TrenchR: An R package for modular and accessible microclimate and biophysical ecology

Abstract

Much understanding of organismal responses to climate change and variability relies on the assumption that body temperatures are equal to temporally averaged air temperatures high above the ground. However, most organisms experience microclimates near the ground and acute exposure to solar and thermal radiation and thermal extremes can substantially elevate or depress their body temperatures. We introduce the TrenchR package, which aids in Translating Environmental Change into organismal responses. The package includes microclimate models to vertically scale weather station data to organismal heights. Additional functions model and temporally partition air and soil temperatures and solar radiation. TrenchR biophysical modeling tools include both general models for heat flows and specific models to predict body temperatures for a variety of ectothermic taxa. We also offer utility functions to aid in estimating the organismal and environmental parameters needed for biophysical ecology. TrenchR focuses on simple and modular functions so users can create transparent and flexible models for biophysical applications. The package aims to introduce and enable microclimate and biophysical modeling to improve ecological and evolutionary forecasting. We further this aim through a series of educational modules that introduce the field of biophysical ecology.