NicheMapR - an R package for biophysical modelling: the endotherm model

Endothermic organisms typically maintain high and relatively constant body temperatures in the face of environmental variation by regulating their metabolic and water loss rates in conjunction with behavioural and postural adjustments. A mechanistic understanding of these processes provides a perspective of the fundamental niches of endotherms by quantifying their energy and water requirements, restrictions on habitat use and survival limits. Here we introduce and document the endotherm model of NicheMapR, an R package that includes a suite of programs for the mechanistic modelling of energy and mass exchange between organisms and their environments. The NicheMapR endotherm model is based on a Fortran program that simultaneously solves for the metabolic rate, water loss rate, fur/feather temperature and skin temperature required to balance the heat budget in a given microclimate. These calculations are a function of traits relating to insulation, shape, physiological and behavioural responses. The program contains algorithms for computing heat transfer through a porous insulative layer (fur/feathers), including solar and infrared radiation fluxes as well as convective and conductive exchange, and can handle differing dorsal and ventral traits and environments. Here we configure the program to be called from R as part of the NicheMapR package and describe the model in detail. We break the program into a set of modules that can be run in isolation, or jointly, and combined in different ways to capture species-specific thermoregulatory responses. We explain the theory and underlying subroutines, and the default thermoregulatory settings. We discuss how the model can be adapted to incorporate species-specific behaviours and extended to incorporate multiple body parts. We also compare the endotherm modelling setup with the ectotherm model of the NicheMapR package and discuss how the different modelling strategies they require reflect fundamental biological issues.