AmPtools

AmPtools analyzes parameter patterns in the Add-my-Pet (AmP) database to summarize and compare Dynamic Energy Budget (DEB) model parameters across animal species.

Key Features:

• Parameter estimation-in-context: Estimates DEB parameters from species-specific empirical datasets to derive species energetic profiles.
• Comparative analysis across species: Standardizes and compares DEB parameters across diverse taxa, including extinct species, enabling cross-species energetic comparisons among ray-finned fish, mollusks, and crustaceans.
• DEB model classification: Classifies animal energetics using a structured family of DEB models based on metabolic acceleration modes.
• Visualization of parameters and derived properties: Visualizes parameter distributions and derived properties at both aggregate and individual species levels.
• Model fit statistics: Reports model fit metrics, including a median relative error of 0.07 across over a thousand animal species.
• Wide body-mass coverage: Handles datasets spanning 16 orders of magnitude in body mass.
• AmP database integration: Operates on Add-my-Pet (AmP) database entries representing full life-cycle energetics from embryonic development to senescence.

Scientific Applications:

• Evolutionary biology: Integrates evolutionary aspects into parameter estimation to study metabolic evolution across taxa.
• Ecology and biodiversity inference: Infers energetic properties of lesser-known or poorly sampled species to expand understanding of biodiversity.
• Comparative energetics and macroecology: Enables studies of metabolic strategies and energetics across the animal kingdom spanning vast body-mass scales.

Methodology:

Uses DEBtool code for parameter estimation from empirical datasets and AmPtool code for pattern analysis of the resulting DEB parameters.