1. Individual-based Modeling Computational Science for NRM D. Wang Individual based modeling and Ecology http://www.humboldt.edu/~ecomodel/book.htm If the system we deal with in ecology are populations, communities, and ecosystems, then why should ecological models be based on individuals? Individuals are building blocks of ecological system; Fitness-seeking adaptation occurs at the individual level; Simspar Package: Developed by Scott M. Duke-Sylvester at TIEM

2. Class Diagram Computational Science for NRM D. Wang The purpose of a class diagram is to depict the classes within a model. In an object oriented application, classes have attributes (member variables), operations (member functions) and relationships with other classes. The UML class diagram can depict all these things quite easily. The fundamental element of the class diagram is an icon the represents a class. A class icon is simply a rectangle divided into three compartments. The topmost compartment contains the name of the class. The middle compartment contains a list of attributes (member variables), and the bottom compartment contains a list of operations (member functions).

3. Class Diagram Computational Science for NRM D. Wang www.tiem.utk.edu/~wang/Driver.h Developed by Scott M. Duke-Sylvester Driver AttributeConfig, Date, IOdevice SparrowPop OperationsInitialization (read parameters, setup data…) Run (Simulation) Shut-Down (IO device, error report…)

4. Class Diagram Computational Science for NRM D. Wang www.tiem.utk.edu/~wang/pop.h Developed by Scott M. Duke-Sylvester SparrowPop AttributeList threshhold OperationsConfig, update (age, mateDate, kill_old/juveniles, etc) Lay_eggs, mate, fledge,move

5. Class Diagram Computational Science for NRM D. Wang www.tiem.utk.edu/~wang/ind.h Developed by Scott M. Duke-Sylvester Sparrow AttributeSparrowIterator, SparrowRef father, mother, mate, self Operationsramdom_mortality, age_mortality,die Lay_eggs, mate, fledge,move

6. Sequence Diagrams Computational Science for NRM D. Wang UML sequence diagrams model the flow of logic in a visual manner, enabling users both to document and validate model logic, and are commonly used for both analysis and design purposes. Sequence diagrams are the most popular UML artifact for dynamic modeling, which focuses on identifying the system’s behaviors. Sequence diagrams, along with class diagrams are in my opinion the most important design-level models for OOP application development.class diagrams

7. Sequence Diagrams Computational Science for NRM D. Wang Driver Initialization Simulation From start_date to end_date Shut-down Pop Update Get_total Sparrow Simulation From first_elmt to last_elmt Age Mate Kill Other

8. How It Works Computational Science for NRM D. Wang Make: a tool which controls the generation of executables and other non-source files of a program from the program's source files. www.tiem.utk.edu/~wang/Makefile_example Source files and header files (define functionalities) Compiler: converts C++ code into machine readable object Linker: links all objects (include library) into an executable image