SORTIE-ND documentation

• SORTIE-ND License
• What's new in the latest version
• Basic SORTIE modeling concepts
• Setting up SORTIE-ND for your site
• The SORTIE-ND plot
• Timesteps and run length
• Trees
  • What is a tree?
  • Tree population - how trees are organized
  • Tree life history stages and transitions
  • Tree allometry
  • Setting up trees: parameters
  • Setting up tree initial conditions
  • Tree data member list
• Behaviors
  • What is a behavior?
  • The relationship of behaviors to trees and grids
  • Choosing behaviors for a run
  • Setting up behaviors: parameters
  • Complete behavior documentation
    • State change behaviors
    • Harvest and disturbance behaviors
    • Management behaviors
    • Light behaviors
    • Growth behaviors
    • Mortality behaviors
    • Substrate behaviors
    • Epiphytic establishment behaviors
    • Mortality utility behaviors
    • Snag dynamics behaviors
    • Disperse behaviors
    • Seed predation behaviors
    • Establishment behaviors
    • Planting behaviors
    • Analysis behaviors
• Grids
  • What is a grid?
  • How grids are created and used
  • Grid cell size
  • Setting up grid initial conditions
  • Individual grid documentation
• Creating a parameter file
• Setting up output
  • Types of output files
  • Output strategies
  • Tree output
  • Grid output
  • Subplots in output
  • Setting up output
  • Using output as input to a new run
• Viewing output
  • Loading and displaying data from an output file
  • Extracting chart data into text format
  • Batch extracting chart data into text format
  • Viewing output data while a run is still in progress
• Output chart types
  • Line graphs
  • Histograms
  • Tree map
  • Grid maps
  • Tables
• Starting and managing a run
• Batching
• Files in SORTIE-ND
  • Parameter files
  • Detailed output files
  • Summary output files
  • Tab-delimited tree map files
• The SORTIE-ND menu
  • File menu
    • Batch setup window
  • Edit menu
    • Model settings window
    • Tree population - edit species list window
    • Tree population - edit initial density size classes window
    • Tree population - manage tree maps window
    • Grid setup window
      • Grid value edit window
    • Model flow window
      • Current run behaviors window
      • Tree behavior edit window
      • Tree assignments window
    • Output options window
      • Setup detailed output file window
        • Setup tree save options window
        • Setup grid save options window
      • Summary output file setup window
        • Edit subplots window
  • Model menu
  • Tools menu
  • Help menu
• Math in SORTIE-ND
• References
• GPL License

Developer Documentation

• Installing the Code
• Software structure
  • Message passing
  • Model I/O
  • Parameter files (and how to hack them)
  • How a run progresses
  • Design philosophy
  • The SORTIE-ND user installation
• The C++ model core
  • Model architecture
  • Exception handling
  • DOS interface
  • Variable naming conventions
  • Behavior versioning
  • C++ code documentation
• The Java GUI
  • Architecture and key classes
  • Exception handling
  • Windows
  • SORTIE-ND help system
  • Java code documentation
• How to write a new behavior
  • Part 1: Design
  • Part 2: Preparing to code
  • Part 3: Writing code and testing
  • Part 4: GUI and user documentation
• Porting to another operating system
• Third-party plug-ins
• Special topic: How light calculations are performed