simplex

simplex simulates ecological systems at the level of individual organisms using individual-based modeling (IBM) to investigate how physiology, life history traits, resource-limited growth, fluctuating environmental conditions, and community assembly produce population- and community-level patterns.

Key Features:

• Comprehensive Simulation Capabilities: Simulates physiology, life history traits, resource-limited growth, fluctuating environmental conditions, and the assembly and structure of communities in both fluid and non-fluid environments.
• Stochastic Modeling: Assembles and runs stochastic ecological models using over 20 state variables combined randomly to explore alternative system outcomes.
• Data Management and Visualization: Stores model outputs and generates animations that represent dynamic ecological processes over time.
• R Markdown Integration: Provides R Markdown files tailored for statistical analysis of simulated datasets.
• Model Description and Quality Assurance: Adheres to the ODD (Overview, Design concepts, Details) protocol and supports community-based revisions, unit testing, and time testing.

Scientific Applications:

• Population Dynamics: Enables mechanistic studies of population dynamics arising from individual physiology and life-history variation.
• Community Ecology: Explores community assembly, species interactions, and community structure under varying environmental conditions.
• Ecosystem Modeling: Supports modeling of ecosystem-level responses to fluctuating environmental conditions and resource limitation.

Methodology:

Individual-based modeling (IBM); assembly and execution of stochastic models with over 20 state variables combined randomly; simulation of physiology, life history, resource-limited growth, fluctuating environmental conditions, and community assembly in fluid and non-fluid environments; storage of model outputs and generation of animations; provision of R Markdown analysis files; adherence to the ODD protocol and inclusion of unit and time testing.