NicheMapR - an R package for biophysical modelling: the ectotherm and Dynamic Energy Budget models

Mechanistic niche models characterise the fundamental niche of an organism by determining thermodynamic constraints on its heat, water and nutritional budget, and the consequences of this for growth, development and reproduction. They can thus quantify constraints on survival, activity and, ultimately, the vital rates that determine population growth, given a sequence of environmental conditions and the key morphological, physiological and behavioural functional traits. Here we introduce and document the ectotherm model of NicheMapR, an R package that includes a suite of programs for the mechanistic modelling of heat, water, energy and mass exchange between any kind of ectothermic organism and its environment. The NicheMapR ectotherm model is based on a Fortran program originally developed by Porter, Mitchell and Beckman for predicting core body temperature and evaporative water loss as a function of microclimatic conditions and behavioural thermoregulation. The model includes routines for computing steady state body temperature and evaporative water loss given two extreme microclimates (minimum and maximum shade) as computed by the NicheMapR microclimate model. Behavioural options include posture and colour change, shade-seeking, panting, climbing and retreating underground. Here we configure the program to be called from R as part of the NicheMapR package and describe the model in detail including new functionality for modelling whole life-cycle energy and water budgets using Dynamic Energy Budget theory. We include scripts for core operation of the ectotherm model as well as stand-alone R scripts for running the DEB model. Example applications are provided in the paper and in the associated vignettes. The integrated microclimate and ectotherm models should provide a strong thermodynamic basis for determining the effects of environmental change on the behaviour, distribution and abundance of ectothermic organisms.