Guidance on the Use of Proprietary Computer Simulation Models

JEED recognizes that many ecological engineering design studies rely on simulation models that are proprietary, commercially licensed, or otherwise not open source. Such models are widely used in practice and are acceptable for publication. To ensure transparency, reproducibility, and credibility, we ask that authors include the following in their submissions.

1. Methodological Transparency

The manuscript should make clear how modeling outputs influenced design choices, scenario evaluation, or performance assessment. The simulation model should not function as a “black box” within the design narrative. A technical manual, previous papers, or other document describing the model structure should be cited, if publicly available.

Authors must describe:

  • Model name, version, hardware and software requirements (e.g., required operating system), and details where the model can be accessed (if available)
  • The conceptual structure, governing processes represented, and fundamental equations/algorithms
  • The temporal and spatial scale at which the model operates (e.g., event-based or continuous simulation, field scale or watershed scale)
  • How the model was configured for the specific site or system
  • Any assumptions embedded in the modeling approach and site configuration

2. Parameterization, Calibration, and Validation

When modeling informs built or proposed interventions, discussion of model sensitivity and sources of uncertainty is strongly encouraged. Authors should document:

  • Key parameter values and their sources
  • Calibration procedures and datasets used
  • Validation approach, if applicable
  • Performance metrics for calibration and validation 
  • Sources of uncertainty and potential impacts on model reliability

3. Reproducibility and Workflow Documentation

While proprietary code need not be shared, authors are expected to provide sufficient documentation to allow readers with access to the same tool to reproduce the analysis. Whenever possible, authors should archive the following documentation in a public repository (examples include GitHub, Zenodo, Figshare, or Hydroshare):

  • Model code or compiled software 
  • Input datasets or detailed information for publicly available sources
  • Parameter files or configuration settings
  • Workflow diagrams or stepwise modeling procedures; a clear visual workflow or modeling schematic is encouraged.

4. Data and Materials Availability Statement

All manuscripts must include a Data Availability Statement describing access to model inputs, outputs, and any supporting materials. If the model requires a commercial license or restricted access, this should be stated clearly. 

5. Disclosure

If authors are developers of the model, affiliated with organizations that distribute it, or otherwise have a financial or professional interest in the tool, this should be disclosed in the manuscript's Conflict of Interest Statement.