HAED, and SFWMMT; Create HMDT_5.4; Analysis of HMDT_5.4 as compared to previous HMDT; Certify HMDT5.4.


Analysis phase of HMDT creation; Modify HRT and HMDT documentation delivered August 2006.

To expedite these changes, weekly conference call involving the main personnel from TIEM, USGS, NPS, JEM, and SFWMD are being held. These meetings last approximately 30 minutes and are preceded by written progress summaries.

In addition to the work on production of HMDT, the associated ATSL and the associated handbooks

  • ATLSS High Resolution Topography (HRT) Manual
  • ATLSS High Resolution Multi-Source Topography (HRMST) Implementation Manual
  • ATLSS HydroSuite (HS) Implementation Manual

are being revised and consolidated into one handbook. The original version, created in 2006, was not sufficiently complete to allow agency personnel in South Florida create ATLSS hydrology independently. A draft of a revised version has been distributed for comments. The consolidated handbook will contain all relevant information for applying the HydroSuite to any new version of the SFWMM.

The development of a new handbook is not simple, as all possible contingencies that might occur in a new version of the Cal/Ver need to be taken into account. For example, A hypothetical would be what would happen if a new FGAP was generated utilizing 2007 imagery. Cal/Ver stops at 2000. Does one have a problem generating hydroperiods that appropriate for the new FGAP?

Planned Products: Several additional ATLSS SESI models will be delivered by the end of October 2007.

ATLSS High Resolution Multi-Date Source Topography (HMDT 5.4)
Consolidated ATLSS High Resolution Topography (HRT), High Resolution Multi-Source Topography (HRMST), HydroSuite (HS) Implementation Manual

As time permits, work will continue on other aspects of ATLSS. A new ATLSS landscape class structure is being developed. There will be continued Testing and Validation of ATLSS Models.

Recent Product:
Fuller, M. M., L. J. Gross, S. M. Duke-Sylvester, and M. Palmer. Testing the robustness of management decisions to uncertainty: Everglades restoration science. Ecological Applications (in press).

Specific Task Products:

Completion of Consolidate HRT, HRMST and HS implementation manual
Completion of training of DOI staff to use ATLSS models
Integration of the vegetation succession model into SESI models
New landscape class structure for models
Tests of one or more SESI models
Perform simulation runs for CERP

Specific Relevance to Information Needs Identified in DOI's Science Plan in Support of Ecosystem Restoration, Preservation, and Protection in South Florida (DOI's Everglades Science Plan) [See Plan on SOFIA's Web site:]: The ATLSS project links detailed biotic models with spatially-explicit abiotic data at regional extents, in order to provide a scientifically-defensible basis for regional planning that accounts for the complexity of biotic responses from individual-organism levels to that of communities (p. 79). ATLSS models were applied extensively in analyzing Restudy and Mod Water plans. ATLSS products are requested regularly by various agencies in South Florida including the South Florida Water Management District, U.S. Fish and Wildlife Service and Everglades National Park.

Key Findings:

  1. Obtaining and examination of Cal/Ver 5.4 data from SFWMD

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