SLAM Species Life-Cycle Analysis Modules Paul McElhany (project manager, scientist) Miroslav Kos (design & development) Anne Mullan (scientist) Howard Coleman (development) 2005-2012, NWFSC/NOAA Species Life Cycle Analysis Modules (SLAM) was developed as a tool to investigate factors limiting recovery of listed salmonids, but can be applied to any species for modeling population survival over stages. [more] The most recent version of SLAM, along with examples and more information, can be found at http://ecologybox.org/user/SLAM/SLAM Table of Contents Acknowledgements.............................................................................................................................................1 Introduction to SLAM........................................................................................................................................3 Opening a sample life cycle model..........................................................................................................4 Adding a scenario to the sample life cycle..............................................................................................6 Running a simulation...............................................................................................................................7 Browsing results......................................................................................................................................8 The SLAM interface................................................................................................................................9 Interface features:..............................................................................................................................9 Theory................................................................................................................................................................11 Biological perspective............................................................................................................................12 Life cycle, season, generation.........................................................................................................12 Simulation scenario.........................................................................................................................12 Biological and mathematical definitions for salmon.............................................................................13 Life cycles...........................................................................................................................................................14 Creating and editing life cycles.............................................................................................................14 Saving life cycles...................................................................................................................................14 Loading existing life cycles...................................................................................................................15 Deleting life cycles................................................................................................................................16 Read-only life cycles..............................................................................................................................17 Creating and editing life stages..............................................................................................................18 Defining stages................................................................................................................................19 Transitions.......................................................................................................................................21 Self-influencing stages....................................................................................................................24 Split influences................................................................................................................................25 Self-influencing splits......................................................................................................................27 Creating and editing environment variables..........................................................................................28 Creating environment variables.......................................................................................................28 Creating environment variable influences.......................................................................................29 Creating and editing dynamic drivers....................................................................................................30 Creating dynamic drivers................................................................................................................30 Connecting dynamic drivers............................................................................................................30 Managing life cycle layout.....................................................................................................................32 SLAM Scenarios................................................................................................................................................33 Creating scenarios..................................................................................................................................33 Loading scenarios..................................................................................................................................33 Saving scenarios.....................................................................................................................................34 Deleting scenarios..................................................................................................................................34 Scenario editor.......................................................................................................................................35 Configuring elements in the scenario editor..........................................................................................37 Element types..................................................................................................................................37 Configuring life cycle stages in the scenario editor........................................................................38 Configuring environment variables in the scenario editor..............................................................43 Configuring dynamic drivers in the scenario editor........................................................................44 Configuring transitions in the scenario editor........................................................................................46 i Table of Contents SLAM Scenarios Transition influences.......................................................................................................................47 Transition functions.........................................................................................................................48 Configuring transition functions.....................................................................................................50 Types of transition functions...........................................................................................................54 Previewing transition functions.......................................................................................................56 SLAM parameters..................................................................................................................................59 Parameter types...............................................................................................................................59 Constant...........................................................................................................................................60 Generated values.............................................................................................................................61 Using existing data points...............................................................................................................63 SLAM scripts.........................................................................................................................................65 How SLAM scripts work................................................................................................................66 The SLAM script editor..................................................................................................................70 Batch substitution..................................................................................................................................86 Creating a batch substitution template............................................................................................87 Selecting scenarios to copy.............................................................................................................89 Simulations in SLAM.......................................................................................................................................91 Running a simulation in SLAM.............................................................................................................92 Simulation length............................................................................................................................92